% This file was created with JabRef 2.5. % Encoding: ISO8859_1 @ARTICLE{Allesen-Holm2006, author = {Allesen-Holm, M. and Barken, K. B. and Yang, L. and Klausen, M. and Webb, J. S. and Kjelleberg, S. and Molin, S. and Givskov, M. and Tolker-Nielsen, T.}, title = {{A} characterization of {DNA} release in \emph{Pseudomonas aeruginosa} cultures and biofilms}, journal = {Mol Microbiol}, year = {2006}, volume = {59}, pages = {1114--1128}, abstract = {Pseudomonas aeruginosa produces extracellular DNA which functions as a cell-to-cell interconnecting matrix component in biofilms. Comparison of extracellular DNA and chromosomal DNA by the use of polymerase chain reaction and Southern analysis suggested that the extracellular DNA is similar to whole-genome DNA. Evidence that the extracellular DNA in P. aeruginosa biofilms and cultures is generated via lysis of a subpopulation of the bacteria was obtained through experiments where extracellular beta-galactosidase released from lacZ-containing P. aeruginosa strains was assessed. Experiments with the wild type and laslrhll, pqsA, pqsL and fliMpilA mutants indicated that the extracellular DNA is generated via a mechanism which is dependent on acyl homoserine lactone and Pseudomonas quinolone signalling, as well as on flagella and type IV pili. Microscopic investigation of flow chamber-grown wild-type P. aeruginosa biofilms stained with different DNA stains suggested that the extracellular DNA is located primarily in the stalks of mushroom-shaped multicellular structures, with a high concentration especially in the outer part of the stalks forming a border between the stalk-forming bacteria and the cap-forming bacteria. Biofilms formed by laslrhll, pqsA and fliMpilA mutants contained less extracellular DNA than biofilms formed by the wild type, and the mutant biofilms were more susceptible to treatment with sodium dodecyl sulphate than the wild-type biofilm.}, c1 = {Tech Univ Denmark, Bioctr, Ctr Biomed Microbiol, DK-2800 Lyngby, Denmark.EOLEOLUniv New S Wales, Sydney, NSW 2052, Australia.}, citedreferences = {AAS FE, 2002, MOL MICROBIOL, V46, P749 ; BHARNSHOLT T, 2005, MICROBIOLOGY, V151, P373 ; CARLSON CA, 1983, J BACTERIOL, V153, P93 ; CLARK DJ, 1967, J MOL BIOL, V23, P99 ; COSTERTON JW, 1995, ANNU REV MICROBIOL, V49, P711 ; COSTERTON JW, 1999, SCIENCE, V284, P1318 ; DARGENIO DA, 2002, J BACTERIOL, V184, P6481 ; DAVEY ME, 2003, J BACTERIOL, V185, P1027 ; DAVIES DG, 1998, SCIENCE, V280, P295 ; DEKIEVIT TR, 2001, APPL ENVIRON MICROB, V67, P1865 ; DIGGLE SP, 2003, MOL MICROBIOL, V50, P29 ; DILLARD JP, 2001, MOL MICROBIOL, V41, P263 ; FRIEDMAN L, 2004, J BACTERIOL, V186, P4457 ; FRIEDMAN L, 2004, MOL MICROBIOL, V51, P675 ; FROSHAUER S, 1996, ANTIMICROB AGENTS CH, V40, P1561 ; GIVSKOV M, 1996, J BACTERIOL, V178, P6618 ; GOTO S, 1971, JAPAN J MICROBIOL, V15, P317 ; HARA T, 1981, AGR BIOL CHEM TOKYO, V45, P2457 ; HARA T, 1981, J GEN APPL MICROBIOL, V27, P109 ; HASSETT DJ, 1999, MOL MICROBIOL, V34, P1082 ; HASSETT DJ, 2005, 10 INT C MARS FRANC ; HENDRICKX L, 2003, APPL ENVIRON MICROB, V69, P1721 ; HENTZER M, 2002, MICROBIOL-SGM 1, V148, P87 ; HENTZER M, 2003, EMBO J, V22, P3803 ; HENTZER M, 2004, MICROBIAL BIOFILMS, P118 ; HOLLOWAY BW, 1986, ANNU REV MICROBIOL, V40, P79 ; KADURUGAMUWA JL, 1996, J BACTERIOL, V178, P2767 ; KLAUSEN M, 2003, MOL MICROBIOL, V48, P1511 ; KLAUSEN M, 2003, MOL MICROBIOL, V50, P61 ; LATIFI A, 1995, MOL MICROBIOL, V17, P333 ; LATIFI A, 1996, MOL MICROBIOL, V21, P1137 ; LEQUETTE Y, 2005, J BACTERIOL, V187, P37 ; LI YH, 2001, J BACTERIOL, V183, P897 ; LORENZ MG, 1991, ARCH MICROBIOL, V156, P319 ; LORENZ MG, 1994, MICROBIOL REV, V58, P563 ; MAGNUSON R, 1994, CELL, V77, P207 ; MASHBURN LM, 2005, NATURE, V437, P422 ; MATSUKAWA M, 2004, J BACTERIOL, V186, P4449 ; MCKNIGHT SL, 2000, J BACTERIOL, V182, P2702 ; MEDINA G, 2003, J BACTERIOL, V185, P377 ; MOLLER S, 1998, APPL ENVIRON MICROB, V64, P721 ; MURAKAWA T, 1973, JPN J MICROBIOL, V17, P273 ; MURAKAWA T, 1973, JPN J MICROBIOL, V17, P513 ; MUTO Y, 1986, MICROBIOL IMMUNOL, V30, P621 ; NEMOTO K, 2003, CHEMOTHERAPY, V49, P121 ; OTOOLE GA, 1998, MOL MICROBIOL, V30, P295 ; PALMEN R, 1995, CURR MICROBIOL, V30, P7 ; PASSADOR L, 1993, SCIENCE, V260, P1127 ; PESCI EC, 1999, P NATL ACAD SCI USA, V96, P11229 ; PESTOVA EV, 1996, MOL MICROBIOL, V21, P853 ; PHILLIPS I, 1987, J ANTIMICROB CHEMOTH, V20, P631 ; RASMUSSEN TB, 2005, J BACTERIOL, V187, P1799 ; RENELLI M, 2004, MICROBIOL-SGM 7, V150, P2161 ; SHIH PC, 2002, J ANTIMICROB CHEMOTH, V49, P309 ; SKERKER JM, 2001, P NATL ACAD SCI USA, V98, P6901 ; STEINMOEN H, 2002, P NATL ACAD SCI USA, V99, P7681 ; STEWART GJ, 1983, J BACTERIOL, V156, P30 ; STOVER CK, 2000, NATURE, V406, P959 ; VALLET I, 2001, P NATL ACAD SCI USA, V98, P6911 ; VANSCHAIK EJ, 2005, J BACTERIOL, V187, P1455 ; WAGNER VE, 2003, J BACTERIOL, V185, P2080 ; WANG BY, 2002, ORAL MICROBIOL IMMUN, V2, P108 ; WEBB JS, 2003, J BACTERIOL, V185, P4585 ; WHITCHURCH CB, 2002, SCIENCE, V295, P1487}, em = {ttn@biocentrum.dtu.dk}, ga = {005CQ}, j9 = {MOL MICROBIOL}, ji = {Mol. Microbiol.}, keywords = {NATURAL GENETIC-TRANSFORMATION; QUORUM-SENSING INHIBITORS; TO-CELL COMMUNICATION; EXTRACELLULAR DNA; MEMBRANE-VESICLES; SLIME PRODUCTION; IV PILI; STREPTOCOCCUS-PNEUMONIAE; NEISSERIA-GONORRHOEAE; HOMOSERINE LACTONE}, la = {English}, nr = {64}, owner = {rec}, pa = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND}, pg = {15}, pi = {OXFORD}, publisher = {Blackwell Publishing}, rp = {Tolker-Nielsen, T, Tech Univ Denmark, Bioctr, Ctr Biomed Microbiol,EOLEOLDK-2800 Lyngby, Denmark.}, sc = {Biochemistry & Molecular Biology; Microbiology}, sn = {0950-382X}, tc = {10}, timestamp = {2007.06.17}, ut = {ISI:000234800600004} } @ARTICLE{Averhoff2003, author = {Averhoff, B. and Friedrich, A.}, title = {{T}ype {IV} pili-related natural transformation systems: {DNA} transport in mesophilic and thermophilic bacteria}, journal = {Arch Microbiol}, year = {2003}, volume = {180}, pages = {385--393}, abstract = {Horizontal gene flow is a driving force for bacterial adaptation. Among the three distinct mechanisms of gene transfer in bacteria, conjugation, transduction, and transformation, the latter, which includes competence induction, DNA binding, and DNA uptake, is perhaps the most versatile mechanism and allows the incorporation of free DNA from diverse bacterial species. Here we review DNA transport machineries mediating uptake of naked DNA in gram-positive and gram-negative bacteria. Different putative models of transformation machineries comprising components similar to proteins of type IV pili are presented. Emphasis is placed on a comparative discussion of the underlying mechanisms of DNA transfer in mesophilic and extremely thermophilic bacteria, highlighting conserved and distinctive features of these transformation machineries.}, c1 = {Univ Munich, Dept Biol 1, Bereich Genet, D-80638 Munich, Germany.}, citedreferences = {AAS FE, 2002, MOL MICROBIOL, V46, P749 ; ARAVIND L, 1998, TRENDS GENET, V14, P442 ; BITTER W, 2003, ARCH MICROBIOL, V179, P307 ; CASTON JR, 1988, FEMS MICROBIOL LETT, V51, P225 ; CHEN I, 2001, J BACTERIOL, V183, P3160 ; CHEN I, 2003, FRONT BIOSCI, V8, P544 ; CHEN LY, 1996, J BIOL CHEM, V271, P2703 ; CLAVERYS JP, 2002, FRONT BIOSCI, V7, P1798 ; COLLINS RF, 2001, J BACTERIOL, V183, P3825 ; DEVRIES J, 2001, FEMS MICROBIOL LETT, V195, P211 ; DOOLITTLE WF, 1999, TRENDS CELL BIOL, V9, P5 ; DOUGHERTY BA, 1999, MICROBIOL-UK 2, V145, P401 ; DUBNAU D, 1999, ANNU REV MICROBIOL, V53, P217 ; FOREST KT, 1997, GENE, V192, P165 ; FRIEDRICH A, 2001, APPL ENVIRON MICROB, V67, P3140 ; FRIEDRICH A, 2002, APPL ENVIRON MICROB, V68, P745 ; FRIEDRICH A, 2003, APPL ENVIRON MICROB, V69, P3695 ; FUSSENEGGER M, 1997, GENE, V192, P125 ; GENIN S, 1994, MOL GEN GENET, V243, P112 ; GRAUPNER S, 2001, J BACTERIOL, V183, P4694 ; HIDAKA Y, 1994, BIOSCI BIOTECH BIOCH, V58, P1338 ; HOBBS M, 1993, MOL MICROBIOL, V10, P233 ; HOFREUTER D, 2001, MOL MICROBIOL, V41, P379 ; KAISER D, 2000, CURR BIOL, V10, R777 ; KANG YW, 2002, MOL MICROBIOL, V46, P427 ; KARUDAPURAM S, 1995, J BACTERIOL, V177, P3235 ; KOYAMA Y, 1986, J BACTERIOL, V166, P338 ; LORENZ MG, 1994, MICROBIOL REV, V58, P563 ; MAIER E, 2001, J BACTERIOL, V183, P800 ; MATTICK JS, 2002, ANNU REV MICROBIOL, V56, P289 ; MERZ AJ, 2000, ANNU REV CELL DEV BI, V16, P423 ; MERZ AJ, 2000, NATURE, V407, P98 ; NELSON KE, 1999, NATURE, V399, P323 ; NOUWEN N, 2000, EMBO J, V19, P2229 ; OCHMAN H, 2000, NATURE, V405, P299 ; PALMEN R, 1997, GENE, V192, P179 ; PESTOVA EV, 1998, J BACTERIOL, V180, P2701 ; PORSTENDORFER D, 1997, APPL ENVIRON MICROB, V63, P4150 ; PROVVEDI R, 1999, MOL MICROBIOL, V31, P271 ; SAUVONNET N, 2000, EMBO J, V19, P2221 ; SMEETS LC, 2002, TRENDS MICROBIOL, V10, P159 ; STROM MS, 1993, ANNU REV MICROBIOL, V47, P565 ; THANASSI DG, 2002, J MOL MICROB BIOTECH, V4, P11 ; TONJUM T, 1997, GENE, V192, P155 ; WHITE O, 1999, SCIENCE, V286, P1571 ; WOLFGANG M, 1998, MOL MICROBIOL, V29, P321 ; WOLFGANG M, 1999, MOL MICROBIOL, V31, P1345 ; YOSHIHARA S, 2001, PLANT CELL PHYSIOL, V42, P63}, de = {natural transformation; competence proteins; type IV pili}, ga = {750TJ}, j9 = {ARCH MICROBIOL}, ji = {Arch. Microbiol.}, keywords = {LATERAL GENE-TRANSFER; THERMUS-THERMOPHILUS; NEISSERIA-GONORRHOEAE; TWITCHING MOTILITY; PROTEIN-SECRETION; OUTER-MEMBRANE; PSEUDOMONAS-STUTZERI; HELICOBACTER-PYLORI; ELECTRON-MICROSCOPY; COMPETENCE GENES}, la = {English}, nr = {48}, owner = {rec}, pa = {175 FIFTH AVE, NEW YORK, NY 10010 USA}, pg = {9}, pi = {NEW YORK}, publisher = {Springer-Verlag}, rp = {Averhoff, B, Univ Munich, Dept Biol 1, Bereich Genet, Maris Ward StrEOLEOL1A, D-80638 Munich, Germany.}, sc = {Microbiology}, sn = {0302-8933}, tc = {12}, timestamp = {2007.06.17}, ut = {ISI:000187013900001} } @ARTICLE{Avery1944, author = {O. T. Avery and C. M. MacLeod and M. McCarty}, title = {{S}tudies on the chemical nature of the substance inducing transformation of pneumococcal types. {I}. {I}nductions of transformation by a desoxyribonucleic acid fraction isolated from \emph{Pneumococcus} type {III}.}, journal = {J Exp Med}, year = {1944}, volume = {79}, pages = {137--157}, keywords = {DNA, Bacterial; Enzymes; History, 20th Century; Streptococcus pneumoniae; Transformation, Genetic}, owner = {rec}, pmid = {33226}, timestamp = {2007.06.17} } @ARTICLE{Bailiff1991, author = {Megan D. Bailiff and David M. Karl}, title = {Dissolved and particulate {DNA} dynamics during a spring bloom in the {A}ntarctic {P}eninsula region, 1986--1987}, journal = {Deep-Sea Res Pt I}, year = {1991}, volume = {38}, pages = {1077--1095}, doi = {DOI: 10.1016/0198-0149(91)90097-Y}, issn = {0198-0149}, owner = {rec}, timestamp = {2010.09.13}, url = {http://www.sciencedirect.com/science/article/B757K-489YKD6-3D/2/f304b4f77da121499ed83bde086fdb0b} } @ARTICLE{Bayer-Giraldi2010, author = {Bayer-Giraldi, M. and Uhlig, C. and John, U. and Mock, T. and Valentin, K.}, title = {Antifreeze proteins in polar sea ice diatoms: diversity and gene expression in the genus \emph{Fragilariopsis}}, journal = {Environ Microbiol}, year = {2010}, volume = {12}, pages = {1041--1052}, abstract = {Summary Fragilariopsis is a dominating psychrophilic diatom genus in polar sea ice. The two species Fragilariopsis cylindrus and Fragilariopsis curta are able to grow and divide below freezing temperature of sea water and above average sea water salinity. Here we show that antifreeze proteins (AFPs), involved in cold adaptation in several psychrophilic organisms, are widespread in the two polar species. The presence of AFP genes (afps) as a multigene family indicated the importance of this group of genes for the genus Fragilariopsis, possibly contributing to its success in sea ice. Protein phylogeny showed the potential mobility of afps, which appear to have crossed kingdom and domain borders, occurring in Bacteria, diatoms, crustaceans and fungi. Our results revealed a broad distribution of AFPs not only in polar organisms but also in taxa apparently not related to cold environments, suggesting that these proteins may be multifunctional. The relevance of AFPs to Fragilariopsis was also shown by gene expression analysis. Under stress conditions typical for sea ice, with subzero temperatures and high salinities, F. cylindrus and F. curta strongly expressed selected afps. An E/G point mutation in the Fragilariopsis AFPs may play a role in gene expression activity and protein function.}, issn = {1462-2920}, owner = {rec}, publisher = {Blackwell Publishing Ltd}, timestamp = {2010.09.13}, url = {http://dx.doi.org/10.1111/j.1462-2920.2009.02149.x} } @ARTICLE{Beiko2005, author = {Beiko, Robert G. and Harlow, Timothy J. and Ragan, Mark A.}, title = {{H}ighways of gene sharing in prokaryotes}, journal = {PNAS}, year = {2005}, volume = {102}, pages = {14332--14337}, abstract = {The extent to which lateral genetic transfer has shaped microbial genomes has major implications for the emergence of community structures. We have performed a rigorous phylogenetic analysis of >220,000 proteins from genomes of 144 prokaryotes to determine the contribution of gene sharing to current prokaryotic diversity, and to identify "highways" of sharing between lineages. The inferred relationships suggest a pattern of inheritance that is largely vertical, but with notable exceptions among closely related taxa, and among distantly related organisms that live in similar environments.}, doi = {10.1073/pnas.0504068102}, keywords = {Bacterial Proteins; Base Sequence; Bayes Theorem; Computational Biology; Evolution, Molecular; Gene Transfer, Horizontal; Genome, Archaeal; Genome, Bacterial; Models, Genetic; Phylogeny; Prokaryotic Cells; Sequence Alignment; Variation (Genetics)}, owner = {rec}, pii = {0504068102}, pmid = {16176988}, timestamp = {2007.06.17}, url = {http://dx.doi.org/10.1073/pnas.0504068102} } @ARTICLE{Belzile2008, author = {Claude Belzile and Sonia Brugel and Christian Nozais and Yves Gratton and Serge Demers}, title = {Variations of the abundance and nucleic acid content of heterotrophic bacteria in {B}eaufort {S}helf waters during winter and spring}, journal = {J Mar Sys}, year = {2008}, volume = {74}, pages = {946--956}, comment = {DOI: 10.1016/j.jmarsys.2007.12.010}, issn = {0924-7963}, keywords = {Heterotrophic bacteria}, owner = {rec}, timestamp = {2011.03.07}, url = {http://www.sciencedirect.com/science/article/B6VF5-4RM1KS7-1/2/65e6b0619b5f02fc4fb2e3b042abb426} } @ARTICLE{Beveridge1997, author = {Beveridge, Terry J and Makin, Stephen A and Kadurugamuwa, Jagath L and Li, Zusheng}, title = {Interactions between biofilms and the environment}, journal = {FEMS Microbiol Rev}, year = {1997}, volume = {20}, pages = {291--303}, abstract = {The surfaces of bacteria are highly interactive with their environment. Whether the bacterium is Gram-negative or Gram-positive, most surfaces are charged at neutral pH because of the ionization of the reactive chemical groups which stud them. Since prokaryotes have a high surface area-to-volume ratio, this can have surprising ramifications. For example, many bacteria can concentrate dilute environmental metals on their surfaces and initiate the development of fine-grained minerals. In natural environments, it is not unusual to find such bacteria closely associated with the minerals which they have helped develop. Bacteria can be free-living (planktonic), but in most natural ecosystems they prefer to grow on interfaces as biofilms; supposedly to take advantage of the nutrient concentrative effect of the interface, although there must also be gained some protective value against predators and toxic agents. Using a Pseudomonas aeruginosa model system, we have determined that lipopolysaccharide is important in the initial attachment of this Gram-negative bacterium to interfaces and that this surface moiety subtly changes during biofilm formation. Using this same model system, we have also discovered that there is a natural tendency for Gram-negative bacteria to concentrate and package periplasmic components into membrane vesicles which bleb-off the surface. Since some of these components (e.g., peptidoglycan hydrolases) can degrade other surrounding cells, the vesicles could be predatory; i.e., a natural system by which neighboring bacteria are targeted and lysed, thereby liberating additional nutrients to the microbial community. This obviously would be of benefit to vesicle-producing bacteria living in biofilms containing mixed microbial populations.}, owner = {rec}, timestamp = {2009.08.22}, url = {http://dx.doi.org/10.1111/j.1574-6976.1997.tb00315.x} } @ARTICLE{Biers2008, author = {Erin J Biers and Kui Wang and Catherine Pennington and Robert Belas and Feng Chen and Mary Ann Moran}, title = {Occurrence and expression of gene transfer agent genes in marine bacterioplankton.}, journal = {Appl Environ Microbiol}, year = {2008}, volume = {74}, pages = {2933--2939}, abstract = {Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine Roseobacter clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured Alphaproteobacteria, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles ( approximately 50 to 70 nm) was demonstrated experimentally for the Roseobacter clade member Silicibacter pomeroyi DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.}, doi = {10.1128/AEM.02129-07}, institution = {Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.}, keywords = {Bacterial Proteins, biosynthesis; Bacteriophages, genetics/ultrastructure; Chromosomes, Bacterial, genetics; DNA, Bacterial, genetics; Gene Expression Profiling; Gene Order; Microscopy, Electron, Transmission; Phylogeny; Plankton, genetics; Prophages, genetics; Rhodobacteraceae, genetics; Sequence Homology, Amino Acid; Transduction, Genetic}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {AEM.02129-07}, pmid = {18359833}, timestamp = {2009.07.27}, url = {http://dx.doi.org/10.1128/AEM.02129-07} } @ARTICLE{Blokesch2008, author = {Melanie Blokesch and Gary K Schoolnik}, title = {The extracellular nuclease {Dns} and its role in natural transformation of \emph{Vibrio cholerae}.}, journal = {J Bacteriol}, year = {2008}, volume = {190}, pages = {7232--7240}, abstract = {Free extracellular DNA is abundant in many aquatic environments. While much of this DNA will be degraded by nucleases secreted by the surrounding microbial community, some is available as transforming material that can be taken up by naturally competent bacteria. One such species is Vibrio cholerae, an autochthonous member of estuarine, riverine, and marine habitats and the causative agent of cholera, whose competence program is induced after colonization of chitin surfaces. In this study, we investigate how Vibrio cholerae's two extracellular nucleases, Xds and Dns, influence its natural transformability. We show that in the absence of Dns, transformation frequencies are significantly higher than in its presence. During growth on a chitin surface, an increase in transformation efficiency was found to correspond in time with increasing cell density and the repression of dns expression by the quorum-sensing regulator HapR. In contrast, at low cell density, the absence of HapR relieves dns repression, leading to the degradation of free DNA and to the abrogation of the transformation phenotype. Thus, as cell density increases, Vibrio cholerae undergoes a switch from nuclease-mediated degradation of extracellular DNA to the uptake of DNA by bacteria induced to a state of competence by chitin. Taken together, these results suggest the following model: nuclease production by low-density populations of V. cholerae might foster rapid growth by providing a source of nucleotides for the repletion of nucleotide pools. In contrast, the termination of nuclease production by static, high-density populations allows the uptake of intact DNA and coincides with a phase of potential genome diversification.}, doi = {10.1128/JB.00959-08}, institution = {Department of Microbiology and Immunology, Beckman Center B237, 279 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305, USA. Blokesch@stanford.edu}, keywords = {Bacterial Proteins, genetics/metabolism/physiology; Biofilms, growth /&/ development; Chitin, metabolism; Deoxyribonucleases, genetics/metabolism; Gene Expression Regulation, Bacterial; Models, Biological; Quorum Sensing, genetics/physiology; Sequence Deletion; Transformation, Genetic, genetics; Vibrio cholerae, genetics/metabolism/physiology}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {JB.00959-08}, pmid = {18757542}, timestamp = {2009.07.27}, url = {http://dx.doi.org/10.1128/JB.00959-08} } @ARTICLE{Bockelmann2006, author = {Bockelmann, U. and Janke, A. and Kuhn, R. and Neu, T. R. and Wecke, J. and Lawrence, J. R. and Szewzyk, U.}, title = {{B}acterial extracellular {DNA} forming a defined network-like structure}, journal = {FEMS Microbiol Lett}, year = {2006}, volume = {262}, pages = {31--38}, abstract = {It is generally assumed that nucleic acids are localized inside of living cells and that their primary function is the storage of information. In contrast, extracellular DNA is mainly considered as a remnant of lysed cells. Here, we report the formation of extracellular bacterial DNA as a spatial structure. An aquatic bacterium, strain F8, was isolated, which produced a stable filamentous network of extracellular DNA. Different staining and enzymatic techniques confirmed that it was DNA. We were able to amplify the 16S rRNA gene from the extracellular DNA. Restriction endonuclease cleavage and randomly amplified polymorphic DNA analysis of extracellular and genomic DNAs revealed major similarities, but also some differences in both sequences. Our data demonstrate a new function and relevance for extracellular DNA.}, af = {Boeckelmann, UtaEOLEOLJanke, AndreaEOLEOLKuhn, RamonaEOLEOLNeu, Thomas R.EOLEOLWecke, JoergEOLEOLLawrence, John R.EOLEOLSzewzyk, Ulrich}, c1 = {Tech Univ Berlin, Dept Environm Microbiol, D-10587 Berlin, Germany.EOLEOLUFZ Ctr Environm Res Leipzig Halle, Dept River Ecol, Magdeburg, Germany.EOLEOLRobert Koch Inst, Berlin, Germany.EOLEOLNatl Water Res Inst Branch, Saskatoon, SK, Canada.}, citedreferences = {BOCKELMANN U, 2000, FEMS MICROBIOL ECOL, V33, P157 ; BOCKELMANN U, 2002, J MICROBIOL METH, V49, P75 ; BRETTAR I, 2002, INT J SYST EVOL MI 5, V52, P1851 ; BRINKMANN V, 2004, SCIENCE, V303, P1532 ; CORINALDESI C, 2005, APPL ENVIRON MICROB, V71, P46 ; DELLANNO A, 2004, APPL ENVIRON MICROB, V70, P4384 ; DELLANNO A, 2005, SCIENCE, V309, P2179 ; LANE DJ, 1991, NUCL ACID TECHNIQUES, P115 ; LIU MZ, 2005, LANGMUIR, V21, P1972 ; NIEMEYER CM, 2000, CURR OPIN CHEM BIOL, V4, P609 ; NISHIMURA S, 2003, NUCL ACIDS RES S, V3, P279 ; OLISHEVSKY S, 2004, EXP ONCOL, V26, P265 ; STEINBERGER RE, 2002, MICROBIAL ECOL, V43, P416 ; STEINBERGER RE, 2005, APPL ENVIRON MICROB, V71, P5404 ; STRUNK O, 1995, ARB SOFTWARE ENV SEQ ; TATON TA, 2001, NATURE, V412, P491 ; VENIERI D, 2004, WATER SCI TECHNOL, V50, P193 ; WATANABE M, 1998, APPL MICROBIOL BIOT, V50, P682 ; WATNICK P, 2000, J BACTERIOL, V182, P2675 ; WHITCHURCH CB, 2002, SCIENCE, V295, P1487 ; ZHOU SQ, 2004, BIOMACROMOLECULES, V5, P1256}, de = {extracellular DNA (eDNA); filamentous network; aquatic bacteria;EOLEOLnanotechnology; nanostructures}, em = {uta.boeckelmann@tu-berlin.de}, ga = {071SF}, j9 = {FEMS MICROBIOL LETT}, ji = {FEMS Microbiol. Lett.}, keywords = {UNSATURATED BIOFILMS; MARINE-SEDIMENTS; NANOSTRUCTURES; HYBRIDIZATION; SEA}, la = {English}, nr = {21}, owner = {rec}, pa = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND}, pg = {8}, pi = {OXFORD}, publisher = {Blackwell Publishing}, rp = {Bockelmann, U, Tech Univ Berlin, Dept Environm Microbiol, FranklinstrEOLEOL29,FR 1-2, D-10587 Berlin, Germany.}, sc = {Microbiology}, sn = {0378-1097}, tc = {0}, timestamp = {2007.06.17}, ut = {ISI:000239621500005} } @ARTICLE{Brown2001a, author = {Brown, J. R.}, title = {{G}enomic and phylogenetic perspectives on the evolution of prokaryotes}, journal = {Syst Biol}, year = {2001}, volume = {50}, pages = {497--512}, abstract = {Prokaryotes have been at the forefront of the genome sequencing revolution. Many genomes have been completely sequenced, revealing much about bacterial and archaeal genome content and organization. Yet, a meaningful evolutionary picture of prokaryotes still eludes us. Much of the problem lies in understanding the mode and tempo of genome evolution. Here phenylalanyl-tRNA synthetase is used as an example of the complex interplay among lateral gene transfer, operon recombination, and gene recruitment in the evolution of some prokaryotic genes. Promising new approaches to genomic analyses, which could add to our understanding prokaryotic evolution and help in their classification, are discussed.}, c1 = {Glaxo SmithKline Pharmaceut, Div Bioinformat, Microbial Bioinformat Dept, Collegeville, PA 19426 USA.}, citedreferences = {ALTSCHUL SF, 1997, NUCLEIC ACIDS RES, V25, P3389 ; BALDAUF SL, 1996, P NATL ACAD SCI USA, V93, P7749 ; BARNS SM, 1994, P NATL ACAD SCI USA, V91, P1609 ; BARNS SM, 1996, P NATL ACAD SCI USA, V93, P9188 ; BOCCHETTA M, 2000, J MOL EVOL, V50, P366 ; BOUCHER Y, 2000, MOL MICROBIOL, V37, P703 ; BROWN JR, 1995, P NATL ACAD SCI USA, V92, P2441 ; BROWN JR, 1997, J MOL EVOL, V45, P9 ; BROWN JR, 1997, MICROBIOL MOL BIOL R, V61, P456 ; BROWN JR, 1998, CURR BIOL, V8, P365 ; BROWN JR, 1998, THERMOPHILES KEYS MO, P217 ; BROWN JR, 1998, TRENDS MICROBIOL, V6, P349 ; BROWN JR, 1999, J MOL EVOL, V49, P485 ; BROWN JR, 2001, IN PRESS NATURE GENE, V28 ; BROWN JW, 1989, CRC CRIT R MICROBIOL, V16, P287 ; BULT CJ, 1996, SCIENCE, V273, P1058 ; BURGGRAF S, 1992, SYST APPL MICROBIOL, V15, P352 ; CAVALIERSMITH T, 1993, MICROBIOL REV, V57, P953 ; CHATTON E, 1937, TITRES TRAVAUZ SCI ; DANDEKAR T, 1998, TRENDS BIOCHEM SCI, V23, P324 ; DANSON MJ, 1993, BIOCH ARCHAEA ARCHAE, P1 ; DAYHOFF MO, 1972, ATLAS PROTEIN SEQUEN, V5, P89 ; DECKERT G, 1998, NATURE, V392, P353 ; DELONG EF, 1992, P NATL ACAD SCI USA, V89, P5685 ; DELONG EF, 1994, NATURE, V371, P695 ; DIAZLAZCOZ Y, 1998, MOL BIOL EVOL, V15, P1548 ; DOOLITTLE WF, 1994, P NATL ACAD SCI USA, V91, P6721 ; DOOLITTLE WF, 1998, CURR BIOL, V8, R209 ; DOOLITTLE WF, 1998, NATURE, V392, P15 ; DOOLITTLE WF, 1999, SCIENCE, V284, P2124 ; EDGELL DR, 1997, CELL, V89, P995 ; FAGUY DM, 2000, TRENDS GENET, V16, P196 ; FELSENSTEIN J, 1993, PHYLIP PHYLOGENY INF ; FITCH WM, 1987, COLD SPRING HARB SYM, V52, P759 ; FLEISCHMANN RD, 1995, SCIENCE, V269, P496 ; FORTERRE P, 1999, BIOESSAYS, V21, P871 ; FORTERRE P, 2000, TRENDS GENET, V16, P152 ; FOX GE, 1977, P NATL ACAD SCI USA, V74, P4537 ; FUHRMAN JA, 1992, NATURE, V356, P148 ; GOGARTEN JP, 1989, P NATL ACAD SCI USA, V86, P6661 ; GOGARTEN JP, 1999, CURR OPIN GENET DEV, V9, P630 ; GOLDGUR Y, 1997, STRUCTURE, V5, P59 ; GRAHAM DE, 2000, P NATL ACAD SCI USA, V97, P3304 ; HENIKOFF S, 1992, P NATL ACAD SCI USA, V89, P10915 ; HILARIO E, 1993, BIOSYSTEMS, V31, P111 ; IBBA M, 1997, SCIENCE, V278, P1119 ; IWABE N, 1989, P NATL ACAD SCI USA, V86, P9355 ; JAIN R, 1999, P NATL ACAD SCI USA, V96, P3801 ; KATES M, 1993, BIOCH ARCHAEA ; KEELING PJ, 1994, CURR OPIN GENE DEV, V4, P816 ; KLENK HP, 1999, J MOL EVOL, V48, P528 ; KOONIN EV, 1996, TRENDS GENET, V12, P334 ; KOONIN EV, 1997, MOL MICROBIOL, V25, P619 ; KUNST F, 1997, NATURE, V390, P249 ; KYRPIDES NC, 1998, P NATL ACAD SCI USA, V95, P224 ; LAKE JA, 1988, NATURE, V331, P184 ; LANDER ES, 2001, NATURE, V409, P860 ; LANGER D, 1995, P NATL ACAD SCI USA, V92, P5768 ; LAWRENCE JG, 1996, GENETICS, V143, P1843 ; LAWRENCE JG, 1997, TRENDS MICROBIOL, V5, P355 ; LAWSON FS, 1996, MOL BIOL EVOL, V13, P970 ; LECHLER A, 1997, FEBS LETT, V420, P139 ; LECHLER A, 1998, J MOL BIOL, V278, P897 ; LOPEZ P, 1999, J MOL EVOL, V49, P496 ; MARCOTTE EM, 1999, SCIENCE, V285, P751 ; MARGULIS L, 1970, ORIGIN EUKARYOTIC CE ; MARTIN W, 1998, NATURE, V392, P37 ; MOREIRA D, 1998, J MOL EVOL, V47, P517 ; OCHMAN H, 2000, NATURE, V405, P299 ; OLSEN GJ, 1994, J BACTERIOL, V176, P1 ; OLSEN GJ, 1997, CELL, V89, P991 ; OVERBEEK R, 1999, P NATL ACAD SCI USA, V96, P2896 ; PACE NR, 1991, CELL, V65, P531 ; PELLEGRINI M, 1999, P NATL ACAD SCI USA, V96, P4285 ; PHILIPPE H, 1999, J MOL EVOL, V49, P509 ; REEVE JN, 1997, CELL, V89, P999 ; RIVERA MC, 1992, SCIENCE, V257, P74 ; RIVERA MC, 1998, P NATL ACAD SCI USA, V95, P6239 ; SALZBERG SL, 2001, SCIENCE, V292, P1903 ; SANNI A, 1991, P NATL ACAD SCI USA, V88, P8387 ; SCHIMMEL P, 2000, TRENDS BIOCHEM SCI, V25, P207 ; SCHOPF JW, 1993, SCIENCE, V260, P640 ; SIMOS G, 1996, EMBO J, V15, P5437 ; SMITH MW, 1992, TRENDS BIOCHEM SCI, V17, P489 ; SNEL B, 1999, NAT GENET, V21, P108 ; STANHOPE MJ, 2001, NATURE, V411, P940 ; STANIER RY, 1941, J BACTERIOL, V42, P437 ; STANIER RY, 1962, ARCH MIKROBIOL, V42, P17 ; STANIER RY, 1970, S SOC GEN MICROBIOL, V20, P1 ; STEIN JL, 1996, P NATL ACAD SCI USA, V93, P6228 ; SWOFFORD DL, 1999, PAUP PHYLOGENETIC AN ; TEICHMANN SA, 1999, J MOL EVOL, V49, P98 ; THOMPSON JD, 1994, NUCLEIC ACIDS RES, V22, P4673 ; WILDING EI, 2000, J BACTERIOL, V182, P4319 ; WOESE CR, 1977, P NATL ACAD SCI USA, V51, P221 ; WOESE CR, 1977, P NATL ACAD SCI USA, V51, P221 ; WOESE CR, 1987, MICROBIOL REV, V51, P221 ; WOESE CR, 1990, P NATL ACAD SCI USA, V87, P4576 ; WOESE CR, 2000, MICROBIOL MOL BIOL R, V64, P202 ; WOLF YI, 1999, GENOME RES, V9, P689 ; ZILLIG W, 1991, CURR OPIN GENE DEV, V1, P457}, de = {Archaea; comparative genomics; eubacteria; phenylalanyl-tRNAEOLEOLsynthetase; universal tree}, ga = {473RD}, j9 = {SYST BIOL}, ji = {Syst. Biol.}, keywords = {TRANSFER-RNA SYNTHETASES; LATERAL GENE-TRANSFER; GLUTAMYL-TRANSFER-RNA; UNIVERSAL TREE; HORIZONTAL TRANSFER; ARCHAEAL DIVERSITY; AQUIFEX-PYROPHILUS; ELONGATION-FACTOR; SELFISH OPERONS; LIFE}, la = {English}, nr = {101}, owner = {rec}, pa = {11 NEW FETTER LANE, LONDON EC4P 4EE, ENGLAND}, pg = {16}, pi = {LONDON}, publisher = {Taylor \& Francis Ltd}, rp = {Brown, JR, Glaxo SmithKline Pharmaceut, Div Bioinformat, MicrobialEOLEOLBioinformat Dept, 1250 S Collegeville Rd,POB 5089,UP1345, Collegeville,EOLEOLPA 19426 USA.}, sc = {Evolutionary Biology}, sn = {1063-5157}, tc = {12}, timestamp = {2007.06.17}, ut = {ISI:000171061000005} } @ARTICLE{Brum2005, author = {Brum, J. R.}, title = {{C}oncentration, production and turnover of viruses and dissolved {DNA} pools at {S}tn. {ALOHA}, {N}orth {P}acific {S}ubtropical {G}yre}, journal = {Aquat Microb Ecol}, year = {2005}, volume = {41}, pages = {103--113}, abstract = {The concentrations,. production rates and turnover times of the components of the dissolved DNA (D-DNA) pool, including viruses, were investigated in a depth profile at Stn ALOHA in the North Pacific Subtropical Gyre. A recently developed centrifugal concentration method was used to quantify the 3 major components of the D-DNA pool: free or enzymatically-hydrolyzable D-DNA (ehD-DNA), D-DNA within viruses and uncharacterized bound D-DNA. The production rates of each of these components of the D-DNA pool were estimated using a dilution technique and the turnover times of each component were calculated. Concentrations of total D-DNA and ehD-DNA were approximately 1.2 and 0.6 ng ml(-1), respectively, throughout the mixed layer (upper 100 m), and decreased with increasing depth to 0.2 and 0.06 ng ml(-1) at 500 m, resulting in ehD-DNA constituting 27 to 51% of the total D-DNA pool. Concentrations of viruses ranged from 0.9 to 1.0 x 10(7) ml(-1) within the mixed layer and also decreased with increasing depth to 0.2 x 10(7) ml-1 at 500 m. The average mass of DNA per viral genome was estimated at each depth with viral genome fingerprinting, and ranged from 62.5 to 69.8 ag DNA per virus. Multiplying the concentration of viruses by the average mass of DNA per virus at each depth revealed the concentration of D-DNA within viruses, which ranged from 0.13 to 0.68 ng ml(-1) and constituted 49 to 63 % of the total D-DNA pool. There was no measurable concentration of uncharacterized bound D-DNA in the depth profile. The production rates of ehD-DNA and D-DNA within viruses ranged from 0.10 to 0.41 and 0.03 to 0.07 ng ml(-1) h(-1), respectively, within the mixed layer, but no production of D-DNA could be measured below the mixed layer. The calculated turnover times of ehD-DNA ranged from 0.97 to 6.2 h within the mixed layer and were 3 to 10 times shorter than the turnover times of D-DNA within viruses, which ranged from 9.6 to 24 h. In addition, the amount of phosphorus that was calculated to be produced within the ehD-DNA was able to support the biologically available phosphorus (BAP) demand, based on previously reported measurements of BAP uptake at Stn ALOHA. Using the measured virus production rates, viruses were estimated to lyse 3.2 to 16.5 % of the standing stock of bacteria at Stn ALOHA h(-1), resulting in the release of ehD-DNA, which was estimated as 11 to 35% of the total ehD-DNA production. This research supports the hypothesis that individual components of the D-DNA pool are cycled at different rates and shows that viruses in open-ocean gyre systems may have large impacts on the microbial community there, including viral-induced mortality and subsequent release of cellular contents to the dissolved organic matter pool.}, c1 = {Univ Hawaii, Sch Ocean & Earth Sci & Technol, Honolulu, HI 96822 USA.}, citedreferences = {ALONSO MC, 2000, J EXP MAR BIOL ECOL, V244, P239 ; AMMERMAN JW, 1985, SCIENCE, V227, P1338 ; BEEBEE TJC, 1991, FRESHWATER BIOL, V25, P525 ; BJORKMAN KM, 2003, LIMNOL OCEANOGR, V48, P1049 ; BOEHME J, 1993, MAR ECOL-PROG SER, V97, P1 ; BRATBAK G, 1994, MICROBIAL ECOL, V28, P209 ; BRUM JR, 2004, LIMNOL OCEANOGR-METH, V2, P248 ; BRUSSAARD CPD, 2004, APPL ENVIRON MICROB, V70, P1506 ; CHROST RJ, 1990, AQUAT MICROB ECOL, P47 ; CULLEY AI, 2002, LIMNOL OCEANOGR, V47, P1508 ; DEFLAUN MF, 1986, APPL ENVIRON MICROB, V52, P654 ; DEFLAUN MF, 1987, MAR ECOL-PROG SER, V38, P65 ; FINKEL SE, 2001, J BACTERIOL, V183, P6288 ; FRISCHER ME, 1990, APPL ENVIRON MICROB, V56, P3439 ; FRISCHER ME, 1994, FEMS MICROBIOL ECOL, V15, P127 ; FUHRMAN J, 1992, PRIMARY PRODUCTIVITY, P361 ; FUHRMAN JA, 1982, MAR BIOL, V66, P109 ; FUHRMAN JA, 1995, LIMNOL OCEANOGR, V40, P1236 ; FUHRMAN JA, 1999, NATURE, V399, P541 ; GUNDERSEN K, 1996, MAR ECOL-PROG SER, V137, P305 ; ISHII N, 1998, HYDROBIOLOGIA, V380, P67 ; JEFFREY WH, 1990, MICROBIAL ECOL, V19, P259 ; JIANG SC, 1995, APPL ENVIRON MICROB, V61, P317 ; JONES DR, 1996, DEEP-SEA RES PT I, V43, P1567 ; JORGENSEN NOG, 1993, MAR ECOL-PROG SER, V98, P135 ; JORGENSEN NOG, 1994, APPL ENVIRON MICROB, V60, P4124 ; JORGENSEN NOG, 1996, AQUAT MICROB ECOL, V11, P263 ; KARL DM, 1989, LIMNOL OCEANOGR, V34, P543 ; KARL DM, 2001, DEEP-SEA RES PT II, V48, P1449 ; KARL DM, 2001, DEEP-SEA RES PT II, V48, P1529 ; KAWABATA Z, 1998, HYDROBIOLOGIA, V385, P71 ; MARUYAMA A, 1993, APPL ENVIRON MICROB, V59, P712 ; MATSUI K, 2001, AQUAT MICROB ECOL, V26, P95 ; MONGER BC, 1993, APPL ENVIRON MICROB, V59, P905 ; NOBLE RT, 1998, AQUAT MICROB ECOL, V14, P113 ; PAUL JH, 1987, APPL ENVIRON MICROB, V53, P170 ; PAUL JH, 1988, APPL ENVIRON MICROB, V54, P1682 ; PAUL JH, 1989, APPL ENVIRON MICROB, V55, P1865 ; PAUL JH, 1990, APPL ENVIRON MICROB, V56, P2957 ; PAUL JH, 1991, APPL ENVIRON MICROB, V57, P2197 ; SIUDA W, 1996, ARCH HYDROBIOL SPEC, V48, P155 ; SIUDA W, 1998, AQUAT MICROB ECOL, V15, P89 ; SIUDA W, 2000, AQUAT MICROB ECOL, V21, P195 ; SKOOG DA, 2000, ANAL CHEM INTRO ; STEWARD GF, 1996, MAR ECOL-PROG SER, V131, P287 ; STEWARD GF, 2000, LIMNOL OCEANOGR, V45, P1697 ; STEWARD GF, 2001, METHOD MICROBIOL, P85 ; TURK V, 1992, APPL ENVIRON MICROB, V58, P3744 ; WEINBAUER MG, 1993, APPL ENVIRON MICROB, V59, P4074 ; WEINBAUER MG, 1995, MICROBIAL ECOL, V30, P25 ; WEINBAUER MG, 1999, AQUAT MICROB ECOL, V18, P217 ; WEN K, 2004, APPL ENVIRON MICROB, V70, P3862 ; WILHELM SW, 1999, BIOSCIENCE, V49, P781 ; WILHELM SW, 2002, MICROBIAL ECOL, V43, P168 ; WOMMACK KE, 2000, MICROBIOL MOL BIOL R, V64, P69}, de = {dissolved DNA; virus; Stn ALOHA; North Pacific Subtropical Gyre}, em = {jbrum@hawaii.edu}, ga = {996EO}, j9 = {AQUAT MICROB ECOL}, ji = {Aquat. Microb. Ecol.}, keywords = {AQUATIC ENVIRONMENTS; MARINE-BACTERIA; HETEROTROPHIC BACTERIOPLANKTON; PHOSPHORUS REGENERATION; NATURAL TRANSFORMATION; MICROBIAL-POPULATIONS; EXTRACELLULAR DNA; NUCLEIC-ACIDS; STATION ALOHA; ADRIATIC SEA}, la = {English}, nr = {55}, owner = {rec}, pa = {NORDBUNTE 23, D-21385 OLDENDORF LUHE, GERMANY}, pg = {11}, pi = {OLDENDORF LUHE}, publisher = {Inter-Research}, rp = {Brum, JR, Univ Hawaii, Sch Ocean & Earth Sci & Technol, 1000 Pope Rd,EOLEOLHonolulu, HI 96822 USA.}, sc = {Ecology; Marine & Freshwater Biology}, sn = {0948-3055}, tc = {0}, timestamp = {2007.06.17}, ut = {ISI:000234157400001} } @ARTICLE{Brum2004, author = {Brum, Jennifer R. and Steward, Grieg F. and Karl, David M.}, title = {{A} novel method for the measurement of dissolved deoxyribonucleic acid in seawater}, journal = {Limnol Oceanogr Methods}, year = {2004}, volume = {2}, pages = {248--255}, owner = {rec}, timestamp = {2007.06.17} } @ARTICLE{Button2001, author = {Button, D. K. and Robertson, Betsy R.}, title = {Determination of {DNA} content of aquatic bacteria by flow cytometry}, journal = {Appl Environ Microbiol}, year = {2001}, volume = {67}, pages = {1636--1645}, abstract = {The distribution of DNA among bacterioplankton and bacterial isolates was determined by flow cytometry of DAPI (4',6'-diamidino-2-phenylindole)-stained organisms. Conditions were optimized to minimize error from nonspecific staining, AT bias, DNA packing, changes in ionic strength, and differences in cell permeability. The sensitivity was sufficient to characterize the small 1- to 2-Mb-genome organisms in freshwater and seawater, as well as low-DNA cells ("dims"). The dims could be formed from laboratory cultivars; their apparent DNA content was 0.1 Mb and similar to that of many particles in seawater. Preservation with formaldehyde stabilized samples until analysis. Further permeabilization with Triton X-100 facilitated the penetration of stain into stain-resistant lithotrophs. The amount of DNA per cell determined by flow cytometry agreed with mean values obtained from spectrophotometric analyses of cultures. Correction for the DNA AT bias of the stain was made for bacterial isolates with known G+C contents. The number of chromosome copies per cell was determined with pure cultures, which allowed growth rate analyses based on cell cycle theory. The chromosome ratio was empirically related to the rate of growth, and the rate of growth was related to nutrient concentration through specific affinity theory to obtain a probe for nutrient kinetics. The chromosome size of a Marinobacter arcticus isolate was determined to be 3.0 Mb by this method. In a typical seawater sample the distribution of bacterial DNA revealed two major populations based on DNA content that were not necessarily similar to populations determined by using other stains or protocols. A mean value of 2.5 fg of DNA cell[-]1 was obtained for a typical seawater sample, and 90% of the population contained more than 1.1 fg of DNA cell[-]1.}, comment = {10.1128/AEM.67.4.1636-1645.2001}, owner = {rec}, timestamp = {2008.07.22} } @ARTICLE{Carmack2004, author = {Carmack, Eddy C. and Macdonald, Robie W. and Jasper, Steve}, title = {Phytoplankton productivity on the {C}anadian {S}helf of the {B}eaufort {S}ea}, journal = {Mar Ecol Prog Ser}, year = {2004}, volume = {277}, pages = {37--50}, date = {August 16, 2004}, doi = {10.3354/meps277037}, owner = {rec}, timestamp = {2010.09.13}, url = {http://www.int-res.com/abstracts/meps/v277/p37-50/} } @ARTICLE{Catlin1956, author = {B. W. Catlin}, title = {Extracellular deoxyribonucleic acid of bacteria and a deoxyribonuclease inhibitor.}, journal = {Science}, year = {1956}, volume = {124}, pages = {441--442}, keywords = {Bacteria, metabolism; DNA, analysis}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {13360267}, timestamp = {2009.07.27} } @ARTICLE{Chamier1993, author = {Bärbel Chamier and Michael G Lorenz and Wilfried Wackernagel}, title = {Natural transformation of \emph{{A}cinetobacter calcoaceticus} by plasmid {DNA} adsorbed on sand and groundwater aquifer material.}, journal = {Appl Environ Microbiol}, year = {1993}, volume = {59}, pages = {1662--1667}, abstract = {It is known that plasmid DNA and linear duplex DNA molecules adsorb to chemically purified mineral grains of sand and to particles of several clay fractions. It seemed desirable to examine whether plasmid DNA would also adsorb to nonpurified mineral materials taken from the environment and, particularly, whether adsorbed plasmid DNA would be available for natural transformation of bacteria. Therefore, microcosms consisting of chemically pure sea sand plus buffered CaCl(2) solution were compared with microcosms consisting of material sampled directly from a groundwater aquifer (GWA) plus groundwater (GW) with respect to the natural transformation of Acinetobacter calcoaceticus by mineral-associated DNA. The GWA minerals were mostly sand with inorganic precipitates and organic material plus minor quantities of silt and clay (illite and kaolinite). The amount of plasmid DNA which adsorbed to GWA (in GW) was about 80\% of the amount which adsorbed to purified sand (in buffered CaCl(2) solution). Plasmid DNA adsorbed on sand transformed A. calcoaceticus significantly less efficiently than did plasmid DNA in solution. In contrast, the transformation by sand-adsorbed chromosomal DNA was as high as that by DNA in solution. In GWA/GW microcosms, the efficiency of transformation by chromosomal DNA was similar to that in sand microcosms, whereas plasmid transformation was not detectable. However, plasmid transformants were found at a low frequency when GWA was loaded with both chromosomal and plasmid DNA. Reasons for the low transformation efficiency of plasmid DNA adsorbed to mineral surfaces are discussed. Control experiments showed that the amounts of plasmid and chromosomal DNA desorbing from sand during incubation with a cell-free filtrate of a competent cell suspension did not greatly contribute to transformation in sand microcosms, suggesting that transformation occurred by direct uptake of DNA from the mineral surfaces. Taken together, the observations suggest that plasmid DNA and chromosomal DNA fragments which are adsorbed on mineral surfaces in a sedimentary or soil habitat may be available (although with different efficiencies for the two DNA species) for transformation of a naturally competent gram-negative soil bacterium.}, institution = {Genetik, Fachbereich Biologie, Universität Oldenburg, D-2900 Oldenburg, Germany.}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {16348943}, timestamp = {2009.07.27} } @ARTICLE{Collins2008, author = {Collins, R. Eric and Carpenter, Shelly D. and Deming, Jody W.}, title = {{S}patial heterogeneity and temporal dynamics of particles, bacteria, and p{EPS} in {A}rctic winter sea ice}, journal = {J Mar Sys}, year = {2008}, volume = {74}, pages = {902--917}, abstract = {Abundances of particles, total bacteria, and particulate extracellular polymeric substances (pEPS) in Arctic sea ice were tracked through a winter season to examine the impact of combined extremes of low temperature and high salinity on the prokaryotic microbial community. Three horizons, centered at depths of 25, 45, and 65 cm from the ice surface, with mean seasonal temperatures of - 20, - 17, and - 13 [degree sign]C, respectively, were sampled 16 times over the course of 12 weeks. Microscopic counts of bacteria (stained with DAPI) and particles (stained with acridine orange) reflected the dynamic conditions of the growing ice sheet, with greater abundances and variability in the upper ice horizons compared to the lower. The trend of higher particle and bacterial abundances in the upper ice was corroborated by several full-depth profiles taken during the expedition, which also displayed significantly decreasing cell abundance with depth. Bacterial abundance declined slowly and significantly with time in the upper and middle ice horizons, but not in the lowest, suggesting that much of the prokaryotic microbial community is resilient to extreme environmental conditions. We found that pEPS concentrations increased significantly with time and with decreasing temperatures in all depth horizons, which may lend support to the argument that sea ice bacteria produce EPS in situ as a cryoprotectant.}, doi = {10.1016/j.jmarsys.2007.09.005}, keywords = {Canada, Northwest Territories, Franklin Bay, Canadian Arctic, Particles, Bacteria, Extracellular polymeric substances, Sea ice, Brine, Winter, Arctic}, owner = {rec}, timestamp = {2008.01.04}, url = {http://dx.doi.org/10.1016/j.jmarsys.2007.09.005} } @ARTICLE{CollinsVirus, author = {Collins, R. E. and Jody W. Deming}, title = {Abundant dissolved genetic material in {A}rctic sea ice, {P}art {II}: {V}iral dynamics during autumn freeze-up}, journal = {Polar Biol}, year = {submitted this issue}, owner = {rec}, timestamp = {2010.09.13} } @ARTICLE{Collins2010, author = {R. Eric Collins and Gabrielle Rocap and Jody W Deming}, title = {Persistence of bacterial and archaeal communities in sea ice through an {A}rctic winter}, journal = {Environ Microbiol}, year = {2010}, volume = {12}, pages = {1828--1841}, abstract = {The structure of bacterial communities in first-year spring and summer sea ice differs from that in source seawaters, suggesting selection during ice formation in autumn or taxon-specific mortality in the ice during winter. We tested these hypotheses by weekly sampling (January-March 2004) of first-year winter sea ice (Franklin Bay, Western Arctic) that experienced temperatures from -9 degrees C to -26 degrees C, generating community fingerprints and clone libraries for Bacteria and Archaea. Despite severe conditions and significant decreases in microbial abundance, no significant changes in richness or community structure were detected in the ice. Communities of Bacteria and Archaea in the ice, as in under-ice seawater, were dominated by SAR11 clade Alphaproteobacteria and Marine Group I Crenarchaeota, neither of which is known from later season sea ice. The bacterial ice library contained clones of Gammaproteobacteria from oligotrophic seawater clades (e.g. OM60, OM182) but no clones from gammaproteobacterial genera commonly detected in later season sea ice by similar methods (e.g. Colwellia, Psychrobacter). The only common sea ice bacterial genus detected in winter ice was Polaribacter. Overall, selection during ice formation and mortality during winter appear to play minor roles in the process of microbial succession that leads to distinctive spring and summer sea ice communities.}, doi = {10.1111/j.1462-2920.2010.02179.x}, institution = {School of Oceanography, Box 357940, 1503 NE Boat St., University of Washington, Seattle, WA 98195, USA. rec3141@ocean.washington.edu}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {EMI2179}, pmid = {20192970}, timestamp = {2010.09.13}, url = {http://dx.doi.org/10.1111/j.1462-2920.2010.02179.x} } @ARTICLE{CoxWeeks1986, author = {Cox, G. F. N. and Weeks, W. F.}, title = {{C}hanges in the salinity and porosity of sea-ice samples during shipping and storage}, journal = {J Glaciol}, year = {1986}, volume = {32}, pages = {371--375}, owner = {rec}, timestamp = {2006.12.11}, ut = {ISI:A1986F839800011} } @ARTICLE{CoxWeeks1983, author = {Cox, G. F. N. and Weeks, W. F.}, title = {{E}quations for determining the gas and brine volumes in sea-ice samples}, journal = {J Glaciol}, year = {1983}, volume = {29}, pages = {306--316}, owner = {rec}, timestamp = {2006.12.11}, ut = {ISI:A1983RQ48200011} } @ARTICLE{Dahlberg1998, author = {Dahlberg, C. and Bergstr\"om, M. and Andreasen, M. and Christensen, B. B. and Molin, S. and Hermansson, M.}, title = {Interspecies bacterial conjugation by plasmids from marine environments visualized by gfp expression}, journal = {Mol Biol Evol}, year = {1998}, volume = {15}, pages = {385--390}, abstract = {Horizontal transmission of DNA between different species may have played an important role in evolutionary history. Gene transfer encoded by bacterial plasmids has occurred between distantly related bacterial species; it may have occurred between species of different kingdoms. We have developed a system to detect conjugal plasmid transfer in situ based on the expression of the green fluorescent protein (GFP). Plasmids were tagged with the gfp gene under the control of a Inc promoter. These plasmids were placed in a Pseudomonas putida strain carrying a chromosomal lac repressor. In conjugation mixtures, the donor strain remained nonfluorescent, but any newly formed transconjugant cell fluoresced. Unlike other assays for conjugation, this assay is sensitive enough to detect the formation of a single transconjugant a short time after it occurs. We tested for the transfer of three plasmids that were originally exogenously isolated from marine bacterial communities. Eleven of the 19 different eubacterial recipients formed transconjugants, including a species only distantly related to the donor, Planctomyces maris. The results imply that interspecies gene transfer mediated by conjugation is common in natural environments, and may explain why similar DNA sequences can be found among distantly related bacterial species.}, c1 = {Univ Gothenburg, Dept Gen & Marine Microbiol, Lundberg Lab, S-40530 Gothenburg, Sweden.EOLEOLTech Univ Denmark, Dept Microbiol, DK-2800 Lyngby, Denmark.}, citedreferences = {ANDREASEN M, 1997, THESIS U COPENHAGEN ; BALE MJ, 1988, APPL ENVIRON MICROB, V54, P972 ; CHALFIE M, 1994, SCIENCE, V263, P802 ; CHRISTENSEN BB, 1996, GENE, V173, P59 ; COUTURIER M, 1988, MICROBIOL REV, V52, P375 ; DAHLBERG C, 1997, APPL ENVIRON MICROB, V63, P4692 ; FARRAND SK, 1993, BACTERIAL CONJUGATIO, P255 ; FRY JC, 1990, BACTERIAL GENETICS N, P55 ; FUERST JA, 1995, MICROBIOL-UK, V141, P1493 ; GROISMAN EA, 1992, EMBO J, V11, P1309 ; GUINEY DG, 1989, PROMISCUOUS PLASMIDS, P27 ; GUINEY DG, 1993, BACTERIAL CONJUGATIO, P75 ; GUISEPPI A, 1991, GENE, V106, P109 ; HEIM R, 1994, P NATL ACAD SCI USA, V91, P12501 ; HEINEMANN JA, 1989, NATURE, V340, P205 ; HERRERO M, 1990, J BACTERIOL, V172, P6557 ; HIRSCH AM, 1995, MOL BIOL EVOL, V12, P16 ; HOYER LL, 1992, MOL MICROBIOL, V6, P873 ; IYER VN, 1989, PROMISCUOUS PLASMIDS, P165 ; JAENECKE S, 1996, MOL MICROBIOL, V21, P293 ; KIDWELL MG, 1993, ANNU REV GENET, V27, P235 ; LAWRENCE JG, 1995, J BACTERIOL, V177, P6371 ; LAWRENCE JG, 1997, J MOL EVOL, V44, P383 ; LEVY SB, 1989, GENE TRANSFER ENV ; MANIATIS T, 1982, MOL CLONING ; MAZODIER P, 1991, ANNU REV GENET, V25, P147 ; SMITH MW, 1992, TRENDS BIOCHEM SCI, V17, P489 ; SOUBRIER F, 1992, GENE, V116, P99 ; SYVANEN M, 1994, ANNU REV GENET, V28, P237 ; VALENTINE CRI, 1989, PROMISCUOUS PLASMIDS, P125}, de = {plasmids; horizontal transfer; broad host range; interspecies; marine;EOLEOLgfp}, ga = {ZF262}, j9 = {MOL BIOL EVOL}, ji = {Mol. Biol. Evol.}, keywords = {GREEN FLUORESCENT PROTEIN; GENE-TRANSFER; HORIZONTAL TRANSFER; CLONING; EVOLUTION; SEQUENCE; MARKER}, la = {English}, nr = {30}, owner = {rec}, pa = {PO BOX 1897, LAWRENCE, KS 66044-8897 USA}, pg = {6}, pi = {LAWRENCE}, publisher = {Soc Molecular Biology Evolution}, rp = {Hermansson, M, Univ Gothenburg, Dept Gen & Marine Microbiol, LundbergEOLEOLLab, Box 462, S-40530 Gothenburg, Sweden.}, sc = {Biochemistry & Molecular Biology; Evolutionary Biology; Genetics &EOLEOLHeredity}, sn = {0737-4038}, tc = {12}, timestamp = {2007.06.17}, ut = {ISI:000072879900004} } @ARTICLE{DeFlaun1987, author = {M.F. DeFlaun and J.H. Paul and W.H. Jeffrey}, title = {Distribution and molecular weight of dissolved {DNA} in subtropical estuarine and oceanic environments}, journal = {Mar Ecol Prog Ser}, year = {1987}, volume = {48}, pages = {65--73}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Dellanno1998, author = {A. Dell'Anno and M. Fabiano and G. C. A. Duineveld and A. Kok and R. Danovaro}, title = {Nucleic acid ({DNA}, {RNA}) quantification and {RNA}/{DNA} ratio determination in marine sediments: comparison of spectrophotometric, fluorometric, and {H}igh {P}erformance {L}iquid {C}hromatography methods and estimation of detrital {DNA}}, journal = {Appl Environ Microbiol}, year = {1998}, volume = {64}, pages = {3238--3245}, abstract = {In this study, we compared three methods for extraction and quantification of RNA and DNA from marine sediments: (i) a spectrophotometric method using the diphenylamine assay; (ii) a fluorometric method utilizing selective fluorochromes (thiazole orange for total nucleic acids and Hoechst 33258 for DNA); and (iii) a high-pressure liquid chromatography (HPLC) method which uses a specific column to separate RNA and DNA and UV absorption of the nucleic acids for quantification. Sediment samples were collected in the oligotrophic Cretan Sea (eastern Mediterranean, from 40 to 1,540 m in depth) and compared to the distribution and composition of the benthic microbial assemblages (i.e., bacteria and microprotozoa). DNA concentrations measured spectrophotometrically and by HPLC were not significantly different, while fluorometric yields were significantly lower. Such differences appear mainly due to fact that the stain-DNA complex is strongly dependent on the DNA composition and structure. RNA concentrations determined by the three methods displayed some differences; fluorometric and spectrophotometric methods obtain RNA concentration by difference and therefore may be biased by DNA estimates. By contrast, the HPLC method provides independent assessments of RNA and DNA concentrations. We tentatively estimated the contribution of the detrital DNA to the total DNA pools in two ways. The two calculations provided quite similar results indicating that the majority of the DNA pool in the deep-sea sediments was detrital. Microbial RNA generally accounted for almost the entire sedimentary RNA pools below 100-m depth. RNA concentrations were found to decrease along the Cretan shelf and slope. The RNA/DNA ratio calculated by using fluorometric DNA concentrations was significantly correlated with values of sediment community oxygen consumption only below 100-m depth (dominated by the microbial biomass). These data suggest that the RNA/DNA ratio, based on fluorometric estimates of DNA, can be used as an indicator of benthic metabolic activity, but only when metazoan contribution to the microbial DNA is negligible.}, institution = {Faculty of Science, Marine Science, University of Ancona, Ancona, Italy.}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {9726866}, timestamp = {2009.11.05} } @ARTICLE{Droge1998, author = {Marcus Dr\"oge and Alfred P\"uhler and Werner Selbitschka}, title = {Horizontal gene transfer as a biosafety issue: A natural phenomenon of public concern}, journal = {J Biotechnol}, year = {1998}, volume = {64}, pages = {75--90}, abstract = {The transfer of genetic information between distantly or even unrelated organisms during evolution had been inferred from nucleotide sequence comparisons. These studies provided circumstantial evidence that in rare cases genes had been laterally transmitted amongst organisms of the domains bacteria, archaea and eukarya. Laboratory-based studies confirmed that the gene pools of the various domains of organisms are linked. Amongst the bacterial gene exchange mechanisms transduction, transformation and conjugation, the latter was identified as the mechanism with potentially the broadest host range of transfer. Previously, the issue of horizontal gene transfer has become important in the context of biosafety. Gene transfer studies carried out under more natural conditions such as in model ecosystems or in the environment established that all gene transfer mechanisms worked under these conditions. Moreover, environmental hot-spots were identified where favourable conditions such as nutrient enrichment increased the probability of genetic exchange among bacteria. In particular, the phytosphere was shown to provide conducive conditions for conjugative gene exchange. Concern has been expressed that transfer of recombinant DNA (e.g. antibiotic resistance genes) from genetically modified organisms (GMOs) such as transgenic plants to phytosphere bacteria may occur and thus contribute to the undesirable spread of antibiotic resistance determinants. Studies which were performed to address this issue clearly showed that such a transfer occurs, if at all, at extremely low frequency.}, doi = {DOI: 10.1016/S0168-1656(98)00105-9}, issn = {0168-1656}, owner = {rec}, timestamp = {2009.08.22} } @ARTICLE{Draghi2006, author = {Jeremy A Draghi and Paul E Turner}, title = {{DNA} secretion and gene-level selection in bacteria.}, journal = {Microbiology}, year = {2006}, volume = {152}, pages = {2683--2688}, abstract = {Natural genetic transformation can facilitate gene transfer in many genera of bacteria and requires the presence of extracellular DNA. Although cell lysis can contribute to this extracellular DNA pool, several studies have suggested that the secretion of DNA from living bacteria may also provide genetic material for transformation. This paper reviews the evidence for specific secretion of DNA from intact bacteria into the extracellular environment and examines this behaviour from a population-genetics perspective. A mathematical model demonstrates that the joint action of DNA secretion and transformation creates a novel type of gene-level natural selection. This model demonstrates that gene-level selection could explain the existence of DNA secretion mechanisms that provide no benefit to individual cells or populations of bacteria. Additionally, the model predicts that any trait affecting DNA secretion will experience selection at the gene level in a transforming population. This analysis confirms that the secretion of DNA from intact bacterial cells is fully explicable with evolutionary theory, and reveals a novel mechanism for bacterial evolution.}, doi = {10.1099/mic.0.29013-0}, institution = {Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA. jeremy.draghi@yale.edu}, keywords = {Bacteria, genetics; DNA, Bacterial, secretion; Evolution; Gene Transfer, Horizontal; Genetics, Population; Models, Genetic; Selection (Genetics); Transformation, Bacterial}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {152/9/2683}, pmid = {16946263}, timestamp = {2009.07.27}, url = {http://dx.doi.org/10.1099/mic.0.29013-0} } @ARTICLE{Edelman1967, author = {M. Edelman and D. Swinton and J. A. Schiff and H. T. Epstein and B. Zeldin}, title = {Deoxyribonucleic Acid of the blue-green algae (\emph{Cyanophyta})}, journal = {Bacteriol Rev}, year = {1967}, volume = {31}, pages = {315--331}, institution = {Department of Biology, Brandeis University, Waltham, Massachusetts 02154.}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {16350207}, timestamp = {2010.09.13} } @ARTICLE{Eicken2005, author = {Eicken, H. and Gradinger, R. and Gaylord, A. and Mahoney, A. and Rigor, I. and Melling, H.}, title = {{S}ediment transport by sea ice in the {C}hukchi and {B}eaufort {S}eas: {I}ncreasing importance due to changing ice conditions?}, journal = {Deep-Sea Res Pt II}, year = {2005}, volume = {52}, pages = {3281--3302}, abstract = {Sediment-laden sea ice is widespread over the shallow, wide Siberian Arctic shelves, with off-shelf export from the Laptev and East Siberian Seas contributing substantially to the Arctic Ocean's sediment budget. By contrast, the North American shelves, owing to their narrow width and greater water depths, have not been deemed as important for basin-wide sediment transport by sea ice. Observations over the Chukchi and Beaufort shelves in 2001/02 revealed the widespread Occurrence of sediment-laden ice over an area of more than 100,000km(2) between 68 and 74 degrees N and 155 and 170 degrees W. Ice stratigraphic studies indicate that sediment inclusions were associated with entrainment of frazil ice into deformed, multiple layers of rafted nilas, indicative of a flaw-lead environment adjacent to the landfast ice of the Chukchi and Beaufort Seas. This is corroborated by buoy trajectories and satellite imagery indicating entrainment in a coastal polynya in the eastern Chukchi Sea in February of 2002 as well as formation of sediment-laden ice along the Beaufort Sea coast as far eastward as the Mackenzie shelf. Moored upward-loo king sonar on the Mackenzie shelf provides further insight into the ice growth and deformation regime governing sediment entrainment. Analysis of Radarsat Synthetic Aperture (SAR) imagery in conj. unction with bathymetric data help constrain the water depth of sediment resuspension and subsequent ice entrainment (> 20 m for the Chukchi Sea). Sediment loads averaged at 128 t km(-2), with sediment occurring in layers of roughly 0.5 m thickness, mostly in the lower ice layers. The total amount of sediment transported by sea ice (mostly Out of the narrow zone between the landfast ice edge and waters too deep for resuspension and entrainment) is at minimum 4 x 10(6) t in the sampling area and is estimated at 5-8 x 10(6) t over the entire Chukchi and Beaufort shelves in 2001/02, representing a significant term in the sediment budget of the western Arctic Ocean. Recent changes in the Chukchi and Beaufort Sea ice regimes (reduced summer minimum ice extent, ice thinning, reduction in multi-year ice extent, altered drift paths and mid-winter landfast ice break-out events) have likely resulted in an increase of sediment-laden ice in the area. Apart from contributing substantially to along- and across-shelf particulate flow, an increase in the amount of dirty ice significantly impacts (sub-)ice algal production and may enhance the dispersal of pollutants. (c) 2005 Elsevier Ltd. All rights reserved.}, owner = {rec}, timestamp = {2007.06.17}, ut = {ISI:000234894300009} } @ARTICLE{Elsas1987, author = {J.D. van Elsas and J.M. Govaert and J.A. van Veen}, title = {Transfer of plasmid {pFT30} between bacilli in soil as influenced by bacterial population dynamics and soil conditions}, journal = {Soil Biol Biochem}, year = {1987}, volume = {19}, pages = {639--647}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Ewert2011, author = {Marcela Ewert and Jody W. Deming}, title = {Selective retention in saline ice of extracellular polysaccharides produced by the cold-adapted marine bacterium \emph{Colwellia psychrerythraea} strain 34H}, journal = {Annal Glaciol}, year = {2011}, volume = {52}, pages = {111--117}, owner = {rec}, timestamp = {2011.05.12} } @ARTICLE{Forest2007, author = {Alexandre Forest and Makoto Sampei and Hiroshi Hattori and Ryosuke Makabe and Hiroshi Sasaki and Mitsuo Fukuchi and Paul Wassmann and Louis Fortier}, title = {Particulate organic carbon fluxes on the slope of the {M}ackenzie {S}helf ({B}eaufort {S}ea): {P}hysical and biological forcing of shelf-basin exchanges}, journal = {J Mar Sys}, year = {2007}, volume = {68}, pages = {39--54}, doi = {DOI: 10.1016/j.jmarsys.2006.10.008}, issn = {0924-7963}, keywords = {Shelf-basin exchange}, owner = {rec}, timestamp = {2010.09.13}, url = {http://www.sciencedirect.com/science/article/B6VF5-4MJJC3G-1/2/79f32e04875e14e9006fa7a706337b2b} } @ARTICLE{Frischer1994, author = {Frischer, M. E. and Stewart, G. J. and Paul, J. H.}, title = {{P}lasmid transfer to indigenous marine bacterial populations by natural transformation}, journal = {FEMS Microbiol Ecol}, year = {1994}, volume = {15}, pages = {127--135}, abstract = {Horizontal gene transfer among microbial populations has been assumed to occur in the environment, yet direct observations of this phenomenon are rare or limited to observations where the mechanism(s) could not be explicitly determined. Here we demonstrate the transfer of exogenous plasmid DNA to members of indigenous marine bacterial populations by natural transformation, the first report of this process for any natural microbial community. Ten percent of marine bacterial isolates examined were transformed by plasmid DNA while 14% were transformed by chromosomal DNA. Transformation of mixed marine microbial assemblages was observed in 5 of 14 experiments. In every case, acquisition of the plasmid by members of the indigenous flora was accompanied by modification (probably from genetic rearrangement or methylation) that altered its restriction enzyme digestion pattern. Estimation of transformation rates in estuarine environments based upon the distribution of competency and transformation frequencies in isolates and mixed populations ranged from 5 x 10(-4) to 1.5 transformants/1 day. Extrapolation of these rates to ecosystem scales suggests that natural transformation may be an important mechanism for plasmid transfer among marine bacterial communities.}, c1 = {UNIV S FLORIDA,DEPT MARINE SCI,ST PETERSBURG,FL 33701.EOLEOLW GEORGIA COLL,DEPT BIOL,CARROLLTON,GA 30118.}, citedreferences = {BAYA AM, 1986, APPL ENVIRON MICROB, V51, P1285 ; BELLIVEAU BH, 1991, CAN J MICROBIOL, V37, P513 ; BURTON NF, 1982, APPL ENVIRON MICROB, V44, P1026 ; DEFLAUN MF, 1987, MAR ECOL-PROG SER, V38, P65 ; DOWSON CG, 1990, P NATL ACAD SCI USA, V87, P5858 ; FREY J, 1989, PROMISCUOUS PLASMIDS, P79 ; FRISCHER ME, 1990, APPL ENVIRON MICROB, V56, P3439 ; FRISCHER ME, 1993, J GEN MICROBIOL, V139, P753 ; FRY JC, 1990, BACTERIAL GENETICS N ; FRY JC, 1990, BACTERIAL GENETICS N, P55 ; GENTHNER FJ, 1988, APPL ENVIRON MICROB, V54, P115 ; GLASSMAN DL, 1981, PLASMID, V5, P231 ; JEFFREY WH, 1990, MICROBIAL ECOL, V19, P259 ; JIANG SC, 1992, MAR ECOL-PROG SER, V80, P101 ; JUNI E, 1972, J BACTERIOL, V112, P917 ; KOBORI H, 1984, APPL ENVIRON MICROB, V48, P515 ; MEYER R, 1982, J BACTERIOL, V152, P140 ; NORELLI JL, 1991, APPL ENVIRON MICROB, V57, P486 ; OGUNSEITAN OA, 1987, J IND MICROBIOL, V1, P311 ; PAUL JH, 1982, APPL ENVIRON MICROB, V43, P939 ; PAUL JH, 1991, APPL ENVIRON MICROB, V57, P1509 ; PAUL JH, 1992, MOL ECOL, V1, P37 ; PICKUP RW, 1989, MICROBIAL ECOL, V18, P211 ; RAY MK, 1991, MICROBIOS, V67, P151 ; RITTMANN BE, 1990, ENVIRON SCI TECHNOL, V24, P23 ; ROCHELLE PA, 1988, J GEN MICROBIOL, V134, P2933 ; SAMBROOK J, 1989, MOL CLONING LABORATO ; SAUNDERS JR, 1988, METHOD MICROBIOL, V21, P79 ; SCHUTT C, 1989, MICROBIAL ECOL, V17, P49 ; SCHUTT C, 1990, AQUATIC MICROBIAL EC ; SIZEMORE RK, 1977, ANTIMICROB AGENTS CH, V12, P373 ; SMETS BF, 1990, ENVIRON SCI TECHNOL, V24, P162 ; SMITH JM, 1991, NATURE, V349, P29 ; THOMAS CM, 1989, PROMISCUOUS PLASMIDS}, de = {NATURAL TRANSFORMATION; PLASMID; MARINE BACTERIA}, ga = {PP793}, j9 = {FEMS MICROBIOL ECOL}, ji = {FEMS Microbiol. Ecol.}, keywords = {BIOLOGICAL PROCESSES; HIGH-FREQUENCY; RESISTANCE; STRAINS; VIBRIO; GENES; DNA; ACINETOBACTER; ENVIRONMENTS; ESTUARINE}, la = {English}, nr = {34}, owner = {rec}, pa = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, pg = {9}, pi = {AMSTERDAM}, publisher = {Elsevier Science Bv}, sc = {Microbiology}, sn = {0168-6496}, tc = {19}, timestamp = {2007.06.17}, ut = {ISI:A1994PP79300015} } @ARTICLE{Frischer1993, author = {Frischer, M. E. and Thurmond, J. M. and Paul, J. H.}, title = {{F}actors affecting competence in a high-frequency of transformation marine \emph{{V}ibrio}}, journal = {J Gen Microbiol}, year = {1993}, volume = {139}, pages = {753--761}, abstract = {Natural plasmid transformation may be a mechanism for the horizontal transfer of non-conjugative plasmids in the marine environment, yet there are few marine model systems available for the study of this process. Using multimers of IncQ/P4 plasmids and a filter transformation assay, we have measured the effects of nutrients, salinity, temperature, as well as the development and maintenance of competence for genetic transformation in the high frequency of transformation (HFT) marine Vibrio strain WJT-1C. Transformation frequency was proportional to the amount of DNA used from 0.1 to 1.0 mug DNA and was saturated at concentrations greater than 1.0 mug. Competence began in the early-exponential phase and reached a maximum at the onset of stationary phase. Once attained, competence was maintained in both spent and nutrient-free media for at least 10 d. Thus, the establishment and maintenance of competence was unique compared to previously described transformation systems. Temperatures ranging from 4 to 33-degrees-C had no significant effect on the maximal transformation frequency of WJT-1C, but at 37-degrees-C the transformation frequency was reduced. However, temperature did affect the rate of the transformation process. Salinities in the range 12 to 50 parts per thousand had no significant effect on the transformation frequency but transformation frequencies were lower at 6 parts per thousand and 63 parts per thousand. Cells were transformed equally well in nutrient-free media or rich media. The ability of this marine HFT Vibrio strain to develop competence under a wide spectrum of conditions and to maintain the competent state indicates that natural plasmid transformation could occur in conditions found in tropical and subtropical estuaries.}, c1 = {UNIV S FLORIDA,DEPT MARINE SCI,140 7TH AVE S,ST PETERSBURG,FL 33701.}, citedreferences = {AHLQUIST EF, 1980, FEMS MICROBIOLOGY LE, V7, P107 ; ALBANO M, 1987, J BACTERIOL, V169, P3110 ; AVERY OT, 1944, J EXP MED, V79, P137 ; BALE MJ, 1987, J GEN MICROBIOL, V133, P3099 ; BALE MJ, 1988, APPL ENVIRON MICROB, V54, P972 ; BAZALYAN VL, 1979, OCEANOLOGY, V19, P30 ; BRODA P, 1979, PLASMIDS ; CARLSON CA, 1985, J BACTERIOL, V163, P291 ; CONTENTE S, 1979, MOL GEN GENET, V167, P251 ; CRUZE JA, 1979, CURR MICROBIOL, V3, P129 ; DEFLAUN MF, 1986, J MICROBIOL METH, V5, P265 ; DEFLAUN MF, 1987, MAR ECOL-PROG SER, V38, P65 ; DEFLAUN MF, 1989, MICROBIAL ECOL, V18, P21 ; FELSENSTEIN KM, 1988, BIOTECHNIQUES, V6, P847 ; FOSTER TJ, 1983, MICROBIOL REV, V47, P361 ; FREY J, 1989, PROMISCUOUS PLASMIDS, P79 ; FRISCHER ME, 1990, APPL ENVIRON MICROB, V56, P3439 ; FRY JC, 1990, BACTERIAL GENETICS N, P55 ; FULTHORPE RR, 1991, APPL ENVIRON MICROB, V57, P1546 ; GRAHAM JB, 1978, MOL GEN GENET, V166, P287 ; GRIFFITH OM, 1988, BIOTECHNIQUES, V6, P725 ; HENSCHKE RB, 1990, CURR MICROBIOL, V20, P105 ; JEFFREY WH, 1990, MICROBIAL ECOL, V19, P259 ; JUNI E, 1972, J BACTERIOL, V112, P917 ; KLINGMULLER W, 1991, FEMS MICROBIOL ECOL, V85, P107 ; LACKS S, 1973, J BACTERIOL, V114, P152 ; MAEDA M, 1974, J EXP MAR BIOL ECOL, V14, P157 ; MEYER R, 1982, J BACTERIOL, V152, P140 ; MORITA RY, 1985, BACTERIA THEIR NATUR, P111 ; NORELLI JL, 1991, APPL ENVIRON MICROB, V57, P486 ; NOVICK RP, 1969, BACTERIOL REV, V33, P210 ; NOVITSKY JA, 1986, APPL ENVIRON MICROB, V52, P504 ; OGRAM A, 1987, J MICROBIOL METH, V7, P57 ; PAKULA R, 1963, J GEN MICROBIOL, V31, P125 ; PAUL JH, 1982, APPL ENVIRON MICROB, V43, P939 ; PAUL JH, 1987, APPL ENVIRON MICROB, V53, P170 ; PAUL JH, 1991, APPL ENVIRON MICROB, V57, P1509 ; PAUL JH, 1992, MOL ECOL, V1, P37 ; PRETORIUSGUTH IM, 1990, APPL ENVIRON MICROB, V56, P2354 ; REDFIELD RJ, 1991, J BACTERIOL, V173, P5612 ; ROCHELLE PA, 1988, J GEN MICROBIOL, V134, P2933 ; ROCHELLE PA, 1989, J GEN MICROBIOL, V135, P409 ; SAMBRI V, 1989, MICROBIOLOGICA, V12, P323 ; SAMBROOK J, 1989, MOL CLONING LABORATO ; SAUNDERS JR, 1988, METHOD MICROBIOL, V21, P79 ; SAYE DJ, 1990, APPL ENVIRON MICROB, V56, P140 ; SCHUTT C, 1990, AQUAT MICROB ECOL, P160 ; SEIFERT HS, 1988, NATURE, V336, P392 ; SMIT E, 1991, APPL ENVIRON MICROB, V57, P3482 ; SMITH HO, 1981, ANN REV BIOCH, V50, P140 ; SMITH JM, 1991, NATURE, V349, P29 ; SPARLING PF, 1966, J BACTERIOL, V92, P1364 ; STEWART GJ, 1986, ANNU REV MICROBIOL, V40, P211 ; STEWART GJ, 1987, ANNU REV MICROBIOL, V68, P1712 ; STEWART GJ, 1989, GENE TRANSFER ENV, P139 ; STEWART GJ, 1990, APPL ENVIRON MICROB, V56, P1818 ; TOMASZ A, 1964, P NATL ACAD SCI USA, V51, P480 ; TREVORS JT, 1986, CAN J MICROBIOL, V32, P610 ; VANELSAS JD, 1989, CURR MICROBIOL, V19, P375 ; ZAR JH, 1984, BIOSTAT ANAL, P162 ; ZERVOS PH, 1988, BIOTECHNIQUES, V6, P238}, ga = {KY980}, j9 = {J GEN MICROBIOL}, ji = {J. Gen. Microbiol.}, keywords = {NATURAL PLASMID TRANSFORMATION; MERCURY-RESISTANCE PLASMIDS; PSEUDOMONAS-AERUGINOSA; BACILLUS-SUBTILIS; CONJUGAL TRANSFER; DISSOLVED DNA; GENE-TRANSFER; BACTERIA; SOIL; STRAINS}, la = {English}, nr = {61}, owner = {rec}, pa = {HARVEST HOUSE 62 LONDON ROAD, READING, BERKS, ENGLAND RG1 5AS}, pg = {9}, pi = {READING}, pn = {Part 4}, publisher = {Soc General Microbiology}, sc = {Microbiology}, sn = {0022-1287}, tc = {12}, timestamp = {2007.06.17}, ut = {ISI:A1993KY98000011} } @ARTICLE{Frischer1990, author = {Frischer, M. E. and Thurmond, J. M. and Paul, J. H.}, title = {{N}atural plasmid transformation in a high-frequency-of-transformation marine\emph{{V}ibrio} strain}, journal = {Appl Environ Microbiol}, year = {1990}, volume = {56}, pages = {3439--3444}, c1 = {UNIV S FLORIDA,DEPT MARINE SCI,140 7TH AVE S,ST PETERSBURG,FL 33701.}, citedreferences = {AHLQUIST EF, 1980, FEMS MICROBIOLOGY LE, V7, P107 ; AVERY OT, 1944, J EXP MED, V79, P137 ; BAGDASARIAN M, 1981, GENE, V16, P237 ; BAUMANN P, 1984, BERGEYS MANUAL SYSTE, V1, P516 ; BERG DE, 1989, GENE TRANSFER ENV, P99 ; BULUWELA L, 1989, NUCLEIC ACIDS RES, V17, P452 ; CARLSON CA, 1985, J BACTERIOL, V163, P291 ; CHRISTOPHER F, 1989, PROMISCUOUS PLASMIDS, P248 ; CHURCH GM, 1984, P NATL ACAD SCI-BIOL, V81, P1991 ; COUGHTER JP, 1989, A VAN LEEUW J MICROB, V55, P15 ; DEFLAUN MF, 1986, J MICROBIOL METH, V5, P265 ; DEFLAUN MF, 1987, MAR ECOL-PROG SER, V38, P65 ; FELSENSTEIN KM, 1988, BIOTECHNIQUES, V6, P847 ; GRIFFITH OM, 1988, BIOTECHNIQUES, V6, P725 ; HENSCHKE RB, 1990, CURR MICROBIOL, V20, P105 ; JEFFREY WH, 1990, APPL ENVIRON MICROB, V56, P1367 ; JEFFREY WH, 1990, MICROBIAL ECOL, V19, P259 ; LEDERBURG J, 1946, NATURE, V260, P40 ; LEVY SB, 1989, GENE TRANSFER ENV ; MANIATIS T, 1982, MOL CLONING ; MARMUR J, 1961, J MOL BIOL, V3, P208 ; MEYER R, 1982, J BACTERIOL, V152, P140 ; MICHOD RE, 1988, GENETICS, V118, P31 ; PAUL JH, 1982, APPL ENVIRON MICROB, V43, P1393 ; PAUL JH, 1982, APPL ENVIRON MICROB, V43, P939 ; PAUL JH, 1988, APPL ENVIRON MICROB, V54, P1682 ; ROCHELLE PA, 1988, J GEN MICROBIOL, V134, P2933 ; SAUNDERS JR, 1988, METHOD MICROBIOL, P79 ; SAYE DJ, 1990, APPL ENVIRON MICROB, V56, P140 ; SISCO KL, 1979, P NATL ACAD SCI USA, V76, P972 ; SMITH HO, 1981, ANN REV BIOCH, V50, P140 ; STEWART GJ, 1986, ANNU REV MICROBIOL, V40, P211 ; STEWART GJ, 1989, GENE TRANSFER ENV, P139 ; STEWART GJ, 1990, APPL ENVIRON MICROB, V56, P1818 ; ZERVOS PH, 1988, BIOTECHNIQUES, V6, P238 ; ZINDER ND, 1952, J BACTERIOL, V64, P679}, ga = {EF663}, j9 = {APPL ENVIRON MICROBIOL}, ji = {Appl. Environ. Microbiol.}, la = {English}, nr = {36}, owner = {rec}, pa = {1325 MASSACHUSETTS AVENUE, NW, WASHINGTON, DC 20005-4171}, pg = {6}, pi = {WASHINGTON}, publisher = {Amer Soc Microbiology}, sc = {Biotechnology & Applied Microbiology; Microbiology}, sn = {0099-2240}, tc = {22}, timestamp = {2007.06.17}, ut = {ISI:A1990EF66300032} } @ARTICLE{Garcia1978, author = {E. Garcia and P. Lopez and M. T. Ureńa and M. Espinosa}, title = {Early stages in \emph{Bacillus subtilis} transformation: association between homologous {DNA} and surface structures.}, journal = {J Bacteriol}, year = {1978}, volume = {135}, pages = {731--740}, abstract = {The addition of ethylenediaminetetraacetate to competent cultures of Bacillus subtilis irreversibly inhibited the transformability as well as the cellular binding of DNA. Our results show that the inhibition of DNA binding by ethylenediaminetetraacetate in whole cells, protoplasts, and membrane vesicles is mainly due to a permanent alteration of the DNA receptors. Transformation absolutely requires free magnesium ions, whereas DNA binding is a magnesium-independent step. In contrast to ethylenediaminetetraacetate, the absence of Mg2+ does not irreversibly affect the capacity of the competent cells to be transformed DNA-binding receptors located at the cell surface remain associated with the plasma membrane after protoplasting and after isolation of membrane vesicles. A Mg2+-dependent endonucleolytic activity associated with the membrane appears to be responsible for the lower levels of binding by protoplasts in the presence of this ion.}, keywords = {Bacillus subtilis, genetics/metabolism; Calcium, pharmacology; Cell Membrane, metabolism; DNA, Bacterial, metabolism; Edetic Acid, pharmacology; Magnesium, pharmacology; Protoplasts, metabolism; Receptors, Drug, drug effects; Transformation, Bacterial, drug effects}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {99433}, timestamp = {2009.07.27} } @ARTICLE{Garcia-Vallve2000a, author = {Garcia-Vallv\'e, S. and Romeu, A. and Palau, J.}, title = {{H}orizontal gene transfer in bacterial and archaeal complete genomes}, journal = {Genome Res}, year = {2000}, volume = {10}, pages = {1719--1725}, abstract = {There is growing evidence that horizontal gene transfer is a potent evolutionary Force in prokaryotes, although exactly how potent is not known. We have developed a statistical procedure for predicting whether genes of a complete genome have been acquired by horizontal gene transfer. It is based on the analysis of G+C contents, codon usage, amino acid usage, and gene position. When we applied this procedure to 17 bacterial complete genomes and seven archaeal ones, we found that the percentage of horizontally transferred genes varied From 1.5% to 14.5%. Archaea and nonpathogenic bacteria had the highest percentages and pathogenic bacteria, except for Mycoplasma genitalium, had the lowest. As reported in the literature, we found that informational genes were less likely to be transferred than operational genes. Most of the horizontally transferred genes were only present in one or two lineages. Some of these transferred genes include genes that form part of prophages, pathogenecity islands, transposases, integrases, recombinases, genes present only in one of the two Helicobacter pylori strains, and regions of genes functionally related. All of these Findings support the important role of horizontal gene transfer in the molecular evolution of microorganisms and speciation.}, c1 = {Univ Rovira & Virgili, Dept Biochem & Biotechnol, E-43005 Tarragona, Catalonia, Spain.}, citedreferences = {ARAVIND L, 1998, TRENDS GENET, V14, P442 ; CHOU KC, 1995, CRIT REV BIOCHEM MOL, V30, P275 ; DOOLITTLE RF, 1998, NATURE, V392, P339 ; DOOLITTLE WF, 1999, SCIENCE, V284, P2124 ; DOOLITTLE WF, 1999, TRENDS BIOCHEM SCI, V24, M5 ; FUCHS TM, 1998, NATURWISSENSCHAFTEN, V85, P99 ; GARCIAVALLVE S, 1999, MOL BIOL EVOL, V16, P1125 ; GARCIAVALLVE S, 2000, MOL BIOL EVOL, V17, P352 ; GRANTHAM R, 1980, NUCLEIC ACIDS RES, V8, P49 ; GUILLESPIE DT, 1977, J PHYS CHEM-US, V81, P2340 ; HILL MO, 1974, J ROY STAT SOC C-APP, V23, P340 ; JAIN R, 1999, P NATL ACAD SCI USA, V96, P3801 ; KAPLAN JB, 1998, FEMS MICROBIOL LETT, V163, P31 ; KARLIN S, 1998, ANNU REV GENET, V32, P185 ; KOONIN EV, 1997, CURR OPIN GENET DEV, V7, P757 ; KOONIN EV, 1997, MOL MICROBIOL, V25, P619 ; KUNST F, 1997, NATURE, V390, P249 ; LAFAY B, 1999, NUCLEIC ACIDS RES, V27, P1642 ; LAWRENCE JG, 1997, J MOL EVOL, V44, P383 ; LAWRENCE JG, 1998, P NATL ACAD SCI USA, V95, P9413 ; LAWRENCE JG, 1999, CURR OPIN MICROBIOL, V2, P519 ; LI WH, 1997, MOL EVOLUTION ; MARTIN W, 1999, BIOESSAYS, V21, P99 ; MCINERNEY JO, 1997, MICROB COMP GENOM, V2, P1 ; MEDIGUE C, 1991, J MOL BIOL, V222, P851 ; MOSZER I, 1998, FEBS LETT, V430, P28 ; MOSZER I, 1999, CURR OPIN MICROBIOL, V2, P524 ; NAVARRO C, 1993, MOL MICROBIOL, V9, P1181 ; NELSON KE, 1999, NATURE, V399, P323 ; OGAWA KI, 1995, J BACTERIOL, V177, P1409 ; OSAWA S, 1992, MICROBIOL REV, V56, P229 ; PENNISI E, 1998, SCIENCE, V280, P672 ; PONTING CP, 1999, J MOL BIOL, V289, P729 ; ROCHA EPC, 1999, MOL MICROBIOL, V32, P11 ; SMITH MW, 1992, TRENDS BIOCHEM SCI, V17, P489 ; STEPHENS RS, 1998, SCIENCE, V282, P754 ; SYVANEN M, 1994, ANNU REV GENET, V28, P237 ; TATUSOV RL, 2000, NUCLEIC ACIDS RES, V28, P33 ; WOLF YI, 1999, TRENDS GENET, V15, P173}, ga = {374VH}, j9 = {GENOME RES}, ji = {Genome Res.}, keywords = {BACILLUS-SUBTILIS; CODON USAGE; SEQUENCE; EVOLUTION; EXCHANGE; TREE; SPECIATION; BIASES; OPERON}, la = {English}, nr = {39}, owner = {rec}, pa = {1 BUNGTOWN RD, PLAINVIEW, NY 11724 USA}, pg = {7}, pi = {PLAINVIEW}, publisher = {Cold Spring Harbor Lab Press}, rp = {Romeu, A, Univ Rovira & Virgili, Dept Biochem & Biotechnol, E-43005EOLEOLTarragona, Catalonia, Spain.}, sc = {Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology;EOLEOLGenetics & Heredity}, sn = {1088-9051}, tc = {83}, timestamp = {2007.06.17}, ut = {ISI:000165364700010} } @ARTICLE{Garneau2008, author = {Garneau, Marie-\{}Eve and Roy, S\{}ebastien and Lovejoy, Connie and Gratton, Yves and Vincent, Warwick F.}, title = {{S}easonal dynamics of bacterial biomass and production in a coastal arctic ecosystem: {F}ranklin {B}ay, western {C}anadian {A}rctic}, journal = {J Geophys Res}, year = {2008}, volume = {113}, pages = {C07S91}, abstract = {The Canadian Arctic Shelf Exchange Study (CASES) included the overwintering deployment of a research platform in Franklin Bay (70°N, 126°W) and provided a unique seasonal record of bacterial dynamics in a coastal region of the Arctic Ocean. Our objectives were (1) to relate seasonal bacterial abundance (BA) and production (BP) to physico-chemical characteristics and (2) to quantify the annual bacterial carbon flux. BA was estimated by epifluorescence microscopy and BP was estimated from 3H-leucine and 3H-thymidine assays. Mean BA values for the water column ranged from 1.0 (December) to 6.8 × 105 cells mL−1 (July). Integral BP varied from 1 (February) to 80 mg C m−2 d−1 (July). During winter-spring, BP was uncorrelated with chlorophyll a (Chl a), but these variables were significantly correlated during summer-autumn (r s = 0.68, p < 0.001, N = 38), suggesting that BP was subject to bottom-up control by carbon supply. Integrated BP data showed three distinct periods: fall-winter, late winter–late spring, and summer. A baseline level of BB and BP was maintained throughout late winter–late spring despite the persistent cold and darkness, with irregular fluctuations that may be related to hydrodynamic events. During this period, BP rates were correlated with colored dissolved organic matter (CDOM) but not Chl a (r s BP.CDOM∣Chl a = 0.20, p < 0.05, N = 176). Annual BP was estimated as 6 g C m−2 a−1, implying a total BP of 4.8 × 1010 g C a−1 for the Franklin Bay region. These results show that bacterial processes continue throughout all seasons and make a large contribution to the total biological carbon flux in this coastal arctic ecosystem.}, issn = {0148-0227}, keywords = {bacterial production, Arctic Ocean, carbon fluxes, 4840 Oceanography: Biological and Chemical: Microbiology and microbial ecology, 4207 Oceanography: General: Arctic and Antarctic oceanography, 4806 Oceanography: Biological and Chemical: Carbon cycling}, owner = {rec}, publisher = {AGU}, timestamp = {2011.03.07}, url = {http://dx.doi.org/10.1029/2007JC004281} } @ARTICLE{Giovannoni2005, author = {Stephen J Giovannoni and H. James Tripp and Scott Givan and Mircea Podar and Kevin L Vergin and Damon Baptista and Lisa Bibbs and Jonathan Eads and Toby H Richardson and Michiel Noordewier and Michael S Rapp\'{e} and Jay M Short and James C Carrington and Eric J Mathur}, title = {Genome streamlining in a cosmopolitan oceanic bacterium}, journal = {Science}, year = {2005}, volume = {309}, pages = {1242--1245}, abstract = {The SAR11 clade consists of very small, heterotrophic marine alpha-proteobacteria that are found throughout the oceans, where they account for about 25\% of all microbial cells. Pelagibacter ubique, the first cultured member of this clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism. In contrast to parasitic bacteria and archaea with small genomes, P. ubique has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. P. ubique has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins; few paralogs; and the shortest intergenic spacers yet observed for any cell.}, doi = {10.1126/science.1114057}, institution = {Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA. steve.giovannoni{at}oregonstate.edu}, keywords = {Alphaproteobacteria, classification/genetics/isolation /&/ purification/physiology; Bacterial Proteins, genetics/metabolism; Base Composition; Carbon, metabolism; Computational Biology; DNA, Bacterial, chemistry/genetics; DNA, Intergenic; Evolution; Gene Expression Regulation, Bacterial; Genes, Bacterial; Genome, Bacterial; Membrane Transport Proteins, genetics/metabolism; Molecular Sequence Data; Oceans and Seas; Phosphates, metabolism; Phylogeny; Seawater, microbiology; Selection (Genetics); Sigma Factor, genetics; Thymidylate Synthase, genetics}, owner = {rec}, pii = {309/5738/1242}, pmid = {16109880}, timestamp = {2008.09.17}, url = {http://dx.doi.org/10.1126/science.1114057} } @ARTICLE{Gleitz1995, author = {Markus Gleitz and M. R. {v.d. Loeff} and David N. Thomas and Gerhard S. Dieckmann and Frank J. Millero}, title = {Comparison of summer and winter inorganic carbon, oxygen and nutrient concentrations in {A}ntarctic sea ice brine}, journal = {Mar Chem}, year = {1995}, volume = {51}, pages = {81--91}, abstract = {During summer (January 1991) and winter (April 1992) cruises to the southern Weddell Sea (Antarctica), brine samples were collected from first year sea ice and analysed for salinity, temperature, dissolved oxygen and major nutrient concentrations. Additionally, the carbonate system was determined from measurements of pH and total alkalinity. During winter, brine chemical composition was largely determined by seawater concentration in the course of freezing. Brine temperatures ranged from -1.9 to -6.7 C. Precipitation of calcium carbonate was not observed at the corresponding salinity range of 34 to 108. Removal of carbon from the total inorganic carbon pool (up to 500 [mu]mol Ct kg-1) was related to reduced nutrient concentrations, indicating the presence of photosynthetically active ice algal assemblages in the winter sea ice. However, nutrient and inorganic carbon concentrations did generally not reach growth limiting levels for phytoplankton. The combined effect of photosynthesis and physical concentration resulted in O2 concentrations of up to 650 [mu]mol kg-1. During summer, brine salinities ranged from 21 to 41 with most values > 28, showing that the net effect of freezing and melting on brine chemical composition was generally slight. Opposite to the winter situation, brine chemical composition was strongly influenced by biological activity. Photosynthetic carbon assimilation resulted in a Ct depletion of up to 1200 [mu]mol kg-1, which was associated with CO2 (aq) exhaustion and O2 concentrations as high as 933 [mu]mol kg-1. The concurrent depletion of major nutrients generally corresponded to uptake ratios predicted from phytoplankton biochemical composition. Primary productivity in summer sea ice is apparently sustained until inorganic resources are fully exhausted, resulting in brine chemical compositions that differ profoundly from those of surface waters. This may have important implications for pathways of ice algal carbon acquisition, carbon isotope fractionation as well as for species distribution in the open water phytoplankton.}, doi = {DOI: 10.1016/0304-4203(95)00053-T}, issn = {0304-4203}, owner = {rec}, timestamp = {2009.08.22} } @ARTICLE{Gogarten2002, author = {Gogarten, J. P. and Doolittle, W. F. and Lawrence, J. G.}, title = {{P}rokaryotic evolution in light of gene transfer}, journal = {Mol Biol Evol}, year = {2002}, volume = {19}, pages = {2226--2238}, abstract = {Accumulating prokaryotic gene and genome sequences reveal that the exchange of genetic information through both homology-dependent recombination and horizontal (lateral) gene transfer (HGT) is far more important, in quantity and quality, than hitherto imagined. The traditional view, that prokaryotic evolution can be understood primarily in terms of clonal divergence and periodic selection, must be augmented to embrace gene exchange as a creative force, itself responsible for much of the pattern of similarities and differences we see between prokaryotic microbes. Rather than replacing periodic selection on genetic diversity, gene loss, and other chromosomal alterations as important players in adaptive evolution, gene exchange acts in concert with these processes to provide a rich explanatory paradigm-some of whose implications we explore here. In particular, we discuss (1) the role of recombination and HGT in giving phenotypic "coherence" to prokaryotic taxa at all levels of inclusiveness, (2) the implications of these processes for the reconstruction and meaning of "phylogeny," and (3) new views of prokaryotic adaptation and diversification based on gene acquisition and exchange.}, c1 = {Univ Pittsburgh, Dept Biol Sci, Pittsburgh, PA 15260 USA.EOLEOLDalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.EOLEOLUniv Connecticut, Dept Mol & Cell Biol, Storrs, CT 06269 USA.}, citedreferences = {ANDERSSON JO, 1999, CURR OPIN GENET DEV, V9, P664 ; ARBER W, 1979, EXPERIENTIA, V35, P287 ; ASAI T, 1999, P NATL ACAD SCI USA, V96, P1971 ; BEJA O, 2001, NATURE, V411, P786 ; BELL ET, 1905, AM J ANAT, V5, P29 ; BETRAN E, 1997, GENETICS, V146, P89 ; BOGARAD LD, 1999, P NATL ACAD SCI USA, V96, P2591 ; BONEN L, 1975, P NATL ACAD SCI USA, V72, P2310 ; BOUCHER Y, 2001, CURR OPIN MICROBIOL, V4, P285 ; BOUCHER Y, 2001, MOL BIOL EVOL, V18, P1378 ; BROCHIER C, 2000, TRENDS GENET, V16, P529 ; BROWN JR, 2001, NAT GENET, V28, P281 ; CERMAKIAN N, 1997, J MOL EVOL, V45, P671 ; CHISTOSERDOVA L, 1998, SCIENCE, V281, P99 ; COHAN FM, 1994, AM NAT, V143, P965 ; COHAN FM, 1994, TRENDS ECOL EVOL, V9, P175 ; COHAN FM, 2001, SYST BIOL, V50, P513 ; DENAMUR E, 2000, CELL, V103, P711 ; DENAMUR E, 2002, J BACTERIOL, V184, P605 ; DEPPENMEIER U, 2002, J MOL MICROB BIOTECH, V4, P453 ; DOOLITTLE RF, 1990, J MOL EVOL, V31, P383 ; DOOLITTLE RF, 1998, CURR OPIN GENET DEV, V8, P630 ; DOOLITTLE WF, 1999, SCIENCE, V284, P2124 ; DOOLITTLE WF, 1999, TRENDS CELL BIOL, V9, P5 ; DOOLITTLE WF, 2000, CURR OPIN STRUC BIOL, V10, P355 ; DYKHUIZEN DE, 1991, J BACTERIOL, V173, P7257 ; FAGUY DM, 2000, TRENDS GENET, V16, P196 ; FEIL EJ, 2001, P NATL ACAD SCI USA, V98, P182 ; FITZGIBBON ST, 1999, NUCLEIC ACIDS RES, V27, P4218 ; FREIDRICH MW, 2002, J BACTERIOL, V184, P278 ; GARCIAVALLVE S, 2000, MOL BIOL EVOL, V17, P352 ; GODDARD MR, 1999, P NATL ACAD SCI USA, V96, P13880 ; GOGARETN JP, 1996, S SOC GEN MICROBIOLO, P267 ; GOGARTEN JP, 1992, J EXP BIOL, V172, P137 ; GOGARTEN JP, 1995, TRENDS ECOL EVOL, V10, P147 ; GOGARTEN JP, 1999, BIOL BULL, V196, P359 ; GOGARTEN JP, 1999, CURR OPIN GENET DEV, V9, P630 ; GOLDING GB, 1998, MOL BIOL EVOL, V15, P355 ; GOLDMAN BS, 1998, MOL MICROBIOL, V27, P871 ; GRAHAM DE, 2000, P NATL ACAD SCI USA, V97, P3304 ; GUPTA RS, 1993, J MOL EVOL, V37, P573 ; GUTTMAN DS, 1994, SCIENCE, V266, P1380 ; HACKER J, 2000, ANNU REV MICROBIOL, V54, P641 ; HAYES WS, 1998, GENOME RES, V8, P1154 ; HEINEMANN JA, 1989, NATURE, V340, P205 ; IBBA M, 1997, P NATL ACAD SCI USA, V94, P14383 ; JAIN R, 1999, P NATL ACAD SCI USA, V96, P3801 ; JIANG WH, 1995, J BACTERIOL, V177, P6411 ; KARLIN S, 1995, TRENDS GENET, V11, P283 ; KARLIN S, 1998, MOL MICROBIOL, V29, P1341 ; KARLIN S, 2000, J BACTERIOL, V182, P5238 ; KATZ LA, 1996, J MOL EVOL, V43, P453 ; KE DB, 2000, J BACTERIOL, V182, P6913 ; KLEIN M, 2001, J BACTERIOL, V183, P6028 ; KLENK HP, 1999, J MOL EVOL, V48, P528 ; KOONIN EV, 1997, MOL MICROBIOL, V25, P619 ; KOONIN EV, 2000, CELL, V101, P573 ; KORBEL JO, 2002, TRENDS GENET, V18, P158 ; KURLAND CG, 2000, EMBO REP, V1, P92 ; LAWRENCE JG, 1997, J MOL EVOL, V44, P383 ; LAWRENCE JG, 1997, TRENDS MICROBIOL, V5, P355 ; LAWRENCE JG, 1998, P NATL ACAD SCI USA, V95, P9413 ; LAWRENCE JG, 1999, CURR OPIN MICROBIOL, V2, P519 ; LAWRENCE JG, 2001, SYST BIOL, V50, P479 ; LAWRENCE JG, 2002, THEOR POPUL BIOL, V61, P449 ; LAWRENCE JG, 2002, TRENDS MICROBIOL, V10, P1 ; LEVIN BR, 1981, GENETICS, V99, P1 ; LEVIN BR, 2000, P NATL ACAD SCI USA, V97, P6981 ; LUDWIG W, 1998, ELECTROPHORESIS, V19, P554 ; MAJEWSKI J, 1998, GENETICS, V148, P13 ; MAJEWSKI J, 1999, GENETICS, V153, P1525 ; MAKAROVA KS, 1999, GENOME RES, V9, P608 ; MAKAROVA KS, 2001, GENOME BIOL, V2 ; MARTIN W, 1999, BIOESSAYS, V21, P99 ; MAYR E, 1942, SYSTEMATICS ORIGIN S ; MAYR E, 1963, ANIMAL SPECIES EVOLU ; MCKANE M, 1995, GENETICS, V139, P35 ; MOSZER I, 1999, CURR OPIN MICROBIOL, V2, P524 ; MYLVAGANAM S, 1992, GENETICS, V130, P399 ; NELSON KE, 1999, NATURE, V399, P323 ; NESBO CL, 2001, J MOL EVOL, V53, P340 ; NESBO CL, 2001, MOL BIOL EVOL, V18, P362 ; NOMURA M, 1968, NATURE, V219, P793 ; OCHMAN H, 2000, NATURE, V405, P299 ; OLENDZENSKI L, 2000, J MOL EVOL, V51, P587 ; OLENDZENSKI L, 2001, SYMBIOSIS MECH MODEL, P65 ; OLIVER A, 2000, SCIENCE, V288, P1251 ; PAPADOPOULOS D, 1999, P NATL ACAD SCI USA, V96, P3807 ; PARKER MA, 2001, APPL ENVIRON MICROB, V67, P2076 ; PENNISI E, 1998, SCIENCE, V280, P672 ; PERNA NT, 2001, NATURE, V409, P529 ; PESOLE G, 1995, MOL BIOL EVOL, V12, P189 ; RAGAN MA, 2001, CURR OPIN GENET DEV, V11, P620 ; RAGAN MA, 2001, FEMS MICROBIOL LETT, V201, P187 ; ROGER AJ, 1996, TRENDS BIOCHEM SCI, V21, P370 ; ROUSVOAL S, 1998, J MOL BIOL, V277, P1047 ; SCHINKEL AH, 1989, TRENDS GENET, V5, P149 ; SENEJANI AG, 2001, BMC BIOCH, V2, P13 ; SHARP PM, 1989, SCIENCE, V246, P808 ; SHARP PM, 1991, J MOL EVOL, V33, P23 ; SHIBUI H, 1997, BIOCHEM BIOPH RES CO, V234, P341 ; SMITH JM, 2000, BIOESSAYS, V22, P1115 ; SMITH NH, 1999, MOL BIOL EVOL, V16, P773 ; SNEATH PHA, 1993, INT J SYST BACTERIOL, V43, P626 ; SNEL B, 1999, NAT GENET, V21, P108 ; SNEL B, 2002, GENOME RES, V12, P17 ; SWEETSER DB, 1994, MOL CELL BIOL, V14, P3863 ; TEKAIA F, 1999, GENOME RES, V9, P550 ; TREVES DS, 1998, MOL BIOL EVOL, V15, P789 ; TURNER SL, 2000, MOL BIOL EVOL, V17, P309 ; UEDA K, 1999, J BACTERIOL, V181, P78 ; UTAKER JB, 2002, J BACTERIOL, V184, P468 ; VULIC M, 1997, P NATL ACAD SCI USA, V94, P9763 ; VULIC M, 1999, P NATL ACAD SCI USA, V96, P7348 ; WANG Y, 1997, J BACTERIOL, V179, P3270 ; WANG Y, 2000, MICROBIOL-UK 11, V146, P2845 ; WARD DM, 1998, CURR OPIN MICROBIOL, V1, P271 ; WERNEGREEN JJ, 2000, J BACTERIOL, V182, P3867 ; WILSON GG, 1991, ANNU REV GENET, V25, P585 ; WILSON RA, 1999, SPECIES NEW INTERDIS ; WOESE CR, 2000, MICROBIOL MOL BIOL R, V64, P202 ; WOESE CR, 2000, P NATL ACAD SCI USA, V97, P8392 ; WOLF YI, 1999, GENOME RES, V9, P689 ; WOLF YI, 2001, GENOME RES, V11, P356 ; WREDE P, 1973, FEBS LETT, V33, P315 ; WRIGHT S, 1932, P INT C GENET, V6, P356 ; WRIGHT S, 1982, ANNU REV GENET, V16, P1 ; XIONG J, 1998, P NATL ACAD SCI USA, V95, P14851 ; YANG D, 1997, MOL CELL BIOL, V17, P3614 ; YAP WH, 1999, J BACTERIOL, V181, P5201 ; ZAWADZKI P, 1995, GENETICS, V140, P917 ; ZHAXYBAYEVA O, 2002, BMC GENOMICS, V3}, de = {lateral gene transfer; horizontal gene transfer; bacterial speciation;EOLEOLrecombination; niche}, ga = {625AT}, j9 = {MOL BIOL EVOL}, ji = {Mol. Biol. Evol.}, keywords = {RIBOSOMAL-RNA GENES; ESCHERICHIA-COLI GENOME; HORIZONTAL TRANSFER; PATHOGENIC BACTERIA; SEQUENCE DIVERGENCE; SALMONELLA-TYPHIMURIUM; MOLECULAR EVOLUTION; THERMOTOGA-MARITIMA; CONVERSION TRACTS; MICROBIAL GENOMES}, la = {English}, nr = {132}, owner = {rec}, pa = {PO BOX 1897, LAWRENCE, KS 66044-8897 USA}, pg = {13}, pi = {LAWRENCE}, publisher = {Soc Molecular Biology Evolution}, rp = {Lawrence, JG, Univ Pittsburgh, Dept Biol Sci, Pittsburgh, PA 15260 USA.}, sc = {Biochemistry & Molecular Biology; Evolutionary Biology; Genetics &EOLEOLHeredity}, sn = {0737-4038}, tc = {156}, timestamp = {2007.06.17}, ut = {ISI:000179795100018} } @ARTICLE{Gowing2002, author = {Gowing, Marcia M. and Riggs, Blake E. and Garrison, David L. and Gibson, Angela H. and Jeffries, Martin O.}, title = {{L}arge viruses in {R}oss {S}ea late autumn pack ice habitats}, journal = {Mar Ecol Prog Ser}, year = {2002}, volume = {241}, pages = {1--11}, owner = {rec}, timestamp = {2007.06.17} } @ARTICLE{Gradinger1999, author = {Gradinger, R. and Friedrich, C. and Spindler, M.}, title = {{A}bundance, biomass and composition of the sea ice biota of the {G}reenland {S}ea pack ice}, journal = {Deep-Sea Res Pt II}, year = {1999}, volume = {46}, pages = {1457--1472}, abstract = {During two cruises to the Greenland Sea, we studied the abundance and biomass of the sea ice biota in summer and late autumn. The mean calculated biomass of the sympagic community was 0.2 g C m(-2) ice. Algae contributed on average 43% to total biomass, followed by bacteria (31%), heterotrophic flagellates (20%), and meiofauna (4%). Diatoms were the main primary producers (60% of total algal biomass), but flagellated cells contributed significantly to the algal biomass. Among the meiofauna, ciliates, nematodes, acoel turbellarians and crustaceans were dominant. Calculated potential ingestion rates of meiofauna (0.6 g C m(-2) (120 d)(-1)) are on the same order of magnitude as annual primary production estimates for Arctic multi-year sea ice. We therefore assume that grazing can control biomass accumulation of primary producers inside the sea ice. (C) 1999 Elsevier Science Ltd. All rights reserved.}, c1 = {Inst Polar Ecol Kiel, D-24148 Kiel, Germany.}, citedreferences = {*HELCOM, 1989, GUID BALT MON PROG D ; ASSUR A, 1958, NAT RES COUNCIL PUBL, V598, P106 ; BARTSCH A, 1989, BER POLARFORSCH, V63, P1 ; BEERS JR, 1970, B SCRIPPS I OCEANOGR, V17, P67 ; BOTTRELL HH, 1976, NORW J ZOOL, V24, P419 ; BUCK KR, 1990, MAR ECOL-PROG SER, V60, P75 ; CAREY AG, 1982, MARINE ECOLOGY PROGR, V8, P1 ; CAREY AG, 1987, MAR ECOL-PROG SER, V40, P247 ; CARMACK EC, 1990, POLAR MARINE DIATOMS, P35 ; CHENGALATH R, 1985, CAN J ZOOL, V63, P2212 ; COTA GF, 1987, J GEOPHYS RES-OCEANS, V92, P1951 ; COTA GF, 1991, J MARINE SYST, V2, P257 ; COTA GF, 1991, J MARINE SYST, V2, P297 ; CROSS WE, 1982, ARCTIC, V35, P13 ; DAHMS HU, 1990, PSZNI MAR ECOL, V11, P207 ; DEMERS S, 1989, POLAR BIOL, V9, P377 ; DEMVENNE HA, 1994, BERICHTE I MEERESKUN, V262, P1 ; EVANS CA, 1983, SCAR BIOMASS HDB, V9, P1 ; FELLER RJ, 1988, INTRO STUDY MEIOFAUN, P181 ; FRANKENSTEIN GE, 1967, J GLACIOL, V6, P943 ; FRIEDRICH C, 1997, BER POLARFORSCH, V246, P1 ; FUTTERER DK, 1991, BERICHTE POLARFORSCH, V107, P1 ; GASOL JM, 1997, LIMNOL OCEANOGR, V42, P1353 ; GLEITZ M, 1996, MAR ECOL-PROG SER, V135, P169 ; GRADINGER R, 1991, POLAR RES, V10, P295 ; GRADINGER R, 1992, POLAR BIOL, V12, P727 ; GRADINGER R, 1995, PHILOS T ROY SOC A, V352, P277 ; GRADINGER R, 1996, P NIPR S POL BIOL, V9, P35 ; GRADINGER R, 1997, POLAR BIOL, V17, P448 ; GRADINGER R, 1998, J PLANKTON RES, V20, P871 ; GRADINGER RR, 1991, MAR BIOL, V111, P311 ; GRAINGER EH, 1985, ARCTIC, V38, P23 ; GRAINGER EH, 1990, OPHELIA, V31, P177 ; GRAINGER EH, 1990, POLAR BIOL, V10, P283 ; HORNER R, 1982, ARCTIC, V35, P485 ; IKAVALKO J, 1997, POLAR BIOL, V17, P473 ; JEROME CA, 1993, J EUKARYOT MICROBIOL, V40, P254 ; KERN JC, 1983, MAR ECOL-PROG SER, V10, P159 ; LAURION I, 1995, MAR ECOL-PROG SER, V120, P77 ; LEGENDRE L, 1992, POLAR BIOL, V12, P429 ; MARTIN T, 1996, ESOP SCI REPORT, V1, P72 ; MAYKUT GA, 1985, SEA ICE BIOTA, P21 ; MEGURO H, 1967, ARCTIC, V20, P114 ; MELNIKOV L, 1997, ARCTIC SEA ICE ECOSY ; MOLONEY CL, 1989, LIMNOL OCEANOGR, V34, P1290 ; MYERS RF, 1967, NEMATOLOGICA, V12, P579 ; NOJI TT, 1996, EUROPEAN SUBPOLAR OC, V2, P540 ; PORTER KG, 1980, LIMNOL OCEANOGR, V25, P943 ; POULIN M, 1990, POLAR MARINE DIATOMS, P1 ; RACHOR E, 1975, METEOR FORSCHUNGSE D, V21, P1 ; RIEMANN F, 1990, MAR BIOL, V104, P453 ; RUTTNERKOLISKO A, 1977, ARCH HYDROBIOL BEIH, V8, P71 ; SLAGSTAD D, 1999, DEEP-SEA RES PT II, V46, P1511 ; SMITH WO, 1990, POLAR OCEANOGRAPHY B, P477 ; SPINDLER M, 1990, GEOLOGICAL HIST POLA, P173 ; VOIGT M, 1978, GEBR BORNTRAEGER BER, V1, P673 ; WARWICK RM, 1984, MAR ECOL-PROG SER, V18, P97 ; WEISSENBERGER J, 1992, LIMNOL OCEANOGR, V37, P179 ; WHEELER PA, 1996, NATURE, V380, P697 ; WIESER W, 1960, LIMNOL OCEANOGR, V5, P121 ; ZHANG Q, IN PRESS BOREAL ENV}, ga = {210TZ}, j9 = {DEEP-SEA RES PT II-TOP ST OCE}, ji = {Deep-Sea Res. Part II-Top. Stud. Oceanogr.}, keywords = {ARCTIC-OCEAN; FROBISHER BAY; BEAUFORT SEA; FRAM STRAIT; COMMUNITIES; PHYTOPLANKTON; MICROALGAE; ASSEMBLAGE; ORGANISMS; COPEPODS}, la = {English}, nr = {61}, owner = {rec}, pa = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, pg = {16}, pi = {OXFORD}, publisher = {Pergamon-Elsevier Science Ltd}, rp = {Gradinger, R, Inst Polar Ecol Kiel, Wischhofstr 1-3,Geb 12, D-24148EOLEOLKiel, Germany.}, sc = {Oceanography}, sn = {0967-0645}, tc = {25}, timestamp = {2007.06.17}, ut = {ISI:000081121900017} } @ARTICLE{Gradinger1998, author = {Gradinger, R. and Ikavalko, J.}, title = {{O}rganism incorporation into newly forming {A}rctic sea ice in the {G}reenland {S}ea}, journal = {J Plankton Res}, year = {1998}, volume = {20}, pages = {871--886}, abstract = {New ice formation, protist incorporation and enrichment in different stages of young Arctic sea ice (grease, nilas and pancake ice) were studied in the Greenlanc Sea in autumn 1995. Nutrients (nitrite, nitrate, phosphate and silicate), salinity and abundance estimates of organisms were analysed from surface water and new ice samples. The abundances of bacteria, diatoms, and photo-and heterotrophic flagellates in the ice and water column were determined using epifluorescence microscopy. An enrichment index was calculated to compare the abundance of organisms in the water column with different stages of young sea ice. The results clearly show that (i) protist incorporation already begins during the first stages of new sea ice formation, (ii) incorporation of protists is selective, showing preference for diatoms with a relatively large cell size and (iii) enrichment of organisms, in particular diatoms, takes place in young sea ice in the Greenland Sea. The selectivity df the incorporation process and the evident preference for diatoms are presumably a result of the larger cell size and/or certain properties of the cell surface (e.g. stickiness) that enhance their incorporation. The calculated enrichment indices were relatively low for bacteria and flagellates.}, c1 = {Inst Polar Ecol, D-24148 Kiel, Germany.EOLEOLUniv Helsinki, Dept Systemat & Ecol, Div Hydrobiol, FIN-00014 Helsinki, Finland.EOLEOLFinnish Inst Marine Res, FIN-00931 Helsinki, Finland.}, citedreferences = {*AB CONC INC, 1995, STATV HDB ; ACKLEY SF, 1982, EOS, V63, P54 ; ASSUR A, 1958, NAT RES COUNCIL PUBL, V598, P106 ; COTA GF, 1991, J MARINE SYST, V2, P297 ; DIECKMANN GS, 1991, J FORAMIN RES, V21, P182 ; DIECKMANN GS, 1991, POLAR BIOL, V11, P449 ; EVANS CA, 1987, SCAR BIOMASS RES SER, V8, P1 ; FRANKENSTEIN GE, 1967, J GLACIOL, V6, P943 ; GARRISON DL, 1983, NATURE, V306, P363 ; GARRISON DL, 1986, POLAR BIOL, V6, P237 ; GLEITZ M, 1993, J EXP MAR BIOL ECOL, V173, P211 ; GRADINGER R, 1991, POLAR RES, V10, P295 ; GRADINGER R, 1992, POLAR BIOL, V12, P727 ; GROSSMANN S, 1993, J EXP MAR BIOL ECOL, V173, P273 ; GROSSMANN S, 1994, APPL ENVIRON MICROB, V60, P2746 ; HORNER R, 1982, ARCTIC, V35, P485 ; HORNER R, 1985, SEA ICE BIOTA ; HORNER R, 1992, POLAR BIOL, V12, P417 ; HOSHIAI T, 1985, ANTARCTIC NUTR CYCLE, P89 ; HSIAO SIC, 1980, ARCTIC, V33, P768 ; IKAVALKO J, 1997, POLAR BIOL, V17, P473 ; KRAUSE G, 1996, BER POLARF, P1 ; LANGE MA, 1989, ANN GLACIOL, V12, P92 ; LANGE MA, 1991, ANN GLACIOL, V15, P210 ; LEGENDRE L, 1992, POLAR BIOL, V12, P429 ; MARTIN S, 1979, J GLACIOL, V22, P473 ; MAYKUT GA, 1985, SEA ICE BIOTA, P21 ; NIEDRAUER TM, 1979, J GEOPHYS RES C, V84, P1176 ; PENNY DM, 1990, EOS, V71, P79 ; PORTER KG, 1980, LIMNOL OCEANOGR, V25, P943 ; REIMNITZ E, 1993, COLD REG SCI TECHNOL, V21, P117 ; RIEBESELL U, 1991, POLAR BIOL, V11, P239 ; SACHS L, 1984, ANGEWANDTE STAT ; SHEN HT, 1990, CRREL MONOGR, V901, P100 ; SPINDLER M, 1986, POLAR BIOL, V5, P185 ; SPINDLER M, 1990, ECOLOGICAL CHANGE CO, P129 ; WADHAMS P, 1987, J GEOPHYS RES, V92, P14535 ; WEISSENBERGER J, 1992, LIMNOL OCEANOGR, V37, P179 ; WHEELER PA, 1996, NATURE, V380, P697}, ga = {ZU413}, j9 = {J PLANKTON RES}, ji = {J. Plankton Res.}, keywords = {FORAMINIFER NEOGLOBOQUADRINA-PACHYDERMA; WEDDELL SEA; STANDING STOCK; ANTARCTICA; ALGAE; PHYTOPLANKTON; COMMUNITIES; MICROALGAE; HABITAT; ECOLOGY}, la = {English}, nr = {39}, owner = {rec}, pa = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND}, pg = {16}, pi = {OXFORD}, publisher = {Oxford Univ Press}, rp = {Gradinger, R, Inst Polar Ecol, Wischhofstr 1-3,Geb 12, D-24148 Kiel,EOLEOLGermany.}, sc = {Marine & Freshwater Biology}, sn = {0142-7873}, tc = {12}, timestamp = {2007.06.17}, ut = {ISI:000074194600005} } @ARTICLE{Griffith1928, author = {Griffith, Fred}, title = {{S}ignificance of pneumococcal types}, journal = {J. Hyg. Cambridge}, year = {1928}, volume = {27}, pages = {113}, owner = {rec}, timestamp = {2007.06.17} } @ARTICLE{Grossmann1994, author = {Grossmann, S. and Dieckmann, G. S.}, title = {{B}acterial standing stock, activity, and carbon production during formation and growth of sea ice in the {W}eddell {S}ea, {A}ntarctica}, journal = {Appl Environ Microbiol}, year = {1994}, volume = {60}, pages = {2746--2753}, abstract = {Bacterial response to formation and growth of sea ice was investigated during autumn in the northeastern Weddell Sea. Changes in standing stock, activity, and carbon production of bacteria were determined in successive stages of ice development. During initial ice formation, concentrations of bacterial cells, in the order of 1 x 10(8) to 3 x 10(8) liter(-1), were not enhanced within the ice matrix. This suggests that physical enrichment of bacteria by ice crystals is not effective. Due to low concentrations of phytoplankton in the water column during freezing, incorporation of bacteria into newly formed ice via attachment to algal cells or aggregates was not recorded in this study. As soon as the ice had formed, the general metabolic activity of bacterial populations was strongly suppressed. Furthermore, the ratio of [H-3]leucine incorporation into proteins to [H-3]thymidine incorporation into DNA changed during ice growth. In thick pack ice, bacterial activity recovered and growth rates up to 0.6 day(-1) indicated actively dividing populations. However, biomass-specific utilization of organic compounds remained tower than in open water. Bacterial concentrations of up to 2.8 x 10(9) cells liter(-1) along with considerably enlarged cell volumes accumulated within thick pack ice, suggesting reduced mortality rates of bacteria within the small brine pores. In the course of ice development, bacterial carbon production increased from about 0.01 to 0.4 mu g of C liter(-1) h(-1). In thick ice, bacterial secondary production exceeded primary production of microalgae.}, owner = {rec}, timestamp = {2006.12.11}, ut = {ISI:A1994NZ70300012} } @ARTICLE{Grossmann1993, author = {Grossmann, S. and Gleitz, M.}, title = {{M}icrobial responses to experimental sea-ice formation: {I}mplications for the establishment of {A}ntarctic sea-ice communities}, journal = {J Exp Mar Biol Ecol}, year = {1993}, volume = {173}, pages = {273--289}, abstract = {The fate of algae and bacteria during the transition from open water to early stages of sea-ice formation was investigated under simulated conditions in the laboratory. Distribution patterns and metabolic activities of three common Southern Ocean diatoms (Nitzschia curta, Thalassiosira tumida, Chaetoceros sp.) and an Antarctic bacterial community were determined after 3 and 14 days of incubation in an insulated 301 plastic vessel. Activity measurements suggest that a close coupling existed between these two groups of organisms prior to ice formation. After 3 days of freezing at -5 degrees C, cell densities and biomasses of algae increased in pore water within an ice-pancake that formed during this period. Accumulation in the pore water exceeded the concentration effect caused by freezing out of water. Bacteria showed similar increases in the presence of algal cells during freezing. As the ice incorporated bacterial populations experienced a strong metabolic inhibition, bacterial growth as a reason for enhanced cell numbers in the pore water seems to be unlikely. Reduced metabolic activities were also recorded for the algal species, most pronounced in T. tumida which showed lowest cell-specific assimilation rates accompanied by a high cell mortality after 3 days of freezing. It is hypothesized that scavenging of algal cells by ice crystals in conjunction with attachment of bacteria onto algal cells was predominantly responsible for the observed enrichment patterns. Different capacities of the algae to concentrate bacterial cells in the pore water were related to differences in algal surface area available for bacterial colonization, which varied among the three species due to different morphologies and cell concentrations. After 2 weeks of incubation under simulated ice conditions and at salinities of 50 parts per thousand, activity of algae and bacteria increased again. In contrast to observations made in open water prior to freezing, no influence of algal species on bacterial activity was recorded after this 2-week period. It is concluded that a bacterial community different to that of the open water had developed which needs a longer time span than employed in the present experiment to establish close metabolic coupling between algae and bacteria as recorded for microbial communities of thick pack and fast ice.}, owner = {rec}, timestamp = {2006.12.11}, ut = {ISI:A1993MK82000008} } @ARTICLE{Hausner1999, author = {Hausner, Martina and Wuertz, Stefan}, title = {High Rates of Conjugation in Bacterial Biofilms as Determined by Quantitative In Situ Analysis}, journal = {Appl Environ Microbiol}, year = {1999}, volume = {65}, pages = {3710--3713}, abstract = {Quantitative in situ determination of conjugative gene transfer in defined bacterial biofilms using automated confocal laser scanning microscopy followed by three-dimensional analysis of cellular biovolumes revealed conjugation rates 1,000-fold higher than those determined by classical plating techniques. Conjugation events were not affected by nutrient concentration alone but were influenced by time and biofilm structure.}, eprint = {http://aem.asm.org/cgi/reprint/65/8/3710.pdf}, owner = {rec}, timestamp = {2009.08.22}, url = {http://aem.asm.org/cgi/content/abstract/65/8/3710} } @ARTICLE{Helmke1995, author = {Helmke, E. and Weyland, H.}, title = {{B}acteria in sea ice and underlying water of the {E}astern {W}eddell {S}ea in midwinter}, journal = {Mar Ecol Prog Ser}, year = {1995}, volume = {117}, pages = {269--287}, abstract = {Bacteria in the water beneath the sea ice of the eastern Weddell Sea were homogeneously distributed. Direct counts resembled values from spring and autumn, whereas viable cell counts, total ATP concentrations, as well as heterotrophic assimilation and extracellular enzymatic activities were very low, implying a metabolic inactive bacterioplankton. The consolidated sea ice had a very heterogeneous horizontal distribution of microbes on large as well as small scales but vertical profiles in low and densely populated ice cores exhibited similar patterns. A close relation between bacterial colonization of sea ice and genetic ice classes was revealed. Sea ice of the 'predominantly congelation ice' had the lowest bacterial biomass and displayed Very low heterotrophic activities which were comparable to those of the water column. Samples of older sea ice belonging to the 'mainly frazil' and 'mixed ice' had maximal numbers of bacteria. They often included high proportions of culturable cells and dividing cells as well as large bacteria. The bacteria of these ice classes were active and contributed significantly to the productivity in the Weddell Sea during winter. 'Predominantly frazil ice' was less colonized; however, selective bacterial growth was also indicated in this typical winter ice by an increase in the proportions of culturable and psychrophilic bacteria with advancing age of the ice. Psychrophilic bacteria dominated in consolidated sea-ice whereas facultative psychrophiles prevailed in young sea-ice and water, corroborating a strict partitioning in a microbial sea-ice and a seawater regime. Generally, temperature does not appear to be the significant factor for the development of bacterial communities in the surface layer of the eastern Weddell Sea in winter since the metabolically active bacterial nora develops in the very cold sea-ice environment. The organic matter supply and its improved usability obviously controls bacterial activity as well as the selective enrichment of psychrophiles.}, owner = {rec}, timestamp = {2007.06.17}, ut = {ISI:A1995QJ84800026} } @ARTICLE{Hermansson1994, author = {Hermansson, M. and Linberg, C.}, title = {{G}ene transfer in the marine environment}, journal = {FEMS Microbiol Ecol}, year = {1994}, volume = {15}, pages = {47--54}, abstract = {This review summarises the literature on bacterial gene transfer in marine ecosystems. Relevant experiments carried out in model systems are also included. Prerequisites for the main gene transfer mechanisms, transformation, transduction and conjugation are discussed, such as concentrations of extracellular DNA in marine waters, numbers of bacteriophages in sea water and frequency of plasmids in marine bacteria. Transfer of chromosomal genes as well as plasmids are considered. We also discuss the possibility that gene transfer is more frequent in surface-associated bacterial communities. Examples of relevant studies using various solid surfaces and from the air-water interface are summarised. We suggest that there is a higher 'flow-rate' of genetic information through surface-associated communities compared to bulk water communities.}, citedreferences = {AARDEMA BW, 1983, APPL ENVIRON MICROB, V46, P417 ; ANGLES ML, 1993, APPL ENVIRON MICROB, V59, P843 ; BARNHARDT BJ, 1963, BIOCHIM BIOPHYS ACTA, V89, P25 ; BAROSS JA, 1978, APPL ENVIRON MICROB, V36, P492 ; BAYA AM, 1986, APPL ENVIRON MICROB, V51, P1285 ; BERGH O, 1989, NATURE, V340, P467 ; BRADLEY DE, 1980, J BACTERIOL, V143, P1466 ; DEFLAUN MF, 1986, APPL ENVIRON MICROB, V52, P654 ; DELONG EF, 1993, LIMNOL OCEANOGR, V38, P924 ; FRISCHER ME, 1993, J GEN MICROBIOL, V139, P753 ; FRY JC, 1990, BACTERIAL GENETICS N ; GAUTHIER MJ, 1985, APPL ENVIRON MICROB, V50, P38 ; GOODMAN AE, 1993, APPL ENVIRON MICROB, V59, P1035 ; GOODMAN AE, 1994, FEMS MICROBIOL ECOL, V15, P55 ; HADA HS, 1981, APPL ENVIRON MICROB, V41, P199 ; HARA T, 1981, AGR BIOL CHEM TOKYO, V11, P1104 ; HERMANSSON M, 1983, MICROBIAL ECOL, V9, P317 ; HERMANSSON M, 1985, MICROBIAL ECOL, V11, P91 ; HERMANSSON M, 1987, APPL ENVIRON MICROB, V53, P2338 ; HERMANSSON M, 1990, BIOL PARTICLES AQUAT, P145 ; HUNTER KA, 1982, LIMNOL OCEANOGR, V27, P322 ; JEFFREY WH, 1990, MICROBIAL ECOL, V19, P259 ; KEYNAN A, 1974, J VIROL, V14, P330 ; KJELLEBERG S, 1987, ANNU REV MICROBIOL, V41, P25 ; KOKJOHN TA, 1989, GENE TRANSFER ENV, P73 ; LEVY SB, 1989, GENE TRANSFER ENV ; LORENZ MG, 1981, MAR BIOL, V64, P225 ; LORENZ MG, 1987, APPL ENVIRON MICROB, V53, P2945 ; PAUL JH, 1987, APPL ENVIRON MICROB, V53, P170 ; PAUL JH, 1991, APPL ENVIRON MICROB, V57, P1509 ; PAUL JH, 1992, MOL ECOL, V1, P37 ; POWER K, 1988, BIOFOULING, V1, P163 ; SANDAA RA, 1992, CAN J MICROBIOL, V38, P1061 ; SAYE DJ, 1987, APPL ENVIRON MICROB, V53, P987 ; SIMONSEN L, 1990, J GEN MICROBIOL 6, V136, P1001 ; SIZEMORE RK, 1977, ANTIMICROB AGENTS CH, V12, P373 ; STEWART GJ, 1988, 1ST INT C REL GEN EN ; STEWART GJ, 1990, APPL ENVIRON MICROB, V56, P1818 ; STEWART GJ, 1991, FEMS MICROBIOL ECOL, V85, P1 ; STEWART GJ, 1992, GENETIC INTERACTIONS, P216 ; STEWART KR, 1980, MAR POLLUT BULL, V11, P130 ; WELLINGTON EMH, 1992, GENETIC INTERACTIONS ; WOMMACK KE, 1992, APPL ENVIRON MICROB, V58, P2965 ; WORTMAN AT, 1988, APPL ENVIRON MICROB, V54, P1284}, de = {GENE TRANSFER; BACTERIA; MARINE ENVIRONMENT; AIR-WATER INTERFACE; SOLIDEOLEOLSURFACE; GMMO}, ga = {PP793}, j9 = {FEMS MICROBIOL ECOL}, ji = {FEMS Microbiol. Ecol.}, keywords = {AIR-WATER-INTERFACE; NATURAL TRANSFORMATION; PLASMID TRANSFER; DRUG-RESISTANCE; AQUATIC ENVIRONMENTS; ESCHERICHIA-COLI; BACTERIA; DNA; SEDIMENT; VIBRIO}, la = {English}, nr = {44}, owner = {rec}, pa = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, pg = {8}, pi = {AMSTERDAM}, publisher = {Elsevier Science Bv}, rp = {HERMANSSON, M, GOTHENBURG UNIV,DEPT GEN & MARINEEOLEOLMICROBIOL,MEDICINAREGATAN 9C,S-41390 GOTHENBURG,SWEDEN.}, sc = {Microbiology}, sn = {0168-6496}, tc = {15}, timestamp = {2007.06.17}, ut = {ISI:A1994PP79300006} } @ARTICLE{Janech2006, author = {Janech, M. G. and Krell, A. and Mock, T. and Kang, J.-S. and Raymond, J. A.}, title = {Ice-binding proteins from sea ice diatoms (\emph{Bacillariophyceae})}, journal = {J Phycol}, year = {2006}, volume = {42}, pages = {410--416}, abstract = {Sea ice diatoms thrive under conditions of low temperature and high salinity, and as a result are responsible for a significant fraction of polar photosynthesis. Their success may be owing in part to secretion of macromolecules that have previously been shown to interfere with the growth of ice and to have the ability to act as cryoprotectants. Here we show that one of these molecules, produced by the sea ice diatom Navicula glaciei Vanheurk, is a āˆ¼25Ā kDa ice-binding protein (IBP). A cDNA obtained from another sea ice diatom, Fragilariopsis cylindrus Grunow, was found to encode a protein that closely matched the partially sequenced N. glaciei IBP, and enabled the amplification and sequencing of an N. glaciei IBP cDNA. Similar proteins are not present in the genome of the mesophilic diatom Thalassiosira pseudonana. Both proteins closely resemble antifreeze proteins from psychrophilic snow molds, and as a group represent a new class of IBPs that is distinct from other IBPs found in fish, insects and plants, and bacteria. The diatom IBPs also have striking similarities to three prokaryotic hypothetical proteins. Relatives of both snow molds and two of the prokaryotes have been found in sea ice, raising the possibility of a fungal or bacterial origin of diatom IBPs.}, issn = {1529-8817}, keywords = {cryoprotection, diatoms, Fragilariopsis cylindrus, ice-binding proteins, Navicula glaciei, sea ice}, owner = {rec}, publisher = {Blackwell Publishing Inc}, timestamp = {2010.09.13}, url = {http://dx.doi.org/10.1111/j.1529-8817.2006.00208.x} } @ARTICLE{Johnson2008, author = {Johnson, Kelsey P. and Blum, Joel D. and Keeler, Gerald J. and Douglas, Thomas A.}, title = {Investigation of the deposition and emission of mercury in arctic snow during an atmospheric mercury depletion event}, journal = {J Geophys Res}, year = {2008}, volume = {113}, pages = {D17304}, abstract = {Mechanisms of air-snow exchange of mercury (Hg) during and after atmospheric mercury depletion events (AMDEs) remain poorly constrained and this has limited our understanding of the arctic Hg cycle. We measured the Hg concentrations of surface snow through time and carried out flux chamber experiments during AMDE and non-AMDE conditions in the spring of 2006 near Barrow, Alaska. Clear skies, low-velocity onshore winds, and a stable boundary layer characterized the meteorology during this AMDE. Surface snow Hg concentrations (upper 1 cm) increased throughout a 9-day AMDE from background levels (4.1ā€“15.5 ng/L) to elevated levels (147 and 237 ng/L) at two sampling sites and returned to near-baseline values within 2 days of AMDE cessation. The Hg concentrations of core samples from the full snowpack did not increase significantly during the AMDE and demonstrate that the Hg enhancement of surface snow resulted from deposition of atmospheric Hg to surface snow. We estimate that complete deposition of background Hg to a height of 200ā€“450 m in the near-surface troposphere could account for the Hg gains to surface snow during this event. Snow incubated in field-based flux chambers emitted 4 to 7% of its total Hg content within 1 day and may represent an upper limit for the photo-reduction rate of ā€œeasilyā€ reducible Hg in snow under post-AMDE conditions. Full-column snow core samples collected in the late springtime have comparable Hg loads to those observed during the AMDE season and imply that a significant fraction of the Hg deposited during the 3-month AMDE season was retained until snowmelt at this location.}, keywords = {Atmospheric mercury depletion event, Arctic, mercury, 0736 Cryosphere: Snow, 0792 Cryosphere: Contaminants, 1065 Geochemistry: Major and trace element geochemistry, 4540 Oceanography: Physical: Ice mechanics and air/sea/ice exchange processes, 1030 Geochemistry: Geochemical cycles}, owner = {rec}, publisher = {American Geophysical Union}, timestamp = {2009.08.21}, url = {http://dx.doi.org/10.1029/2008JD009893} } @ARTICLE{Junge2004, author = {Junge, K. and Eicken, H. and Deming, J. W.}, title = {{B}acterial activity at --2 to --20 degrees {C} in {A}rctic wintertime sea ice}, journal = {Appl Environ Microbiol}, year = {2004}, volume = {70}, pages = {550--557}, abstract = {Arctic wintertime sea-ice cores, characterized by a temperature gradient of -2 to -20degreesC, were investigated to better understand constraints on bacterial abundance, activity, and diversity at subzero temperatures. With the fluorescent stains 4',6'-diamidino-2-phenylindole 2HCl (DAPI) (for DNA) and 5-cyano-2,3-ditoyl tetrazolium chloride (CTC) (for O-2-based respiration), the abundances of total, particle-associated (>3-mum), free-living, and actively respiring bacteria were determined for ice-core samples melted at their in situ temperatures -2 to -20degreesC and at the corresponding salinities of their brine inclusions (38 to 209 ppt). Fluorescence in situ hybridization was applied to determine the proportions of Bacteria, Cytophaga-Flavobacteria-Bacteroides (CFB), and Archaea. Microtome-prepared ice sections also were examined microscopically under in situ conditions to evaluate bacterial abundance (by DAPI staining) and particle associations within the brine-inclusion network of the ice. For both melted and intact ice sections, more than 50% of cells were found to be associated with particles or surfaces (sediment grains, detritus, and ice-crystal boundaries). CTC-active bacteria (0.5 to 4% of the total) and cells detectable by rRNA probes (18 to 86% of the total) were found in all ice samples, including the coldest (-20degreesC), where virtually all active cells were particle associated. The percentage of active bacteria associated with particles increased with decreasing temperature, as did the percentages of CFB (16 to 82% of Bacteria) and Archaea (0.0 to 3.4% of total cells). These results, combined with correlation analyses between bacterial variables and measures of particulate matter in the ice as well as the increase in CFB at lower temperatures, confirm the importance of particle or surface association to bacterial activity at subzero temperatures. Measuring activity down to -20degreesC adds to the concept that liquid inclusions in frozen environments provide an adequate habitat for active microbial populations on Earth and possibly elsewhere.}, owner = {rec}, timestamp = {2007.06.17}, ut = {ISI:000188115300069} } @ARTICLE{Junge2001, author = {Junge, K. and Krembs, C. and Deming, J. and Stierle, A. and Eicken, H.}, title = {{A} microscopic approach to investigate bacteria under in situ conditions in sea-ice samples}, journal = {Annal Glaciol}, year = {2001}, volume = {33}, pages = {304--310}, abstract = {Microbial populations and activity within sea ice have been well described based on bulk measurements from melted sea-ice samples. However, melting destroys the micro-environments within the ice matrix and does not allow for examination of microbial populations at a spatial scale relevant to the organism. Here, we describe the development of a new method allowing for microscopic observations of bacteria localized within the three-dimensional network of brine inclusions in sea ice under in situ conditions. Conventional bacterial staining procedures, using the DNA-specific fluorescent stain DAPI, epifluorescence microscopy and image analysis, were adapted to examine bacteria and their associations with various surfaces within microtomed sections of sea ice at temperatures from -2degrees to 15degreesC. The utility and sensitivity of the method were demonstrated by analyzing artificial sea-ice preparations of decimal dilutions of a known bacterial culture. When applied to natural, particle-rich sea ice, the method allowed distinction between bacteria and particles at high magnification. At lower magnifications, observations of bacteria could be combined with those of other organisms and with morphology and particle content of the pore space. The method described here may ultimately aid in discerning constraints on microbial life at extremely low temperatures.}, owner = {rec}, se = {ANNALS OF GLACIOLOGY}, timestamp = {2006.12.11}, ut = {ISI:000173446300047} } @ARTICLE{Koenneke2005, author = {Martin K\"{o}nneke and Anne E Bernhard and Jos\'{e} R de la Torre and Christopher B Walker and John B Waterbury and David A Stahl}, title = {Isolation of an autotrophic ammonia-oxidizing marine archaeon.}, journal = {Nature}, year = {2005}, volume = {437}, pages = {543--546}, abstract = {For years, microbiologists characterized the Archaea as obligate extremophiles that thrive in environments too harsh for other organisms. The limited physiological diversity among cultivated Archaea suggested that these organisms were metabolically constrained to a few environmental niches. For instance, all Crenarchaeota that are currently cultivated are sulphur-metabolizing thermophiles. However, landmark studies using cultivation-independent methods uncovered vast numbers of Crenarchaeota in cold oxic ocean waters. Subsequent molecular surveys demonstrated the ubiquity of these low-temperature Crenarchaeota in aquatic and terrestrial environments. The numerical dominance of marine Crenarchaeota--estimated at 10(28) cells in the world's oceans--suggests that they have a major role in global biogeochemical cycles. Indeed, isotopic analyses of marine crenarchaeal lipids suggest that these planktonic Archaea fix inorganic carbon. Here we report the isolation of a marine crenarchaeote that grows chemolithoautotrophically by aerobically oxidizing ammonia to nitrite--the first observation of nitrification in the Archaea. The autotrophic metabolism of this isolate, and its close phylogenetic relationship to environmental marine crenarchaeal sequences, suggests that nitrifying marine Crenarchaeota may be important to global carbon and nitrogen cycles.}, doi = {10.1038/nature03911}, institution = {Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, USA.}, keywords = {Aerobiosis; Ammonia, metabolism; Carbon, metabolism; Crenarchaeota, genetics/isolation /&/ purification/metabolism/ultrastructure; Marine Biology; Molecular Sequence Data; Nitrites, metabolism; Nitrogen, metabolism; Oxidation-Reduction; Oxidoreductases, genetics; Phylogeny; RNA, Ribosomal, 16S, genetics; Seawater, chemistry}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {nature03911}, pmid = {16177789}, timestamp = {2009.07.27}, url = {http://dx.doi.org/10.1038/nature03911} } @ARTICLE{Karl1989, author = {Karl, David M. and Bailiff, Megan D.}, title = {The Measurement and Distribution of Dissolved Nucleic Acids in Aquatic Environments}, journal = {Limnol Oceanogr}, year = {1989}, volume = {34}, pages = {543--558}, abstract = {Nucleic acids (DNA and RNA) are ubiquitous components of the dissolved organic matter (DOM) pool of all oceanic, neritic, estuarine, and freshwater habitats studied to date. A new method for the quantitative determination of dissolved nucleic acids (DNA and RNA) in water and sediment samples was developed, evaluated, and utilized in a study of various marine and freshwater ecosystems. Under appropriate reaction conditions, dissolved DNA (D-DNA) and dissolved RNA (D-RNA) are efficiently removed from solution with the addition of cetyltrimethylammonium bromide (CTAB) and subsequent formation of insoluble CTA-nucleic acid salts. The insoluble salts are collected, by filtration, onto glass-fiber filters and analyzed for DNA and RNA with fluorometric and colorimetric procedures, respectively. The performance of this CTAB method is simple, reliable, and reproducible for measuring dissolved nucleic acids in natural aquatic environments. For the ecosystems investigated herein. D-DNA and D-RNA concentrations ranged from $0.56 to 88 \mug liter^-1$ and 4.03 to $871 \mug liter^-1$; the ratio of D-RNA to D-DNA ranged from 4.1 to 11.5.}, copyright = {Copyright © 1989 American Society of Limnology and Oceanography}, issn = {00243590}, jstor_articletype = {primary_article}, jstor_formatteddate = {May, 1989}, owner = {rec}, publisher = {American Society of Limnology and Oceanography}, timestamp = {2009.11.05}, url = {http://www.jstor.org/stable/2837370} } @ARTICLE{Kiko2010, author = {Kiko, Rainer}, title = {Acquisition of freeze protection in a sea-ice crustacean through horizontal gene transfer?}, journal = {Polar Biol}, year = {2010}, volume = {33}, pages = {543--556}, abstract = {Sea ice is permeated by small brine channels, which are characterised by sub-zero temperatures and varying salinities. Despite sometimes extreme conditions a diverse fauna and flora thrives within the brine channels. The dominant calanoid copepods of Antarctic sea ice are Stephos longipes and Paralabidocera antarctica. Here, I report for the first time thermal hysteresis (TH) in the haemolymph of a crustacean, S. longipes, whereas P. antarctica has no such activity. TH, the non-colligative prevention of ice growth, seems to enable S. longipes to exploit all available microhabitats within sea ice, especially the surface layer, in which strong temperature fluctuations can occur. In contrast, P. antarctica only thrives within the lowermost centimetres of sea ice, where temperature fluctuations are moderate. S. longipes possesses two isoforms of a protein with TH activity. A high homology to a group of (putative) antifreeze proteins from diatoms, bacteria and a snow mold and, in contrast, no homologs in any metazoan lineage suggest that this protein was obtained through horizontal gene transfer (HGT). Further analysis of available sequence data from sea-ice organisms indicates that these antifreeze proteins were probably transferred horizontally several times. Temperature and salinity fluctuations within the brine channel system are proposed to provide natural transformation conditions enabling HGT and thus making this habitat a potential hot spot for HGT.}, affiliation = {Institute for Polar Ecology, Wischhofstr. 1-3, Bldg. 12, 24148 Kiel, Germany}, doi = {10.1007/s00300-009-0732-0}, issn = {0722-4060}, issue = {4}, keyword = {Biomedical and Life Sciences}, owner = {rec}, publisher = {Springer Berlin / Heidelberg}, timestamp = {2010.09.13}, url = {http://dx.doi.org/10.1007/s00300-009-0732-0} } @ARTICLE{Kirchman2005, author = {D.L. Kirchman and R.R. Malmstrom and M.T. Cottrell}, title = {Control of bacterial growth by temperature and organic matter in the {W}estern {A}rctic}, journal = {Deep-Sea Res Pt II}, year = {2005}, volume = {52}, pages = {3386--3395}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Kobori1984, author = {Kobori, Hiromi and Sullivan, Cornelius W and Shizuya, Hiroaki}, title = {{B}acterial plasmids in {A}ntarctic natural microbial assemblages.}, journal = {Appl Environ Microbiol}, year = {1984}, volume = {48}, pages = {515--518}, abstract = {Samples of psychrophilic and psychrotrophic bacteria were collected from sea ice, seawater, sediments, and benthic or ice-associated animals in McMurdo Sound, Antarctica. A total of 155 strains were isolated and tested for the presence of plasmids by DNA agarose gel electrophoresis. Thirty-one percent of the isolates carried at least one kind of plasmid. Bacterial isolates taken from sediments showed the highest plasmid incidence (42\%), and isolates from seawater showed the lowest plasmid incidence (20\%). Plasmids were significantly more frequent in the strains which had been first isolated from low-nutrient media (46\%) than in the strains which had been isolated from high-nutrient media (25\%). Multiple forms of plasmids were observed in two-thirds of the plasmid-carrying strains. A majority of the plasmids detected were estimated to have a mass of 10 megadaltons or less. Among 48 plasmid-carrying strains, 7 showed antibiotic resistance. It is concluded that bacterial plasmids are ubiquitous in natural microbial assemblages of the pristine marine ecosystem of Antarctica.}, owner = {rec}, pmid = {16346621}, timestamp = {2007.06.17} } @INCOLLECTION{Kokjohn1989, author = {Kokjohn, T.A.}, title = {Transduction: mechanism and potential for gene transfer in the environment.}, booktitle = {Gene transfer in the environment}, publisher = {McGraw-Hill Publishing Co., New York.}, year = {1989}, editor = {Levy, SB and Miller, RV}, pages = {73--97}, owner = {rec}, timestamp = {2009.08.22} } @INCOLLECTION{Krembs2008, author = {Krembs, Christopher and Deming, Jody W.}, title = {The role of exopolymers in microbial adaptation to sea ice}, booktitle = {Psychrophiles: from Biodiversity to Biotechnology}, publisher = {Springer Berlin / Heidelberg}, year = {2008}, editor = {Rosa Margesin and Franz Schinner and Jean-Claude Marx and Charles Gerday}, pages = {247--264}, abstract = {The cellular exterior that a microbe presents to its surroundings marks its first line of defense against environmental pressures that range from energy deprivation and other extreme conditions, including ionic and thermal stress, to viral and higherorder attack. The production of exopolymers, whether to provide an immediate individual coating of multiple functions or to be freely released and shared by other organisms in consortial arrangements or biofilm formations, is a hallmark of microbial life in soil, water, and host (plant and animal)-associated environments. The basic features of exopolymers and their functions pertain to all manner of environments and microbial adaptation, largely independently of ambient temperature. At extreme temperatures, however, where phase changes come into play, special considerations arise.}, doi = {http://dx.doi.org/10.1007/978-3-540-74335-4_15}, owner = {rec}, timestamp = {2008.04.11} } @ARTICLE{Krembs2011, author = {Krembs, Christopher and Eicken, Hajo and Deming, Jody W.}, title = {Exopolymer alteration of physical properties of sea ice and implications for ice habitability and biogeochemistry in a warmer {A}rctic}, journal = {Proc Natl Acad Sci U S A}, year = {2011}, volume = {108}, pages = {3653--3658}, __markedentry = {[rec]}, abstract = {The physical properties of Arctic sea ice determine its habitability. Whether ice-dwelling organisms can change those properties has rarely been addressed. Following discovery that sea ice contains an abundance of gelatinous extracellular polymeric substances (EPS), we examined the effects of algal EPS on the microstructure and salt retention of ice grown from saline solutions containing EPS from a culture of the sea-ice diatom, Melosira arctica. We also experimented with xanthan gum and with EPS from a culture of the cold-adapted bacterium Colwellia psychrerythraea strain 34H. Quantitative microscopic analyses of the artificial ice containing Melosira EPS revealed convoluted ice-pore morphologies of high fractal dimension, mimicking features found in EPS-rich coastal sea ice, whereas EPS-free (control) ice featured much simpler pore geometries. A heat-sensitive glycoprotein fraction of Melosira EPS accounted for complex pore morphologies. Although all tested forms of EPS increased bulk ice salinity (by 11ā€“59%) above the controls, ice containing native Melosira EPS retained the most salt. EPS effects on ice and pore microstructure improve sea ice habitability, survivability, and potential for increased primary productivity, even as they may alter the persistence and biogeochemical imprint of sea ice on the surface ocean in a warming climate.}, doi = {10.1073/pnas.1100701108}, eprint = {http://www.pnas.org/content/108/9/3653.full.pdf+html}, owner = {rec}, timestamp = {2011.05.12}, url = {http://www.pnas.org/content/108/9/3653.abstract} } @ARTICLE{Krembs2000, author = {C. Krembs and R. Gradinger and M. Spindler}, title = {{I}mplications of brine channel geometry and surface area for the interaction of sympagic organisms in {A}rctic sea ice}, journal = {J Exp Mar Biol Ecol}, year = {2000}, volume = {243}, pages = {55--80}, __markedentry = {[rec]}, abstract = {Dynamic temporal and spatial changes of physical, chemical and spatial properties of sea ice pose many challenges to the sympagic community which inhabit a network of brine channels in its interior. Experiments were conducted to reveal the influence of the internal surface area and the structure of the network on species composition and distribution within sea ice. The surface of the brine channel walls was measured via a newly developed method using a fluorogenic tracer. These measurements allowed us to quantify the internal surface area accessible for predators of different sizes, at different ice temperatures and in different ice textures. Total internal surface area ranged from 0.6 to 4 m2 kg-1 ice and declined with decreasing ice temperature. Potentially, 6 to 41% of the area at -2°C is covered by micro-organisms. Cooling from -2 to -6°C drastically increases the coverage of organisms in brine channels due to a surface reduction. A combination of brine channel frequency measurements with an artificial brine network experiment suggests that brine channels <=200 [mu]m comprise a spatial refuge with microbial community concentrations one to two magnitudes higher than in the remaining channel network. The plasticity of predators to traverse narrow passages was experimentally tested for representative Arctic sympagic rotifers, turbellarians, and nematodes. By conforming to the osmotic pressure of the brine turbellaria match their body dimensions to the fluctuating dimensions of the brine channel system during freezing. Rotifers penetrate very narrow passages several times their body length and 57% their body diameter. In summary, ice texture, temperature, and bulk salinity influence the predatory-prey interactions by superimposing its structural component on the dynamic of the sympagic food web. Larger predators are excluded from brine channels depending on the architecture of the channel network. However, extreme body flexibility allows some predators to traverse structural impasses in the brine channel network.}, comment = {DOI: 10.1016/S0022-0981(99)00111-2}, issn = {0022-0981}, keywords = {Adaptation}, owner = {rec}, timestamp = {2011.03.08}, url = {http://www.sciencedirect.com/science/article/B6T8F-3XXCXYP-4/2/4e445853a74208e863ade514d9f71af6} } @ARTICLE{Krishnamurthy2001, author = {R. V. Krishnamurthy and Madhav Machavaram and M. Baskaran and James M. Brooks and Michael A. Champ}, title = {{O}rganic Carbon Flow in the {O}b, {Y}enisey Rivers and {K}ara {S}ea of the {A}rctic Region}, journal = {Mar Pollut Bull}, year = {2001}, volume = {42}, pages = {726--732}, abstract = {Stable carbon isotope and elemental C/N ratios of the organic fraction of a set of samples along a transect in the Ob and Yenisey Rivers into the Kara Sea in the Arctic were measured. Previously, the concentrations of 239,240Pu and 137Cs in these same samples had been determined. The coupled measurements were carried out to assess possible connectivity between organic carbon flow into the Kara Sea and transport of radioactive nuclides in this marine environment. Organic carbon flow into the Kara Sea is influenced significantly by terrigenous sources carried by the Ob and Yenisey Rivers. The carbon isotope-organic carbon relationship provides evidence that a rich source of terrigenous carbon exists in the riverine system. A weak, but significant relationship between stable carbon isotope ratio and 137Cs suggests that most of the 137Cs is derived from riverine particles, as compared to Pu which is also derived from in situ scavenging within the water column.}, comment = {DOI: 10.1016/S0025-326X(00)00202-2}, issn = {0025-326X}, owner = {rec}, timestamp = {2011.03.08}, url = {http://www.sciencedirect.com/science/article/B6V6N-43VRR6M-F/2/4fb263c0a65330bf40535f614a252e41} } @ARTICLE{Kurland2003, author = {Kurland, C. G. and Canback, B. and Berg, O. G.}, title = {{H}orizontal gene transfer: {A} critical view}, journal = {PNAS}, year = {2003}, volume = {100}, pages = {9658--9662}, abstract = {It has been suggested that horizontal gene transfer (HGT) is the "essence of phylogeny." In contrast, much data suggest that this is an exaggeration resulting in part from a reliance on inadequate methods to identify HGT events. In addition, the assumption that HGT is a ubiquitous influence throughout evolution is questionable. instead, rampant global HGT is likely to have been relevant only to primitive genomes. In modern organisms we suggest that both the range and frequencies of HGT are constrained most often by selective barriers. As a consequence those HGT events that do occur most often have little influence on genome phylogeny. Although HGT does occur with important evolutionary consequences, classical Darwinian lineages seem to be the dominant mode of evolution for modern organisms.}, c1 = {Uppsala Univ, Evolutionary Biol Ctr, Dept Mol Evolut, S-75236 Uppsala, Sweden.}, citedreferences = {ANDERSSON DI, 1999, CURR OPIN MICROBIOL, V2, P487 ; ANDERSSON SGE, 1998, NATURE, V396, P133 ; ARAVIND L, 1998, TRENDS GENET, V14, P442 ; ASAI T, 1999, P NATL ACAD SCI USA, V96, P1971 ; BERG OG, 1995, J THEOR BIOL, V173, P307 ; BERG OG, 2002, MOL BIOL EVOL, V19, P2265 ; BERGSTROM CT, 2000, GENETICS, V155, P1505 ; BJORKMAN J, 2000, SCIENCE, V287, P1479 ; BORMAN AM, 1996, J GEN VIROL 3, V77, P419 ; BROWN JR, 2001, NAT GENET, V28, P281 ; CANBACK B, 2002, P NATL ACAD SCI USA, V99, P6097 ; COWEN LE, 2001, J BACTERIOL, V183, P2971 ; DELACRUZ F, 2000, TRENDS MICROBIOL, V8, P128 ; DONG HJ, 1996, J MOL BIOL, V260, P649 ; DOOLITTLE RF, 1996, SCIENCE, V271, P470 ; DOOLITTLE WF, 1999, SCIENCE, V284, P2124 ; DYKHUIZEN DE, 1991, J BACTERIOL, V173, P7257 ; EHRENBERG M, 1984, Q REV BIOPHYS, V17, P45 ; FALUSH D, 2001, P NATL ACAD SCI USA, V98, P15056 ; FELSENSTEIN J, 2001, J MOL EVOL, V53, P447 ; FENG DF, 1997, P NATL ACAD SCI USA, V94, P13028 ; FITZGIBBON ST, 1999, NUCLEIC ACIDS RES, V27, P4218 ; GALTIER N, 1995, P NATL ACAD SCI USA, V92, P11317 ; GALTIER N, 1999, SCIENCE, V283, P220 ; GOGARTEN JP, 1996, SCIENCE, V274, P1750 ; GOGARTEN JP, 2002, MOL BIOL EVOL, V19, P2226 ; GRAHAM DE, 2000, P NATL ACAD SCI USA, V97, P3304 ; GRAY MW, 1999, SCIENCE, V283, P1476 ; GUINDON S, 2001, MOL BIOL EVOL, V18, P1838 ; HANSKI I, 1998, NATURE, V396, P41 ; HARTMAN H, 2002, P NATL ACAD SCI USA, V99, P1420 ; HOOPER SD, 2002, J MOL EVOL, V54, P734 ; HUYNEN M, 1999, SCIENCE, V286, P1443 ; KARLBERG O, 2000, YEAST, V17, P170 ; KIMURA M, 1983, NEUTRAL THEORY EVOLU ; KORBEL JO, 2002, TRENDS GENET, V18, P158 ; KOSKI LB, 2001, MOL BIOL EVOL, V18, P404 ; KURLAND CG, 1992, ANNU REV GENET, V26, P29 ; KURLAND CG, 2000, EMBO REP, V1, P92 ; LANDER ES, 2001, NATURE, V409, P860 ; LAWRENCE JG, 1997, J MOL EVOL, V44, P383 ; LAWRENCE JG, 1998, P NATL ACAD SCI USA, V95, P9413 ; LINZ B, 2000, MOL MICROBIOL, V36, P1049 ; LOCKHART PJ, 1994, MOL BIOL EVOL, V11, P605 ; LOPEZ P, 1999, J MOL EVOL, V49, P496 ; LOPEZGARCIA P, 1999, TRENDS BIOCHEM SCI, V24, P88 ; LYNCH M, 2001, GENETICS, V159, P1789 ; MACROTTE EMM, 2000, P NATL ACAD SCI USA, V97, P12115 ; MARTIN W, 1998, NATURE, V392, P37 ; MARUYAMA T, 1980, P NATL ACAD SCI-BIOL, V77, P6710 ; MAYNARDSMITH J, 1974, GENET RES, V23, P23 ; MEDIGUE C, 1991, J MOL BIOL, V222, P851 ; MIRA A, 2001, TRENDS GENET, V17, P589 ; MYLVAGANAM S, 1992, GENETICS, V130, P399 ; NELSON KE, 1999, NATURE, V399, P323 ; OCHMAN H, 1987, ESCHERICHIA COLI SAL, P1649 ; OCHMAN H, 2000, EMBO J, V19, P6637 ; OCHMAN H, 2000, NATURE, V405, P299 ; OHNISHI M, 1999, J BACTERIOL, V181, P1281 ; OLSEN GJ, 1996, TRENDS GENET, V12, P377 ; PHILIPPE H, 1999, J MOL EVOL, V49, P509 ; RAO AR, 2001, EMBO J, V20, P2977 ; RAYMOND J, 2002, SCIENCE, V298, P1616 ; RIVERA MC, 1998, P NATL ACAD SCI USA, V95, P6239 ; SALZBERG SL, 2001, SCIENCE, V292, P1903 ; SMITH MW, 1992, TRENDS BIOCHEM SCI, V17, P489 ; SNEL B, 2002, GENOME RES, V12, P17 ; TADEI F, 1997, NATURE, V387, P700 ; TEKAIA F, 1999, GENOME RES, V9, P550 ; THORSNESS PE, 1993, GENETICS, V134, P21 ; WHITLOCK MC, 1997, GENETICS, V146, P427 ; WOESE C, 1998, P NATL ACAD SCI USA, V95, P6854 ; WOESE CR, 1965, P NATL ACAD SCI USA, V54, P1546 ; WOESE CR, 1977, J MOL EVOL, V10, P1 ; WOESE CR, 1983, EVOLUTION MOL MEN, P209 ; WOESE CR, 2000, MICROBIOL MOL BIOL R, V64, P202 ; WOESE CR, 2000, P NATL ACAD SCI USA, V97, P8392 ; WOESE CR, 2002, P NATL ACAD SCI USA, V99, P8742 ; WRIGHT S, 1951, ANN EUGEN, V15, P323 ; YANG ZH, 1995, GENETICS, V139, P993 ; YAP WH, 1999, J BACTERIOL, V181, P5201}, ga = {714QY}, j9 = {PROC NAT ACAD SCI USA}, ji = {Proc. Natl. Acad. Sci. U. S. A.}, keywords = {DETERMINING DIVERGENCE TIMES; RIBOSOME RECYCLING FACTOR; ESCHERICHIA-COLI; GENOME SEQUENCE; UNIVERSAL TREE; DNA-SEQUENCES; PROTEIN CLOCK; EVOLUTION; RNA; ORIGIN}, la = {English}, nr = {81}, owner = {rec}, pa = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA}, pg = {5}, pi = {WASHINGTON}, publisher = {Natl Acad Sciences}, rp = {Berg, OG, Uppsala Univ, Evolutionary Biol Ctr, Dept Mol Evolut,EOLEOLNorbyvagen 22, S-75236 Uppsala, Sweden.}, sc = {Multidisciplinary Sciences}, sn = {0027-8424}, tc = {84}, timestamp = {2007.06.17}, ut = {ISI:000184926000007} } @ARTICLE{Lang2007, author = {Andrew S. Lang and J. Thomas Beatty}, title = {Importance of widespread gene transfer agent genes in {A}lphaproteobacteria}, journal = {Trends Microbiol}, year = {2007}, volume = {15}, pages = {54--62}, abstract = {The gene transfer agent produced by Rhodobacter capsulatus (RcGTA) is a model for several virus-like elements that seem to function solely for mediating gene exchange. Several genes that encode RcGTA are clearly related to bacteriophage genes but the cellular regulatory mechanisms that control RcGTA production indicate that RcGTA is more than just a defective prophage. Genome sequencing projects show that seemingly functional RcGTA-like structural gene clusters are present in many other species of [alpha]-proteobacteria, which might also produce RcGTA-like particles. Here, we use the genomic sequence data that are currently available to identify candidate GTA-producing species and propose an evolutionary scheme for RcGTA-like elements in the [alpha]-proteobacteria.}, doi = {DOI: 10.1016/j.tim.2006.12.001}, issn = {0966-842X}, owner = {rec}, timestamp = {2009.08.22} } @ARTICLE{Lawrence2003, author = {Lawrence, J. G. and Hendrickson, H.}, title = {{L}ateral gene transfer: when will adolescence end?}, journal = {Mol Microbiol}, year = {2003}, volume = {50}, pages = {739--749}, abstract = {The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fuelled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints probably stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Here, we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.}, c1 = {Univ Pittsburgh, Pittsburgh Bacteriophage Inst, Pittsburgh, PA 15260 USA.EOLEOLUniv Pittsburgh, Dept Biol Sci, Pittsburgh, PA 15260 USA.}, citedreferences = {ANDERSSON JO, 1999, CURR OPIN GENET DEV, V9, P664 ; ANDERSSON JO, 1999, MOL BIOL EVOL, V16, P1178 ; BARINAGA M, 1996, SCIENCE, V272, P1261 ; BAUMLER AJ, 2000, SCIENCE, V287, P50 ; BERG OG, 2002, MOL BIOL EVOL, V19, P2265 ; BROCHIER C, 2000, TRENDS GENET, V16, P529 ; BROWN JR, 2001, NAT GENET, V28, P281 ; CAPIAUX H, 2001, BIOCHIMIE, V83, P161 ; COHAN FM, 2001, SYST BIOL, V50, P513 ; COLE ST, 2001, NATURE, V409, P1007 ; DAUBIN V, 2003, SCIENCE, V301, P829 ; DAVIDOFF AJ, 1996, INT J TECHNOL ASSESS, V12, P9 ; DOOLITTLE RF, 1990, J MOL EVOL, V31, P383 ; DOOLITTLE RF, 1998, CURR OPIN GENET DEV, V8, P630 ; DOOLITTLE WF, 1999, SCIENCE, V284, P2124 ; DOOLITTLE WF, 2003, PHILOS T ROY SOC B, V358, P39 ; DYKHUIZEN DE, 1991, J BACTERIOL, V173, P7257 ; FEIL EJ, 2001, P NATL ACAD SCI USA, V98, P182 ; FITZGIBBON ST, 1999, NUCLEIC ACIDS RES, V27, P4218 ; FLEISCHMANN RD, 1995, SCIENCE, V269, P496 ; GARCIAVALLVE S, 2000, GENOME RES, V10, P1719 ; GARCIAVALLVE S, 2000, MOL BIOL EVOL, V17, P352 ; GOGARTEN JP, 1992, J EXP BIOL, V172, P137 ; GOGARTEN JP, 1995, TRENDS ECOL EVOL, V10, P147 ; GOGARTEN JP, 1999, BIOL BULL, V196, P359 ; GOGARTEN JP, 2002, MOL BIOL EVOL, V19, P2226 ; GORDON DM, 2001, MICROBIOL-UK 5, V147, P1079 ; GORDON DM, 2002, MICROBIOL-SGM 5, V148, P1513 ; GUTTMAN DS, 1997, TRENDS ECOL EVOL, V12, P16 ; HALL RM, 1997, CIBA F SYMP, V207, P192 ; HAYES WS, 1998, GENOME RES, V8, P1154 ; IBBA M, 1997, P NATL ACAD SCI USA, V94, P14383 ; JAIN R, 1999, P NATL ACAD SCI USA, V96, P3801 ; JORDAN IK, 2001, GENOME RES, V11, P555 ; KARLIN S, 1998, CURR OPIN MICROBIOL, V1, P598 ; KIMURA M, 1983, NEUTRAL THEORY MOL E ; KLENK HP, 1999, J MOL EVOL, V48, P528 ; KOONIN EV, 2001, ANNU REV MICROBIOL, V55, P709 ; KUNIN V, 2003, GENOME RES, V13, P1589 ; KURLAND CG, 2000, EMBO REP, V1, P92 ; LAWRENCE JG, 1996, GENETICS, V143, P1843 ; LAWRENCE JG, 1997, J MOL EVOL, V44, P383 ; LAWRENCE JG, 1997, TRENDS MICROBIOL, V5, P355 ; LAWRENCE JG, 1998, P NATL ACAD SCI USA, V95, P9413 ; LAWRENCE JG, 1999, CURR OPIN MICROBIOL, V2, P519 ; LAWRENCE JG, 2001, SYST BIOL, V50, P479 ; LAWRENCE JG, 2002, J BACTERIOL, V184, P4891 ; LAWRENCE JG, 2002, THEOR POPUL BIOL, V61, P449 ; LAWRENCE JG, 2002, TRENDS MICROBIOL, V10, P1 ; LEVIN BR, 1981, GENETICS, V99, P1 ; LOBRY JR, 1996, MOL BIOL EVOL, V13, P660 ; LOBRY JR, 2002, GENOME BIOL, V3 ; LOBRY JR, 2003, CURR OPIN MICROBIOL, V6, P101 ; LUDWIG W, 1998, ELECTROPHORESIS, V19, P554 ; LYNCH M, 2001, GENETICS, V159, P1789 ; MAJEWSKI J, 1999, GENETICS, V153, P1525 ; MAKAROVA KS, 1999, GENOME RES, V9, P608 ; MAKAROVA KS, 2001, GENOME BIOL, V2, P1 ; MEDIGUE C, 1991, J MOL BIOL, V222, P851 ; MIRKIN BG, 2003, BMC EVOL BIOL, V3 ; MORAN NA, 2000, TRENDS ECOL EVOL, V15, P321 ; MYLVAGANAM S, 1992, GENETICS, V130, P399 ; NELSON KE, 1999, NATURE, V399, P323 ; NESBO CL, 2001, J MOL EVOL, V53, P340 ; OCHMAN H, 2000, NATURE, V405, P299 ; OKADA S, 2001, MOL ECOL, V10, P2499 ; PEDULLA ML, 2003, CELL, V113, P171 ; RABSCH W, 2002, INFECT IMMUN, V70, P2249 ; RAGAN MA, 2001, CURR OPIN GENET DEV, V11, P620 ; RAGAN MA, 2001, FEMS MICROBIOL LETT, V201, P187 ; SERRES MH, 2000, MICROB COMP GENOMICS, V5, P205 ; SIMMONS MP, 2002, MOL BIOL EVOL, V19, P14 ; SNEL B, 1999, NAT GENET, V21, P108 ; SNEL B, 2002, GENOME RES, V12, P17 ; STILLER JW, 1999, MOL BIOL EVOL, V16, P1270 ; STOLTZFUS A, 1999, J MOL EVOL, V49, P169 ; TAMAS I, 2002, SCIENCE, V296, P2376 ; TEKAIA F, 1999, GENOME RES, V9, P550 ; VOGEL J, 2003, APPL ENVIRON MICROB, V69, P1482 ; WOESE CR, 1987, MICROBIOL REV, V51, P221 ; WOESE CR, 2000, MICROBIOL MOL BIOL R, V64, P202 ; WOESE CR, 2002, P NATL ACAD SCI USA, V99, P8742 ; WORNING P, 2000, NUCLEIC ACIDS RES, V28, P706 ; YAP WH, 1999, J BACTERIOL, V181, P5201 ; ZAWADZKI P, 1995, GENETICS, V140, P917 ; ZUCKERKANDL E, 1965, J THEOR BIOL, V8, P357}, ga = {733FC}, j9 = {MOL MICROBIOL}, ji = {Mol. Microbiol.}, keywords = {ESCHERICHIA-COLI POPULATIONS; TRANSFER-RNA SYNTHETASES; BACTERIAL GENOMES; EVOLUTIONARY HISTORY; THERMOTOGA-MARITIMA; NATURAL-POPULATIONS; HORIZONTAL TRANSFER; MICROBIAL GENOMES; SELFISH OPERONS; RIBOSOMAL-RNA}, la = {English}, nr = {86}, owner = {rec}, pa = {9600 GARSINGTON RD, OXFORD OX4 2DG, OXON, ENGLAND}, pg = {11}, pi = {OXFORD}, publisher = {Blackwell Publishing Ltd}, rp = {Lawrence, JG, Univ Pittsburgh, Pittsburgh Bacteriophage Inst, 352EOLEOLCrawford Hall, Pittsburgh, PA 15260 USA.}, sc = {Biochemistry & Molecular Biology; Microbiology}, sn = {0950-382X}, tc = {54}, timestamp = {2007.06.17}, ut = {ISI:000185988400003} } @ARTICLE{Lederberg1946, author = {Lederberg, Joshua and Tatum, Edward L.}, title = {{G}ene {R}ecombination in \emph{Escherichia coli}}, journal = {Nature}, year = {1946}, volume = {158}, pages = {558}, owner = {rec}, timestamp = {2007.06.17} } @ARTICLE{Lennon2007, author = {Jay T Lennon}, title = {Diversity and metabolism of marine bacteria cultivated on dissolved {DNA}.}, journal = {Appl Environ Microbiol}, year = {2007}, volume = {73}, pages = {2799--2805}, abstract = {Dissolved DNA (dDNA) is a potentially important source of energy and nutrients in aquatic ecosystems. However, little is known about the identity, metabolism, and interactions of the microorganisms capable of consuming dDNA. Bacteria from Eel Pond (Woods Hole, MA) were cultivated on low-molecular-weight (LMW) or high-molecular-weight (HMW) dDNA, which served as the primary source of carbon, nitrogen, and phosphorus. Cloning and sequencing of 16S rRNA genes revealed that distinct bacterial assemblages with comparable levels of taxon richness developed on LMW and HMW dDNA. Since the LMW and HMW dDNA used in this study were stoichiometrically identical, the results confirm that the size alone of dissolved organic matter can influence bacterial community composition. Variation in the growth and metabolism of isolates provided insight into mechanisms that may have generated differences in bacterial community composition. For example, bacteria from LMW dDNA enrichments generally grew better on LMW dDNA than on HMW dDNA. In contrast, bacteria isolated from HMW dDNA enrichments were more effective at degrading HMW dDNA than bacteria isolated from LMW dDNA enrichments. Thus, marine bacteria may experience a trade-off between their ability to compete for LMW dDNA and their ability to access HMW dDNA via extracellular nuclease production. Together, the results of this study suggest that dDNA turnover in marine ecosystems may involve a succession of microbial assemblages with specialized ecological strategies.}, doi = {10.1128/AEM.02674-06}, institution = {W. K. Kellogg Biological Station and Department of Microbiology and Molecular Genetics, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA. lennonja@msu.edu}, keywords = {Bacteria, growth /&/ development/metabolism; Base Sequence; Biodiversity; Cloning, Molecular; Cluster Analysis; Computational Biology; DNA, metabolism; Massachusetts; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S, genetics; Seawater, chemistry/microbiology; Sequence Analysis, DNA; Water Microbiology}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {AEM.02674-06}, pmid = {17337557}, timestamp = {2009.07.27}, url = {http://dx.doi.org/10.1128/AEM.02674-06} } @ARTICLE{Lorenz1981, author = {Lorenz, M.G. and Aardema, B.W. and Krumbein, W.E.}, title = {{I}nteraction of marine sediment with {DNA} and {DNA} availability to nucleases}, journal = {Mar Biol}, year = {1981}, volume = {64}, pages = {225--230}, owner = {rec}, timestamp = {2007.06.17} } @ARTICLE{Lorenz1988, author = {M. G. Lorenz and B. W. Aardema and W. Wackernagel}, title = {Highly efficient genetic transformation of \emph{Bacillus subtilis} attached to sand grains}, journal = {J Gen Microbiol}, year = {1988}, volume = {134}, pages = {107--112}, abstract = {Genetic transformation at the solid/liquid interface was studied using Bacillus subtilis 1G20 (trpC2) with a flow-through system of columns filled with chemically pure sea sand. Studies were done at 23 degrees C. In one type of experiment, competent cultures were incubated with sand-adsorbed DNA, and in another, competent cultures were exposed to sand and then incubated with dissolved DNA for transformation. Of the applied cells, around 10\% were retained in columns filled with DNA-loaded sand and around 1\% in columns with pure sand. Reversible attachment of some of the cells to surfaces of sand grains could be demonstrated. The overall transformation frequencies obtained were 25- to 50-fold higher than in a standard liquid culture procedure. In this standard procedure, transformation was sensitive to DNAase I concentrations above 50 ng ml-1, whereas in sand columns it was resistant to DNAase I concentrations up to 1 microgram ml-1. Quantification of transformants eluting from columns indicated that sand-attached cells detach at some point after DNA binding or uptake.}, institution = {Arbeitsgruppe Genetik, Fachbereich Biologie, Universität Oldenburg, FRG.}, keywords = {Adsorption; Bacillus subtilis, genetics/ultrastructure; DNA, Bacterial, metabolism; Deoxyribonuclease I, pharmacology; Microscopy, Electron, Scanning; Transformation, Genetic, drug effects}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {3141561}, timestamp = {2009.07.27} } @INCOLLECTION{Lorenz1992a, author = {M. G. Lorenz and W. Wackernagel}, title = {{DNA} binding to various clay inerals and retarded enzymatic degradation of {DNA} in a sand/clay microcosm}, booktitle = {Gene transfers and environment}, publisher = {Springer-Verlag KG, Berlin}, year = {1992}, editor = {M. J. Gauthier}, pages = {103--113}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Lorenz1994, author = {Lorenz, M. G. and Wackernagel, W.}, title = {{B}acterial gene transfer by natural genetic transformation in the environment}, journal = {Microbiol Rev}, year = {1994}, volume = {58}, pages = {563--602}, abstract = {Natural genetic transformation is the active uptake of free DNA by bacterial cells and the heritable incorporation of its genetic information. Since the famous discovery of transformation in Streptococcus pneumoniae by Griffith in 1928 and the demonstration of DNA as the transforming principle by Avery and coworkers in 1944, cellular processes involved in transformation have been studied extensively by in vitro experimentation with a few transformable species. Only more recently has it been considered that transformation may be a powerful mechanism of horizontal gene transfer in natural bacterial populations. In this review the current understanding of the biology of transformation is summarized to provide the platform on which aspects of bacterial transformation in water soil, and sediments and the habitat of pathogens are discussed. Direct and indirect evidence for gene transfer routes by transformation within species and between different species will be presented, along with data suggesting that plasmids as well as chromosomal DNA are subject to genetic exchange via transformation. Experiments exploring the prerequisites for transformation in the environment, including the production and persistence of free DNA and factors important for the uptake of DNA by cells, will be compiled, as well as possible natural barriers to transformation. The efficiency of gene transfer by transformation in bacterial habitats is possibly genetically adjusted to submaximal levels. The fact that natural transformation has been detected among bacteria from all trophic and taxonomic groups including archaebacteria suggests that transformability evolved early in phylogeny. Probable functions of DNA uptake other than gene acquisition will be discussed. The body of information presently available suggests that transformation has a great impact on bacterial population dynamics as well as on bacterial evolution and speciation.}, citedreferences = {AARDEMA BW, 1983, APPL ENVIRON MICROB, V46, P417 ; AHRENHOLTZ I, 1994, ARCH MICROBIOL, V161, P176 ; ALBANO M, 1987, J BACTERIOL, V169, P3110 ; ALBRITTON WL, 1982, J BACTERIOL, V152, P1066 ; ALBRITTON WL, 1984, MOL GEN GENET, V193, P358 ; ALLISON DG, 1987, J GEN MICROBIOL, V133, P1319 ; ANDERSON G, 1958, SOIL SCI, V86, P169 ; ANDERSON G, 1961, SOIL SCI, V91, P156 ; ATLAS M, 1981, MICROBIAL ECOLOGY FU ; AVERY OT, 1944, J EXP MED, V79, P137 ; BAGCI H, 1979, MOL GEN GENET, V175, P175 ; BAKER RT, 1977, NZ J SCI, V20, P439 ; BASHAN Y, 1987, J GEN MICROBIOL, V133, P3473 ; BASHAN Y, 1988, AZOSPIRILLUM, V4, P166 ; BASHAN Y, 1988, J GEN MICROBIOL 7, V134, P1811 ; BASSE G, IN PRESS J MICROBIOL ; BASSE G, UNPUB ; BAZELYAN VL, 1979, OCEANOLOGY, V19, P30 ; BEHNKE D, 1981, MOL GEN GENET, V181, P490 ; BERGAN T, 1983, ZBL BAKT MIKR HYG A, V254, P214 ; 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Rev.}, keywords = {POLYMERASE CHAIN-REACTION; CYANOBACTERIUM ANACYSTIS-NIDULANS; COMPETENT BACILLUS-SUBTILIS; STUTZERI STRAIN ZOBELL; MARKER RESCUE TRANSFORMATION; PENICILLIN-RESISTANT STRAINS; AZOSPIRILLUM-BRASILENSE CD; BINDING PROTEIN GENES; INFLUENZAE TYPE-B; ESCHERICHIA-COLI}, la = {English}, nr = {404}, owner = {rec}, pa = {1325 MASSACHUSETTS AVENUE, NW, WASHINGTON, DC 20005-4171}, pg = {40}, pi = {WASHINGTON}, publisher = {Amer Soc Microbiology}, rp = {LORENZ, MG, UNIV OLDENBURG, FACHBEREICH BIOL, POSTFACH 2503, D-26111EOLEOLOLDENBURG, GERMANY.}, sc = {Microbiology}, sn = {0146-0749}, tc = {397}, timestamp = {2007.06.17}, ut = {ISI:A1994PE73000009} } @ARTICLE{Lorenz1990, author = {M. G. Lorenz and W. Wackernagel}, title = {{N}atural genetic transformation of \emph{Pseudomonas stutzeri} by sand-adsorbed {DNA}}, journal = {Arch Microbiol}, year = {1990}, volume = {154}, pages = {380--385}, abstract = {In a soil/sediment model system we have shown recently that a gram-positive bacterium with natural competence (Bacillus subtilis) can take up transforming DNA adsorbed to sand minerals. Here we examined whether also a naturally transformable soil bacterium of the gram-negative pseudomonad (Pseudomonas stutzeri) can be transformed by mineral-associated DNA. For these studies the transformation protocol of this species was further improved and characterized. The peak of competence during growth of P. stutzeri was determined to occur at the beginning of the stationary phase. The competence state was conserved during shock freezing and thawing of cells in 10\% glycerol. Kinetic experiments showed that transformant formation after addition of DNA to competent cells proceeded for more than 2 h with DNA adsorption to cells being the rate limiting step. By means of the defined protocol P. stutzeri was shown to be transformed by sand-adsorbed DNA. Transformation by adsorbed or dissolved DNA occurred between 16 degrees and 44 degrees C. Efficiency and DNaseI-sensitivity of transformation by DNA adsorbed to sand or in liquid were comparable. It is concluded that uptake of particle-bound DNA by P. stutzeri in soil is possible. This finding adds evidence to the view that transformation occurs in natural environments where DNA is assumed to be significantly associated with mineral/particulate material and thereby is protected against enzymatic degradation.}, keywords = {Adsorption; Centrifugation, Density Gradient; DNA, Bacterial; Filtration; Kinetics; Pseudomonas; Soil Microbiology; Transformation, Bacterial}, owner = {rec}, pmid = {2244790}, timestamp = {2007.06.17} } @ARTICLE{Lorenz1987, author = {M. G. Lorenz and W. Wackernagel}, title = {{A}dsorption of {DNA} to sand and variable degradation rates of adsorbed {DNA}}, journal = {Appl Environ Microbiol}, year = {1987}, volume = {53}, pages = {2948--2952}, abstract = {Adsorption and desorption of DNA and degradation of adsorbed DNA by DNase I were studied by using a flowthrough system of sand-filled glass columns. Maximum adsorption at 23 degrees C occurred within 2 h. The amounts of DNA which adsorbed to sand increased with the salt concentration (0.1 to 4 M NaCl and 1 mM to 0.2 M MgCl2), salt valency (Na+ less than Mg2+ and Ca2+), and pH (5 to 9). Maximum desorption of DNA from sand (43 to 59\%) was achieved when columns were eluted with NaPO4 and NaCl for 6 h or with EDTA for 1 h. DNA did not desorb in the presence of detergents. It is concluded that adsorption proceeded by physical and chemical (Mg2+ bridging) interaction between the DNA and sand surfaces. Degradability by DNase I decreased upon adsorption of transforming DNA. When DNA adsorbed in the presence of 50 mM MgCl2, the degradation rate was higher than when it adsorbed in the presence of 20 mM MgCl2. The sensitivity to degradation of DNA adsorbed to sand at 50 mM MgCl2 decreased when the columns were eluted with 0.1 mM MgCl2 or 100 mM EDTA before application of DNase I. This indicates that at least two types of DNA-sand complexes with different accessibilities of adsorbed DNA to DNase I existed. The degradability of DNA adsorbed to minor mineral fractions (feldspar and heavy minerals) of the sand differed from that of quartz-adsorbed DNA.}, keywords = {Adsorption; Animals; DNA; Deoxyribonucleases; Hydrogen-Ion Concentration; Kinetics; Soil; Temperature}, owner = {rec}, pmid = {3435148}, timestamp = {2007.06.17} } @ARTICLE{Lorenzen1967, author = {Lorenzen, C.J.}, title = {Determination of chlorophyll and phaeopigments: spectrophotometric equations}, journal = {Limnol Oceanogr}, year = {1967}, volume = {12}, pages = {343--346}, owner = {rec}, timestamp = {2011.03.07} } @ARTICLE{Maranger1995, author = {R Maranger and DF Bird}, title = {Viral abundance in aquatic systems: a comparison between marine and fresh waters}, journal = {Mar Ecol Prog Ser}, year = {1995}, volume = {121}, pages = {217--226}, owner = {rec}, timestamp = {2009.08.22} } @ARTICLE{Maranger1994, author = {Maranger, R. and Bird, D. F. and Juniper, S. K.}, title = {{V}iral and bacterial dynamics in {A}rctic sea-ice during the spring algal bloom near {R}esolute, {NWT}, {C}anada}, journal = {Mar Ecol Prog Ser}, year = {1994}, volume = {111}, pages = {121--127}, abstract = {High virus counts were found in Arctic sea ice samples taken during the spring ice algal bloom near Resolute, Northwest Territories, Canada. Viral abundances in the sea ice ranged from 3.7 x 10(11) viruses m(-2) (or 9.0 x 10(6) ml(-1)) to 4.9 x 10(12) m(-2) (1.3 x 10(8) ml(-1)) which is 10- to 100-fold greater than the concentration of viruses in the underlying water column (1.1 x 10(6) ml(-1)). This increase in viral abundance corresponds with the 10- to 100-fold increase in bacterial abundance in sea ice as compared with the water column. Bacterial abundances ranged from 6.1 x 10(9) bacteria m(-2) (1.5 x 10(5) ml(-1)) to 4.2 x 10(11) m(-2) (1.0 x 10(7) ml(-1)) from early to late spring respectively. The virus-to-bacteria ratios (VBR) were among the highest reported in natural samples. The greatest viral abundances occurred in the 0.5 to 1.5 cm layer of the ice profile, where the bacteria were most active. The VBR generally decreased during the spring although viruses were increasing in abundance. The disequilibrium between phage and bacterial growth and abundance maxima during the spring bloom is suggested to be due to (1) a change in the makeup of the bacterial community, such that phage-resistant bacteria proliferated later in the spring, or (2) an increase in viral lytic activity with higher bacterial cell-specific growth rates; both viral lytic activity and bacterial growth rates declined later in the spring as the bacterial population reached its peak.}, owner = {rec}, timestamp = {2007.06.17}, ut = {ISI:A1994PB96700013} } @ARTICLE{Meibom2005, author = {Meibom, K. L. and Blokesch, M. and Dolganov, N. A. and Wu, C. Y. and Schoolnik, G. K.}, title = {{C}hitin induces natural competence in \emph{Vibrio cholerae}}, journal = {Science}, year = {2005}, volume = {310}, pages = {1824--1827}, abstract = {The mosaic-structured Vibrio cholerae genome points to the importance of horizontal gene transfer (HGT) in the evolution of this human pathogen. We showed that V. cholerae can acquire new genetic material by natural transformation during growth on chitin, a biopolymer that is abundant in aquatic habitats (e.g., from crustacean exoskeletons), where it lives as an autochthonous microbe. Transformation competence was found to require a type IV pilus assembly complex, a putative DNA binding protein, and three convergent regulatory cascades, which are activated by chitin, increasing cell density, and nutrient limitation, a decline in growth rate, or stress.}, c1 = {Stanford Univ, Div Infect Dis & Geog Med, Dept Microbiol & Immunol, Stanford, CA 94305 USA.EOLEOLStanford Univ, Stanford Inst Environm, Stanford, CA 94305 USA.}, citedreferences = {BAUR B, 1996, APPL ENVIRON MICROB, V62, P3673 ; CHEN I, 2004, NAT REV MICROBIOL, V2, P241 ; FARUQUE SM, 2003, TRENDS MICROBIOL, V11, P505 ; HAHN J, 1993, MOL MICROBIOL, V10, P99 ; LIPP EK, 2002, CLIN MICROBIOL REV, V15, P757 ; LORENZ MG, 1994, MICROBIOL REV, V58, P563 ; MEIBOM KL, 2004, P NATL ACAD SCI USA, V101, P2524 ; MILLER MB, 2002, CELL, V110, P303 ; PALMEN R, 1995, CURR MICROBIOL, V30, P7 ; PURDY A, 2005, J BACTERIOL, V187, P2992 ; REDFIELD RJ, 2005, J MOL BIOL, V347, P735 ; SILVA AJ, 2004, J BACTERIOL, V186, P6374 ; STEINMOEN H, 2002, P NATL ACAD SCI USA, V99, P7681 ; SUZUKI MT, 2004, MICROBIAL ECOL, V48, P473 ; THOMPSON JR, 2005, SCIENCE, V307, P1311 ; WALDOR MK, 1996, SCIENCE, V272, P1910 ; WHITCHURCH CB, 2002, SCIENCE, V295, P1487 ; YILDIZ FH, 2004, MOL MICROBIOL, V53, P497 ; ZHU J, 2002, P NATL ACAD SCI USA, V99, P3129 ; ZULTY JJ, 1995, P NATL ACAD SCI USA, V92, P3616}, em = {kmeibom@necker.frEOLEOLschoolni@cmgm.stanford.edu}, ga = {995II}, j9 = {SCIENCE}, ji = {Science}, keywords = {GENETIC-TRANSFORMATION; HAEMOPHILUS-INFLUENZAE; DNA; EXPRESSION; IDENTIFICATION; POPULATION; INDUCTION; VIRULENCE; LYSIS}, la = {English}, nr = {20}, owner = {rec}, pa = {1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA}, pg = {4}, pi = {WASHINGTON}, publisher = {Amer Assoc Advancement Science}, rp = {Meibom, KL, Stanford Univ, Div Infect Dis & Geog Med, Dept Microbiol &EOLEOLImmunol, Stanford, CA 94305 USA.}, sc = {Multidisciplinary Sciences}, sn = {0036-8075}, tc = {12}, timestamp = {2007.06.17}, ut = {ISI:000234093600049} } @ARTICLE{Meiners2003, author = {Meiners, K. and R. Gradinger and J. Fehling and G. Civitarese and M. Spindler}, title = {{V}ertical distribution of exopolymer particles in sea ice of the {F}ram {S}trait ({A}rctic) during autumn}, journal = {Mar Ecol Prog Ser}, year = {2003}, volume = {248}, pages = {1--13}, owner = {rec}, timestamp = {2011.03.08} } @ARTICLE{MurrayJackson1993, author = {Murray, A. G. and Jackson, G. A.}, title = {Viral dynamics {II}: a model of the interaction of ultraviolet light and mixing processes on virus survival in seawater}, journal = {Mar Ecol Prog Ser}, year = {1993}, volume = {102}, pages = {105-114}, owner = {rec}, timestamp = {2009.08.22} } @ARTICLE{MurrayJackson1992, author = {Murray, A. G. and Jackson, G. A.}, title = {Viral dynamics: a model of the effects of size shape, motion and abundance of single-celled planktonic organisms and other particles}, journal = {Mar Ecol Prog Ser}, year = {1992}, volume = {89}, pages = {103--116}, owner = {rec}, timestamp = {2009.08.22} } @ARTICLE{Nurnberg1994, author = {Nurnberg, D. and Wollenburg, I. and Dethleff, D. and Eicken, H. and Kassens, H. and Letzig, T. and Reimnitz, E. and Thiede, J.}, title = {{S}ediments in {A}rctic sea ice -- {I}mplications for entrainment, transport and release}, journal = {Mar Geol}, year = {1994}, volume = {119}, pages = {185--214}, abstract = {Despite the Arctic sea ice cover's recognized sensitivity to environmental change, the role of sediment inclusions in lowering ice albedo and affecting ice ablation is poorly understood. Sea ice sediment inclusions were studied in the central Arctic Ocean during the Arctic 91 expedition and in the Laptev Sea (East Siberian Arctic Region Expedition 1992). Results from these investigations are here combined with previous studies performed in major areas of ice ablation and the southern central Arctic Ocean. This study documents the regional distribution and composition of particle-laden ice, investigates and evaluates processes by which sediment is incorporated into the ice cover, and identifies transport paths and probable depositional centers for the released sediment. In April 1992, sea ice in the Laptev Sea was relatively clean. The sediment occasionally observed was distributed diffusely over the entire ice column, forming turbid ice. Observations indicate that frazil and anchor ice formation occurring in a large coastal polynya provide a main mechanism for sediment entrainment. In the central Arctic Ocean sediments are concentrated in layers within or at the surface of ice floes due to melting and refreezing processes. The surface sediment accumulation in central Arctic multi-year sea ice exceeds by far the amounts observed in first-year ice from the Laptev Sea in April 1992. Sea ice sediments are generally fine grained, although coarse sediments and stones up to 5 cm in diameter are observed. Component analysis indicates that quartz and clay minerals are the main terrigenous sediment particles. The biogenous components, namely shells of pelecypods and benthic foraminiferal tests, point to a shallow, benthic, marine source area. Apparently, sediment inclusions were resuspended from shelf areas before and incorporated into the sea ice by suspension freezing. Clay mineralogy of ice-rafted sediments provides information on potential source areas. A smectite maximum in sea ice sediment samples repeatedly occurred between 81 degrees N and 83 degrees N along the Arctic 91 transect, indicating a rather stable and narrow smectite rich ice drift stream of the Transpolar Drift. The smectite concentrations are comparable to those found in both Laptev Sea shelf sediments and anchor ice sediments, pointing to this sea as a potential source area for sea ice sediments. In the central Arctic Ocean sea ice clay mineralogy is significantly different from deep-sea clay mineral distribution patterns. The contribution of sea ice sediments to the deep sea is apparently diluted by sedimentary material provided by other transport mechanisms.}, owner = {rec}, timestamp = {2007.06.17}, ut = {ISI:A1994PC28100002} } @ARTICLE{Page1982a, author = {W.J. Page}, title = {Optimal conditions for induction of competence in nitrogen-fixing \emph{Azotobacter vinelandii}}, journal = {Can J Microbiol}, year = {1982}, volume = {28}, pages = {389--397}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Paget1992, author = {E.L. Paget and J. Simonet and P. Monrozier}, title = {Adsorption of {DNA} on clay minerals: protection against {DNaseI} and influence on gene transfer}, journal = {FEMS Microbiol Ecol}, year = {1992}, volume = {97}, pages = {31--40}, owner = {rec}, timestamp = {2009.07.27} } @MANUAL{Parsons1984, title = {A manual of chemical and biological methods for seawater analysis}, author = {T. R. Parsons and Y. Maita and C. M. Lalli}, organization = {Pergamon}, year = {1984}, owner = {rec}, pages = {4829--4833}, timestamp = {2011.05.12} } @ARTICLE{Paul1984, author = {J.H. Paul and D.J. Carlson}, title = {Genetic material in the marine environment: implication for bacterial {DNA}}, journal = {Limnol Oceanogr}, year = {1984}, volume = {29}, pages = {1091--1097}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Paul1988, author = {John H Paul and Mary F Deflaun and Wade H Jeffrey and Andrew W David}, title = {Seasonal and Diel Variability in Dissolved {DNA} and in Microbial Biomass and Activity in a Subtropical Estuary.}, journal = {Appl Environ Microbiol}, year = {1988}, volume = {54}, pages = {718--727}, abstract = {Dissolved DNA and microbial biomass and activity parameters were measured over a 15-month period at three stations along a salinity gradient in Tampa Bay, Fla. Dissolved DNA showed seasonal variation, with minimal values in December and January and maximal values in summer months (July and August). This pattern of seasonal variation followed that of particulate DNA and water temperature and did not correlate with bacterioplankton (direct counts and [H]thymidine incorporation) or phytoplankton (chlorophyll a and CO(2) fixation) biomass and activity. Microautotrophic populations showed maxima in the spring and fall, whereas microheterotrophic activity was greatest in late summer (September). Both autotrophic and heterotrophic microbial activity was greatest at the high estuarine (low salinity) station and lowest at the mouth of the bay (high salinity station), irrespective of season. Dissolved DNA carbon and phosphorus constituted 0.11 +/- 0.05\% of the dissolved organic carbon and 6.6 +/- 6.5\% of the dissolved organic phosphorus, respectively. Strong diel periodicity was noted in dissolved DNA and in microbial activity in Bayboro Harbor during the dry season. A noon maximum in primary productivity was followed by an 8 p.m. maximum in heterotrophic activity and a midnight maximum in dissolved DNA. This diel periodicity was less pronounced in the wet season, when microbial parameters were strongly influenced by episodic inputs of freshwater. These results suggest that seasonal and diel production of dissolved DNA is driven by primary production, either through direct DNA release by phytoplankton, or more likely, through growth of bacterioplankton on phytoplankton exudates, followed by excretion and lysis.}, institution = {Department of Marine Science, University of South Florida, 140 7th Avenue South, St. Petersburg, Florida 33701.}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {16347583}, timestamp = {2009.11.05} } @ARTICLE{Perovich1993, author = {Perovich, D. K.}, title = {A Theoretical Model of Ultraviolet Light Transmission Through {A}ntarctic Sea Ice}, journal = {J Geophys Res}, year = {1993}, volume = {98}, pages = {22579--22587}, abstract = {Much of the region of the Earth most affected by stratospheric ozone depletion is covered by a seasonal or perennial sea ice cover, which is the habitat of a productive and extensive sea ice microbial community. To assess the impact of enhanced incident ultraviolet irradiance on this community, a knowledge of the amount of light transmitted through a sea ice cover is necessary. A two-stream radiative transfer model is used to estimate the penetration of ultraviolet radiation through Antarctic sea ice. Sea ice optical properties were used as proxies to infer scattering and absorption coefficients at ultraviolet wavelengths. Case studies are reported for sea ice in McMurdo Sound and in the Weddell Sea. Values of spectral transmittance are computed as well as integrated transmitted UV-B, UV-A, biologically effective irradiance (BEI), and photosynthetically active radiation (PAR). UV-B light levels under meter-thick ice are a few percent of incident values. The presence of a snow cover results in a large decrease in transmitted ultraviolet. Snow and ice ameliorate the biological impact of enhanced levels of incident ultraviolet radiation by reducing the BEI relative to the PAR.}, owner = {rec}, publisher = {American Geophysical Union}, timestamp = {2009.11.05}, url = {http://dx.doi.org/10.1029/93JC02563} } @ARTICLE{Petersen2005, author = {Fernanda C Petersen and Lin Tao and Anne A Scheie}, title = {{DNA} binding-uptake system: a link between cell-to-cell communication and biofilm formation.}, journal = {J Bacteriol}, year = {2005}, volume = {187}, pages = {4392--4400}, abstract = {DNA has recently been described as a major structural component of the extracellular matrix in biofilms. In streptococci, the competence-stimulating peptide (CSP) cell-to-cell signal is involved in competence for genetic transformation, biofilm formation, and autolysis. Among the genes regulated in response to the CSP are those involved in binding and uptake of extracellular DNA. We show in this study that a functional DNA binding-uptake system is involved in biofilm formation. A comGB mutant of Streptococcus mutans deficient in DNA binding and uptake, but unaffected in signaling, showed reduced biofilm formation. During growth in the presence of DNase I, biofilm was reduced in the wild type to levels similar to those found with the comGB mutant, suggesting that DNA plays an important role in the wild-type biofilm formation. We also showed that growth in the presence of synthetic CSP promoted significant release of DNA, with similar levels in the wild type and in the comGB mutant. The importance of the DNA binding-uptake system in biofilm formation points to possible novel targets to fight infections.}, doi = {10.1128/JB.187.13.4392-4400.2005}, institution = {Department of Oral Biology, Faculty of Dentistry, University of Oslo, N0316 Oslo, Norway. cpaiva@odont.uio.no}, keywords = {Bacterial Proteins, chemical synthesis/pharmacology; Biofilms, drug effects/growth /&/ development; DNA, Bacterial, metabolism; Deoxyribonuclease I, pharmacology; Signal Transduction; Streptococcus mutans, genetics/growth /&/ development/physiology; Transformation, Bacterial}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {187/13/4392}, pmid = {15968048}, timestamp = {2009.07.27}, url = {http://dx.doi.org/10.1128/JB.187.13.4392-4400.2005} } @ARTICLE{Proctor1990, author = {Proctor, L.M. and Fuhrman, J.A.}, title = {{V}iral mortality of marine bacteria and cyanobacteria}, journal = {Nature}, year = {1990}, volume = {343}, pages = {60--62}, owner = {rec}, timestamp = {2007.06.17} } @MANUAL{RProject, title = {R: A Language and Environment for Statistical Computing}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2011}, note = {{ISBN} 3-900051-07-0}, url = {http://www.R-project.org} } @ARTICLE{Raymond2007, author = {James A Raymond and Christian Fritsen and Kate Shen}, title = {An ice-binding protein from an {A}ntarctic sea ice bacterium}, journal = {FEMS Microbiol Ecol}, year = {2007}, volume = {61}, pages = {214--221}, abstract = {An Antarctic sea ice bacterium of the Gram-negative genus Colwellia, strain SLW05, produces an extracellular substance that changes the morphology of growing ice. The active substance was identified as a approximately 25-kDa protein that was purified through its affinity for ice. The full gene sequence was determined and was found to encode a 253-amino acid protein with a calculated molecular mass of 26,350 Da. The predicted amino acid sequence is similar to predicted sequences of ice-binding proteins recently found in two species of sea ice diatoms and a species of snow mold. A recombinant ice-binding protein showed ice-binding activity and ice recrystallization inhibition activity. The protein is much smaller than bacterial ice-nucleating proteins and antifreeze proteins that have been previously described. The function of the protein is unknown but it may act as an ice recrystallization inhibitor to protect membranes in the frozen state.}, doi = {10.1111/j.1574-6941.2007.00345.x}, institution = {School of Life Sciences, University of Nevada, Las Vegas, NV, USA. raymond@unlv.nevada.edu}, keywords = {Alteromonadaceae, genetics/metabolism; Amino Acid Sequence; Antarctic Regions; Bacterial Proteins, chemistry/genetics/physiology; Base Sequence; Ice; Molecular Sequence Data; Sequence Analysis, Protein}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {FEM345}, pmid = {17651136}, timestamp = {2010.09.13}, url = {http://dx.doi.org/10.1111/j.1574-6941.2007.00345.x} } @ARTICLE{Raymond2009, author = {J. A. Raymond and M. G. Janech and C. H. Fritsen}, title = {Novel ice-binding proteins from a psychrophilic {A}ntarctic alga ({C}hlamydomonadaceae, {C}hlorophyceae)}, journal = {J Phycol}, year = {2009}, volume = {45}, pages = {130--136}, owner = {rec}, timestamp = {2011.05.13} } @ARTICLE{Redfield2001, author = {Redfield, Rosemary J.}, title = {Do bacteria have sex?}, journal = {Nature Rev Genet}, year = {2001}, volume = {2}, pages = {634--639}, comment = {10.1038/35084593}, issn = {1471-0056}, owner = {rec}, timestamp = {2009.08.22}, url = {http://dx.doi.org/10.1038/35084593} } @ARTICLE{Riedel2006, author = {Riedel, A. and Michel, C. and Gosselin, M.}, title = {{S}easonal study of sea-ice exopolymeric substances on the {M}ackenzie shelf: implications for transport of sea-ice bacteria and algae}, journal = {Aquat Microb Ecol}, year = {2006}, volume = {45}, pages = {195-206}, abstract = {Bottom sea ice, from under high and low snow cover, and surface water samples were collected in Franklin Bay (Mackenzie shelf) on 21 occasions between 24 February and 20 June 2004 and analyzed for exopolymeric substances (EPS), particulate organic carbon (POC) and chlorophyll a (chl a). Concentrations of EPS were measured using Alcian blue staining of melted ice samples. Chl a and bacterial sinking velocities were also assessed with settling columns, to determine the potential role of EPS in the transport of sea-ice biomass. EPS concentrations in the bottom ice were consistently low in March (avg. 185 µg xanthan equivalents l?1), after which they increased to maximum values of 4930 and 10500 µg Xequiv. l?1 under high and low snow cover, respectively. EPS concentrations in the surface water were consistently 2 orders of magnitude lower than in the sea ice. Sea-ice EPS concentrations were significantly correlated with sea-ice chl a biomass (? = 0.70, p < 0.01). Sea-ice algae were primarily responsible for EPS production within the sea ice, whereas bacteria produced insignificant amounts of sea-ice EPS. EPS-carbon contributed, on average, 23% of POC concentrations within the sea ice, with maximum values reaching 72% during the melt period. Median chl a sinking velocities were 0.11 and 0.44 m d?1 under high and low snow cover, respectively. EPS had little effect on chl a sinking velocities. However, bacterial sinking velocities did appear to be influenced by diatom-associated and free EPS within the sea ice. Diatom-associated EPS could facilitate the attachment of bacteria to algae thereby increasing bacterial sinking velocities, whereas the sinking velocities of bacteria associated with positively buoyant, free EPS, could be reduced. EPS contributed significantly to the sea-ice carbon pool and influenced the sedimentation of sea-ice biomass, which emphasizes the important role of EPS in carbon cycling on Arctic shelves.}, comment = {http://www.int-res.com/abstracts/ame/v45/n2/p195-206/}, owner = {rec}, timestamp = {2006.12.30} } @ARTICLE{Riedel2007, author = {Andrea Riedel and Christine Michel and Michel Gosselin and Bernard LeBlanc}, title = {Enrichment of nutrients, exopolymeric substances and microorganisms in newly formed sea ice on the {M}ackenzie shelf}, journal = {Mar Ecol Prog Ser}, year = {2007}, volume = {342}, pages = {55--67}, owner = {rec}, timestamp = {2011.03.08} } @ARTICLE{Ripp1995, author = {S. Ripp and R. V. Miller}, title = {Effects of Suspended Particulates on the Frequency of Transduction among \emph{Pseudomonas aeruginosa} in a Freshwater Environment.}, journal = {Appl Environ Microbiol}, year = {1995}, volume = {61}, pages = {1214--1219}, abstract = {Transduction has been shown to play a significant role in the transfer of plasmid and chromosomal DNA in aquatic ecosystems. Such ecosystems contain a multitude of environmental factors, any one of which may influence the transduction process. It was the purpose of this study to show how one of these factors, particulate matter, affects the frequency of transduction. In situ transduction rates were measured in lake water microcosms containing either high or low concentrations of particulate matter. The microcosms were incubated in a freshwater lake in central Oklahoma. Transduction frequencies were found to be enhanced as much as 100-fold in the presence of particulates. Our results suggest that aggregations of bacteriophages and bacterial cells are stimulated by the presence of these suspended particulates. This aggregation increases the probability of progeny phages and transducing particles finding and infecting new host cells. Consequently, both phage production and transduction frequencies increase in the presence of particulate matter.}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {16534986}, timestamp = {2009.07.27} } @ARTICLE{Romanowski1991, author = {G. Romanowski and M. G. Lorenz and W. Wackernagel}, title = {Adsorption of plasmid {DNA} to mineral surfaces and protection against {DNase I}}, journal = {Appl Environ Microbiol}, year = {1991}, volume = {57}, pages = {1057--1061}, abstract = {The adsorption of [3H]thymidine-labeled plasmid DNA (pHC314; 2.4 kb) of different conformations to chemically pure sand was studied in a flowthrough microenvironment. The extent of adsorption was affected by the concentration and valency of cations, indicating a charge-dependent process. Bivalent cations (Mg2+, Ca2+) were 100-fold more effective than monovalent cations (Na+, K+, NH4+). Quantitative adsorption of up to 1 microgram of negatively supercoiled or linearized plasmid DNA to 0.7 g of sand was observed in the presence of 5 mM MgCl2 at pH 7. Under these conditions, more than 85\% of DNA adsorbed within 60 s. Maximum adsorption was 4 micrograms of DNA to 0.7 g of sand. Supercoil molecules adsorbed slightly less than linearized or open circular plasmids. An increase of the pH from 5 to 9 decreased adsorption at 0.5 mM MgCl2 about eightfold. It is concluded that adsorption of plasmid DNA to sand depends on the neutralization of negative charges on the DNA molecules and the mineral surfaces by cations. The results are discussed on the grounds of the polyelectrolyte adsorption model. Sand-adsorbed DNA was 100 times more resistant against DNase I than was DNA free in solution. The data support the idea that plasmid DNA can enter the extracellular bacterial gene pool which is located at mineral surfaces in natural bacterial habitats.}, institution = {Genetik, Fachbereich Biologie, Universität Oldenburg, Germany.}, keywords = {Adsorption; Ammonia, metabolism; Calcium, metabolism; DNA, Bacterial, chemistry/metabolism; Deoxyribonuclease I, metabolism; Electrochemistry; Environmental Microbiology; Escherichia coli, genetics/metabolism; Kinetics; Magnesium, metabolism; Minerals, metabolism; Nucleic Acid Conformation; Plasmids; Potassium, metabolism; Silicon Dioxide; Sodium, metabolism; on}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {1647748}, timestamp = {2009.07.27} } @ARTICLE{Schooling2009, author = {Sarah R Schooling and Amanda Hubley and Terry J Beveridge}, title = {Interactions of {DNA} with biofilm-derived membrane vesicles.}, journal = {J Bacteriol}, year = {2009}, volume = {191}, pages = {4097--4102}, abstract = {The biofilm matrix contributes to the chemistry, structure, and function of biofilms. Biofilm-derived membrane vesicles (MVs) and DNA, both matrix components, demonstrated concentration-, pH-, and cation-dependent interactions. Furthermore, MV-DNA association influenced MV surface properties. This bears consequences for the reactivity and availability for interaction of matrix polymers and other constituents.}, doi = {10.1128/JB.00717-08}, institution = {Department of Physics, and AFMNet-NCE, College of Biological Science, University of Guelph, Guelph, Ontario, Canada. sschooli@uoguelph.ca}, keywords = {Biofilms; Cell Membrane, metabolism/ultrastructure; DNA, Bacterial, metabolism/ultrastructure; Microscopy, Electron, Transmission; Microscopy, Fluorescence; Pseudomonas aeruginosa, growth /&/ development/metabolism}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {JB.00717-08}, pmid = {19429627}, timestamp = {2009.07.27}, url = {http://dx.doi.org/10.1128/JB.00717-08} } @ARTICLE{Sikorski1998, author = {Sikorski, J. and Graupner, S. and Lorenz, M. G. and Wackernagel, W.}, title = {{N}atural genetic transformation of \emph{Pseudomonas stutzeri} in a non-sterile soil}, journal = {Microbiology}, year = {1998}, volume = {144}, pages = {569--576}, abstract = {Natural transformation of the soil bacterium Pseudomonas stutzeri JM300 in a non-sterile brown earth microcosm was studied. For this purpose, the microcosm was loaded with purified DNA (plasmid or chromosomal DNA, both containing a high-frequency-transformation marker, his(+), of the P. stutzeri genome), the non-adsorbed DNA was washed out with soil extract and then the soil was charged with competent cells (his-1). Both chromosomal and plasmid transformants were found among the P. stutzeri cells recovered from the soil. The number of plasmid transformants increased in a linear fashion with the amount of DNA added [10-600 ng (0.7 g soil)(-1)]. The observed efficiency of transformation, the time course of transformant formation and the complete inhibition of transformation by DNase I, when added to the soil, were similar to that seen in optimized transformations in nutrient broth. Addition of cells as late as 3 d after loading the soil with plasmid DNA still yielded 3% of the initial transforming activity. This suggests that nucleases indigenous to the soil destroyed the transforming DNA, but at a rate allowing considerable DNA persistence. Transformants were also obtained when intact P. stutzeri cells were introduced into the soil to serve as plasmid DNA donors. Apparently, DNA was released from the cells, adsorbed to the soil material and subsequently taken up by recipient cells. The results indicate that competent cells of P. stutzeri were able to find access to and take up DNA bound on soil particles in the presence of micro-organisms and DNases indigenous to the soil.}, c1 = {Univ Oldenburg, Fachbereich Biol, D-26111 Oldenburg, Germany.}, citedreferences = {ARBER W, 1995, J MOL EVOL, V40, P7 ; BAGDASARIAN M, 1981, GENE, V16, P237 ; BLUM SAE, 1997, SYST APPL MICROBIOL, V20, P513 ; CANOSI U, 1981, MOL GEN GENET, V181, P434 ; CARLSON CA, 1983, J BACTERIOL, V153, P93 ; CARLSON CA, 1984, ARCH MICROBIOL, V140, P134 ; COHAN FM, 1995, EVOLUTION, V49, P164 ; DOYLE JD, 1995, ADV APPL MICROBIOL, V40, P237 ; DUBNAU D, 1991, MOL MICROBIOL, V5, P11 ; DUBNAU D, 1993, BACILLUS SUBTILIS OT, P555 ; GOODMAN AE, 1994, FEMS MICROBIOL ECOL, V15, P55 ; HOLMES DS, 1981, ANAL BIOCHEM, V114, P193 ; KOKJOHN TA, 1989, GENE TRANSFER ENV, P73 ; LOPEZ P, 1982, J BACTERIOL, V150, P692 ; LORENZ MG, 1987, APPL ENVIRON MICROB, V53, P2948 ; LORENZ MG, 1988, J GEN MICROBIOL, V134, P107 ; LORENZ MG, 1990, ARCH MICROBIOL, V154, P380 ; LORENZ MG, 1991, APPL ENVIRON MICROB, V57, P1246 ; LORENZ MG, 1992, MICROB RELEASES, V1, P173 ; LORENZ MG, 1994, MICROBIOL REV, V58, P563 ; LORENZ MG, 1996, TRANSGENIC ORGANISMS, P45 ; LORENZ MG, 1998, HORIZONTAL GENE TRAN ; LORENZ MG, 1998, IN PRESS MICROBIAL I ; LYNCH JM, 1982, J GEN MICROBIOL, V128, P405 ; MAZODIER P, 1991, ANNU REV GENET, V25, P147 ; NIELSEN KM, 1997, APPL ENVIRON MICROB, V63, P1945 ; PAGET E, 1994, FEMS MICROBIOL ECOL, V15, P109 ; PAGET E, 1997, CAN J MICROBIOL, V43, P78 ; SAMBROOK J, 1989, MOL CLONING LAB MANU ; SMITH JM, 1991, NATURE, V349, P29 ; SMITH JM, 1993, P NATL ACAD SCI USA, V90, P4384 ; SOLOMON JM, 1996, TRENDS GENET, V12, P150 ; STEWART GJ, 1991, FEMS MICROBIOL ECOL, V85, P1 ; STOTZKY G, 1986, ADV APPL MICROBIOL, V31, P93 ; STOTZKY G, 1989, GENE TRANSFER ENV, P165 ; STOTZKY G, 1990, ADV APPL MICROBIOL, V35, P57 ; TADDEI F, 1995, P NATL ACAD SCI USA, V92, P11736 ; THOMAS CM, 1994, MICROBIOL-SGM 8, V140, P1799 ; TIEDJE JM, 1989, ECOLOGY, V70, P298 ; TRAVISANO M, 1995, EVOLUTION, V49, P189}, de = {natural transformation; soil; Pseudomonas stutzeri; DNA release; DNAEOLEOLdegradation}, em = {lorenz@biologie.uni-oldenburg.de}, ga = {YW937}, j9 = {MICROBIOLOGY-UK}, ji = {Microbiology-(UK)}, keywords = {BACILLUS-SUBTILIS; ADSORBED DNA; BACTERIA; ENVIRONMENTS; POPULATIONS; PLASMIDS; SAND; COMPETENCE}, la = {English}, nr = {40}, owner = {rec}, pa = {MARLBOROUGH HOUSE, BASINGSTOKE RD, SPENCERS WOODS, READING, BERKS,EOLEOLENGLAND RG7 1AE}, pg = {8}, pi = {READING}, pn = {Part 2}, publisher = {Soc General Microbiology}, rp = {Lorenz, MG, Univ Oldenburg, Fachbereich Biol, Postfach 2503, D-26111EOLEOLOldenburg, Germany.}, sc = {Microbiology}, sn = {1350-0872}, tc = {45}, timestamp = {2007.06.17}, ut = {ISI:000071989700036} } @ARTICLE{Smalla2002, author = {Kornelia Smalla and Patricia A Sobecky}, title = {The prevalence and diversity of mobile genetic elements in bacterial communities of different environmental habitats: insights gained from different methodological approaches.}, journal = {FEMS Microbiol Ecol}, year = {2002}, volume = {42}, pages = {165--175}, abstract = {Abstract The pool of mobile genetic elements (MGE) in microbial communities consists of plasmids, bacteriophages and other elements that are either self-transmissible or use mobile plasmids and phages as vehicles for their dissemination. By facilitating horizontal gene exchange, the horizontal gene pool (HGP) promotes the evolution and adaptation of microbial communities. Efforts to characterise MGE from bacterial populations resident in a variety of ecological habitats have revealed a surprisingly vast and seemingly untapped diversity. MGE, conferring such selectable traits as mercury or antibiotic resistance and degradative functions, have been readily acquired from diverse microbial communities. To circumvent the need to isolate microbial hosts, polymerase chain reaction (PCR)-based detection methods have frequently been used to assess the prevalence of MGE-specific sequences resident in the 'microbial community' HGP. As studies continue to reveal novel and distinct MGE, sequencing of newly isolated MGE from diverse habitats is essential for the continued development of DNA probes, PCR primers as well as for gene array and proteomics-based approaches. This minireview highlights insight gained from different methodological approaches, biased albeit largely toward plasmids in Gram-negative bacteria, used to study the HGP of naturally occurring microbial communities from various aquatic and terrestrial habitats.}, doi = {10.1111/j.1574-6941.2002.tb01006.x}, institution = {Federal Biological Research Centre for Agriculture and Forestry, Institute for Plant Virology, Microbiology and Biosafety, Messeweg 11-12, D-38104 Braunschweig, Germany.}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {FEM165}, pmid = {19709276}, timestamp = {2010.09.13}, url = {http://dx.doi.org/10.1111/j.1574-6941.2002.tb01006.x} } @ARTICLE{Sobecky2002, author = {Patricia A Sobecky}, title = {Approaches to investigating the ecology of plasmids in marine bacterial communities.}, journal = {Plasmid}, year = {2002}, volume = {48}, pages = {213--221}, abstract = {To better understand prokaryotic gene flux in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of plasmid populations in marine bacterial communities, information on the distribution, diversity, and ecological traits of marine plasmids is necessary. This mini-review highlights recent insights gained into the molecular diversity and ecology of plasmids occurring in marine microbial communities.}, institution = {School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA. patricia.sobecky@biology.gatech.edu}, keywords = {DNA, genetics/metabolism; Databases as Topic; Ecology; Ecosystem; Escherichia coli, metabolism; Genetic Techniques; Marine Biology; Models, Genetic; Plasmids, genetics/metabolism; Random Amplified Polymorphic DNA Technique}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {S0147619X02001105}, pmid = {12460537}, timestamp = {2010.09.13} } @ARTICLE{Steinberger2005, author = {Steinberger, R. E. and Holden, P. A.}, title = {{E}xtracellular {DNA} in single- and multiple-species unsaturated biofilms}, journal = {Appl Environ Microbiol}, year = {2005}, volume = {71}, pages = {5404--5410}, abstract = {The extracellular polymeric substances (EPS) of bacterial biofilms form a hydrated barrier between cells and their external environment. Better characterization of EPS could be useful in understanding biofilm physiology. The EPS are chemically complex, changing with both bacterial strain and culture conditions. Previously, we reported that Pseudomonas aeruginosa unsaturated biofilm EPS contains large amounts of extracellular DNA (eDNA) (R. E. Steinberger, A. R. Allen, H. G. Hansma, and P. A. Holden, Microb. Ecol. 43:416-423,2002). Here, we investigated the compositional similarity of eDNA to cellular DNA, the relative quantity of eDNA, and the terminal restriction fragment length polymorphism (TRFLP) community profile of eDNA in multiple-species biofilms. By randomly amplified polymorphic DNA analysis, cellular DNA and eDNA appear identical for P. aeruginosa biofilms. Significantly more eDNA was produced in P. aeruginosa and Pseudomonas putida biofilms than in Rhodococcus erythropolis or Variovorax paradoxus biofilms. While the amount of eDNA in dual-species biofilms was of the same order of magnitude as that of of single-species biofilms, the amounts were not predictable from single-strain measurements. By the Shannon diversity index and principle components analysis of TRFLP profiles generated from 16S rRNA genes, eDNA of four-species biofilms differed significantly from either cellular or total DNA of the same biofilm. However, total DNA- and cellular DNA-based TRFLP analyses of this biofilm community yielded identical results. We conclude that extracellular DNA production in unsaturated biofilms is species dependent and that the phylogenetic information contained in this DNA pool is quantifiable and distinct from either total or cellular DNA.}, c1 = {Univ Calif Santa Barbara, Donald Bren Sch Environm Sci & Management, Santa Barbara, CA 93106 USA.}, citedreferences = {AARDEMA BW, 1983, APPL ENVIRON MICROB, V46, P417 ; AGNELLI A, 2004, SOIL BIOL BIOCHEM, V36, P859 ; ALVAREZ AJ, 1998, MOL ECOL, V7, P775 ; AUERBACH ID, 2000, J BACTERIOL, V182, P3809 ; BALLMANN M, 2002, J CYST FIBROS, V1, P35 ; BERGE MT, 2003, J CYSTIC FIBROSIS, V2, P183 ; BRODIE E, 2003, FEMS MICROBIOL ECOL, V45, P105 ; CRECCHIO C, 1998, SOIL BIOL BIOCHEM, V30, P1061 ; DELLANNO A, 2002, LIMNOL OCEANOGR, V47, P899 ; DUNBAR J, 2000, APPL ENVIRON MICROB, V66, P2943 ; EILER A, 2003, APPL ENVIRON MICROB, V69, P3701 ; EMTIAZI F, 2004, WATER RES, V38, P1197 ; FIERER N, 2003, SOIL BIOL BIOCHEM, V35, P167 ; FINKEL SE, 2001, J BACTERIOL, V183, P6288 ; FORNEY LJ, 2004, CURR OPIN MICROBIOL, V7, P210 ; FROSTEGARD A, 1999, APPL ENVIRON MICROB, V65, P5409 ; GABOR EM, 2003, FEMS MICROBIOL ECOL, V44, P153 ; GREAVES MP, 1970, SOIL BIOL BIOCHEM, V2, P257 ; HARA T, 1981, AGR BIOL CHEM TOKYO, V45, P2457 ; HARUTA S, 2002, APPL MICROBIOL BIOT, V60, P224 ; HOLBEN WE, 1988, APPL ENVIRON MICROB, V54, P703 ; HOLDEN PA, 2001, MICROBIAL ECOL, V42, P256 ; JACKSON DA, 1997, ECOLOGY, V78, P929 ; LAMONTAGNE MG, 2003, MICROBIAL ECOL, V46, P216 ; LAMONTAGNE MG, 2003, MICROBIAL ECOL, V46, P228 ; LEWIS K, 2000, MICROBIOL MOL BIOL R, V64, P503 ; LIESACK W, 1992, J BACTERIOL, V174, P5072 ; LIU WT, 1997, APPL ENVIRON MICROB, V63, P4516 ; LORENZ MG, 1981, MAR BIOL, V64, P225 ; LUKOW T, 2000, FEMS MICROBIOL ECOL, V32, P241 ; MADSEN EL, 2000, HYDROGEOL J, V8, P112 ; MAHENTHIRALINGAM E, 1996, J CLIN MICROBIOL, V34, P1129 ; MARSTORP H, 2000, SOIL BIOL BIOCHEM, V32, P879 ; MATSUI K, 2003, APPL ENVIRON MICROB, V69, P2399 ; MAY TB, 1994, METHOD ENZYMOL, V235, P295 ; MOLIN S, 2003, CURR OPIN BIOTECH, V14, P255 ; NIEMEYER J, 2002, J PLANT NUTR SOIL SC, V165, P121 ; OGRAM A, 1987, J MICROBIOL METH, V7, P57 ; OSBORN AM, 2000, ENVIRON MICROBIOL, V2, P39 ; PAGET E, 1998, EUR J SOIL BIOL, V34, P81 ; PALMER MW, 1993, ECOLOGY, V74, P2215 ; PAUL JH, 1987, APPL ENVIRON MICROB, V53, P170 ; PIETRAMELLARA G, 2001, BIOL FERT SOILS, V33, P402 ; RAMSEY BW, 1993, AM REV RESPIR DIS, V148, P145 ; ROBE P, 2003, EUR J SOIL BIOL, V39, P183 ; ROBERSON EB, 1992, APPL ENVIRON MICROB, V58, P1284 ; SMALLA K, 1993, J APPL BACTERIOL, V74, P78 ; SMITH NR, 2003, WATER RES, V37, P4873 ; SPONZA DT, 2003, ENZYME MICROB TECH, V32, P375 ; STEINBERGER RE, 2002, MICROBIAL ECOL, V43, P416 ; STEINBERGER RE, 2004, BIOFILMS, V1, P37 ; STEWART PS, 1996, ANTIMICROB AGENTS CH, V40, P2517 ; STEWART PS, 1998, BIOTECHNOL BIOENG, V59, P261 ; STOVER CK, 2000, NATURE, V406, P959 ; TORSVIK V, 1990, APPL ENVIRON MICROB, V56, P782 ; WEBB JS, 2003, J BACTERIOL, V185, P4585 ; WEBSTER G, 2003, J MICROBIOL METH, V55, P155 ; WHITCHURCH CB, 2002, SCIENCE, V295, P1487 ; WINGENDER J, 1999, MICROBIAL EXTRACELLU, P1 ; WOBUS A, 2003, FEMS MICROBIOL ECOL, V46, P331 ; WOLFAARDT GM, 1994, MICROBIAL ECOL, V27, P279 ; WOLFAARDT GM, 1995, APPL ENVIRON MICROB, V61, P152 ; ZHOU JZ, 1996, APPL ENVIRON MICROB, V62, P316}, em = {holden@bren.ucsb.edu}, ga = {964RE}, j9 = {APPL ENVIRON MICROBIOL}, ji = {Appl. Environ. Microbiol.}, keywords = {16S RIBOSOMAL-RNA; FRAGMENT-LENGTH-POLYMORPHISMS; BACTERIAL COMMUNITY STRUCTURE; MICROBIAL DIVERSITY; CYSTIC-FIBROSIS; SOIL; EXTRACTION; SEDIMENTS; BIOACCUMULATION; QUANTIFICATION}, la = {English}, nr = {63}, owner = {rec}, pa = {1752 N ST NW, WASHINGTON, DC 20036-2904 USA}, pg = {7}, pi = {WASHINGTON}, publisher = {Amer Soc Microbiology}, rp = {Holden, PA, Univ Calif Santa Barbara, Donald Bren Sch Environm Sci &EOLEOLManagement, Bren Hall, Santa Barbara, CA 93106 USA.}, sc = {Biotechnology & Applied Microbiology; Microbiology}, sn = {0099-2240}, tc = {10}, timestamp = {2007.06.17}, ut = {ISI:000231897400060} } @ARTICLE{Steward2000, author = {G.F. Steward and J.L. Montiel and F. Azam}, title = {Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments.}, journal = {Limnol Oceanogr}, year = {2000}, volume = {45}, pages = {1697--1706}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Stewart1991, author = {Stewart, G. J. and Sinigalliano, C. D. and Garko, K. A.}, title = {{B}inding of exogenous {DNA} to marine sediments and the effect of {DNA}/sediment binding on natural transformation of \emph{Pseudomonas stutzeri} strain {Z}obell in sediment columns}, journal = {FEMS Microbiol Ecol}, year = {1991}, volume = {85}, pages = {1--8}, abstract = {The capacity of marine sediments of facilitate natural transformation of Pseudomonas stutzeri strain ZoBell was investigated. The role of DNA/sediment binding on transformation frequency was also explored. While transformation frequencies increased as a function of DNA concentrations from 0 to 1.0-mu-g of DNA from rifampin-resistant strains for filter transformations, transformation in autoclaved sediment columns displayed a reduction in transformation frequency in response to low DNA concentrations (0-1.0-mu-g/cm3 sediment). Maximum transformation frequencies were obtained on filters at 1.0-mu-g exogenous DNA, however, maximum frequencies were not reached in sediments until a DNA concentration of 3.0-mu-g/cm3 sediment was added. When autoclaved sediments were pre-loaded with excess calf thymus DNA, this reduction in response of transformation frequency (cf. filter transformation) was eliminated, i.e., tranformation frequencies reached saturation in the preloaded sediments at 1.0-mu-g DNA/cm3. Autoclaved sediments were shown to bind DNA at a concentration of about 3.6-mu-g/cm3 sediment, and maximum transformation frequencies were only obtained when these sediments were saturated with DNA. These data indicate that autoclaved marine sediments have the capacity to bind DNA in a form that prevents its availability for natural transformation and only after sediments are saturated with DNA does exogenous DNA become biologically active for natural transformation.}, citedreferences = {AARDEMA BW, 1983, APPL ENVIRON MICROB, V46, P417 ; CARLSON CA, 1983, J BACTERIOL, V153, P93 ; COUGHTER JP, 1989, A VAN LEEUW J MICROB, V55, P15 ; DEFLAUN MF, 1986, APPL ENVIRON MICROB, V52, P654 ; DEFLAUN MF, 1987, MAR ECOL PROGR SER, V33, P29 ; DOHLER K, 1987, INT J SYST BACTERIOL, V37, P1 ; JOHNSON JL, 1981, MANUAL METHODS GEN B, P450 ; LORENZ MG, 1981, MAR BIOL, V64, P225 ; LORENZ MG, 1987, APPL ENVIRON MICROB, V53, P2948 ; LORENZ MG, 1988, J GEN MICROBIOL, V134, P107 ; MANIATIS T, 1982, MOL CLONING ; MATSUBARA T, 1982, J BACTERIOL, V149, P816 ; MINEAR RA, 1972, ENVIRON SCI TECHNOL, V6, P431 ; OGRAM A, 1987, J MICROBIOL METH, V7, P57 ; PAUL JH, 1982, APPL ENVIRON MICROB, V43, P1393 ; PAUL JH, 1987, APPL ENVIRON MICROB, V53, P170 ; PILLAI TNV, 1972, J MAR BIOL ASSOC IND, V14, P384 ; PILLAI TVN, 1970, CURR SCI, V22, P501 ; SMITH HO, 1981, ANNU REV BIOCHEM, V50, P41 ; STEFFAN RJ, 1988, APPL ENVIRON MICROB, V54, P2908 ; STEWART GJ, 1986, ANNU REV MICROBIOL, V40, P211 ; STEWART GJ, 1989, ARCH MICROBIOL, V152, P520 ; STEWART GJ, 1989, GENE TRANSFER ENV, P139 ; STEWART GJ, 1990, APPL ENVIRON MICROB, V56, P1818 ; STOTZKY G, 1990, GENE TRANSFER ENV, P165}, de = {GENE TRANSFER; PSEUDOMONAS GENETICS; DISSOLVED DNA}, ga = {FB274}, j9 = {FEMS MICROBIOL ECOL}, ji = {FEMS Microbiol. Ecol.}, keywords = {GENETIC-TRANSFORMATION; ENVIRONMENT}, la = {English}, nr = {25}, owner = {rec}, pa = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, pg = {8}, pi = {AMSTERDAM}, publisher = {Elsevier Science Bv}, rp = {STEWART, GJ, UNIV S FLORIDA,DEPT BIOL,LIF-169,TAMPA,FL 33620.}, sc = {Microbiology}, sn = {0168-6496}, tc = {21}, timestamp = {2007.06.17}, ut = {ISI:A1991FB27400001} } @ARTICLE{Stierle2002, author = {Stierle, A. P. and Eicken, H.}, title = {{S}ediment inclusions in {A}laskan coastal sea ice: {S}patial distribution, interannual variability, and entrainment requirements}, journal = {Arctic Antarctic Alpine Res}, year = {2002}, volume = {34}, pages = {465--476}, abstract = {We investigated the spatial characteristics of sedimentary inclusions and elucidated processes controlling their spatial and temporal variability in the fast ice cover of the shallow-marine environment of Elson Lagoon near Barrow, Alaska. This was accomplished by examining the frazil ice layer of sea-ice cores representing the 1998, 1999, and 2000 fall freeze-up periods and comparing the results with a sediment resuspension model. Sediments occur exclusively as aggregates of clay to fine-silt sized particles that were confined to brine inclusions in the frazil ice. The average cross-sectional area of these aggregates is positively correlated with sediment concentration of the frazil ice (R-2=0.82, P<0.01). The minimum distance between neighboring aggregates (nearest-neighbor distance) is negatively correlated with sediment concentration (R-2=0.78, P<0.01). However, little correlation exists between the number of aggregates and sediment concentration. Sediment concentrations ranged from 24 to 1470 mg L-1 and sediment loads ranged from 2 g m(-2) to 384 g m(-2), with 1998 and 2000 sediment loads being one to two orders of magnitude smaller than 1999 sediment loads. Similarly, the potential for bottom-sediment resuspension was greater in 1999 than in 1998 and 2000 by more than a factor of two. Resuspension potential is controlled spatially by the local bathymetry and interannually by wind velocity and fetch. At submeter scales, increases in bottom sediment resuspension result in greater sea-ice sediment concentrations, larger aggregates, and smaller nearest-neighbor distances.}, owner = {rec}, timestamp = {2007.06.17}, ut = {ISI:000183096400013} } @ARTICLE{Svarachorn1991, author = {A. Svarachorn and T. Tsuchido and A. Shinmyo and M. Takano}, title = {Dependence of autolysis of \emph{Bacillus subtilis} induced by low temperature}, journal = {J Ferment Bioeng}, year = {1991}, volume = {71}, pages = {281--283}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Svarachorn1989, author = {A. Svarachorn and T. Tsuchido and A. Shinmyo and M. Takano}, title = {Dependence of autolysis of \emph{Bacillus subtilis} cells on macromolecule synthesis under nutrient limitation}, journal = {J Ferment Bioeng}, year = {1989}, volume = {68}, pages = {252--256}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Thomas2002, author = {Thomas, D. N. and Dieckmann, G. S.}, title = {{A}ntarctic Sea Ice--a Habitat for Extremophiles}, journal = {Science}, year = {2002}, volume = {295}, pages = {641--644}, doi = {10.1126/science.1063391}, eprint = {http://www.sciencemag.org/cgi/reprint/295/5555/641.pdf}, owner = {rec}, timestamp = {2009.08.22} } @ARTICLE{Thomas1995, author = {Thomas, D. N. and Lara, R. J. and Eicken, H. and Kattner, G. and Skoog, A.}, title = {{D}issolved organic matter in {A}rctic multiyear sea ice during winter: {M}ajor components and relationship to ice characteristics}, journal = {Polar Biol}, year = {1995}, volume = {15}, pages = {477--483}, abstract = {Ice cores were collected between 10.03.93 and 15.03.93 along a 200 m profile on a large ice flee in Fram Strait. The ice was typical of Arctic multi-year ice, having a mean thickness along the profile of 2.56 +/- 0.53 m. It consisted mostly of columnar ice (83%) grown through congelation of seawater at the ice bottom, and the salinity profiles were characterized by a linear increase from 0 psu at the top to values ranging between 3 and 5 psu at depth. Distributions of dissolved organic carbon (DOC) and nitrogen (DON) and major nutrients were compared with ice texture, salinity and chlorophyll a. DOC, DON, dissolved inorganic nitrogen (DIN), NH4+ and NO2- were present in concentrations in excess of that predicted by dilution curves derived from Arctic surface water values. Only NO3- was depleted, although not exhausted. High DOC and DON values in conjunction with high NH+4 levels indicated that a significant proportion of the dissolved organic matter (DOM) was a result of decomposition/grazing of ice algae and/or detritus. The combination of high NH4+ and NO2- points to regeneration of nitrogen compounds. There was no significant correlation between DOC and Chl a in contrast to DON, which had a positively significant correlation with both salinity and Chl a, and the distribution of DOM in the cores might best be described as a combination of both physical and biological processes. There was no correlation between DOC and DON suggesting an uncoupling of DOC and DON dynamics in multi year ice.}, owner = {rec}, timestamp = {2007.06.17}, ut = {ISI:A1995RR49900003} } @ARTICLE{Turk1992, author = {Turk, V. and Rehnstam, A. S. and Lundberg, E. and Hagstrom, A.}, title = {{R}elease of bacterial {DNA} by marine nanoflagellates, an intermediate step in phosphorus regeneration}, journal = {Appl Environ Microbiol}, year = {1992}, volume = {58}, pages = {3744--3750}, abstract = {The concentrations of dissolved DNA and nanoflagellates were found to covary during a study of diel dynamics of the microbial food web in the Adriatic Sea. This observation was further investigated in a continuous seawater culture when nanoflagellates were fed bacteria grown in filtered seawater. Analysis of dissolved organic phosphorus and dissolved DNA showed a sixfold increase of dissolved DNA in the presence of the nanoflagellates (Ochromonas sp.). The amount of DNA released suggested that the majority of the consumed bacterial DNA was ejected. Phagotrophic nanoflagellates thus represent an important source of origin for dissolved DNA. The rate of breakdown of dissolved DNA and release of inorganic phosphorus in the pelagic ecosystem is suggested to be dependent on the ambient phosphate pool. In the P-limited northern Adriatic Sea, rapid degradation of the labelled DNA could be demonstrated, whereas the N-limited southern California bight water showed a much lower rate. Phosphorus originating from dissolved DNA was shown to be transferred mainly to organisms in the <3-mum-size fractions. On the basis of the C/P ratios, we suggest that a significant fraction of the phosphorus demand by the autotrophs may be sustained by the released DNA during stratified conditions. Thus, the nucleic acid-rich bacterial biomass grazed by protozoa plays an important role in the biogeochemical cycling of phosphorus in the marine environment.}, c1 = {INST BIOL,MARINE BIOL STN,CS-66330 PIRAN,CZECHOSLOVAKIA.EOLEOLUNIV UMEA,UMEA MARINE SCI CTR,S-90304 UMEA,SWEDEN.EOLEOLUMEA UNIV,DEPT MICROBIOL,S-90187 UMEA,SWEDEN.}, citedreferences = {AMMERMAN JW, 1985, SCIENCE, V227, P1338 ; AMMERMAN JW, 1991, LIMNOL OCEANOGR, V36, P1437 ; ANDERSEN OK, 1986, MAR ECOL-PROG SER, V31, P47 ; ANDERSSON A, 1985, MAR ECOL-PROG SER, V23, P99 ; ANDERSSON A, 1986, MAR ECOL-PROG SER, V33, P51 ; ANDERSSON A, 1989, MICROBIAL ECOL, V17, P251 ; AZAM F, 1983, MAR ECOL-PROG SER, V10, P257 ; BERLAND BR, 1980, OCEANOL ACTA, V3, P135 ; BLOEM J, 1988, APPL ENVIRON MICROB, V54, P3113 ; BORSHEIM KY, 1990, APPL ENVIRON MICROB, V56, P352 ; BRATBAK G, 1990, APPL ENVIRON MICROB, V56, P1400 ; CARON DA, 1983, APPL ENVIRON MICROB, V46, P491 ; CARON DA, 1985, MAR ECOL-PROG SER, V24, P243 ; CHO BC, 1988, ERGEB LIMNOL, V31, P153 ; CONCINO MF, 1982, J BACTERIOL, V152, P441 ; DEFLAUN MF, 1986, APPL ENVIRON MICROB, V52, P654 ; DEFLAUN MF, 1987, MAR ECOL-PROG SER, V38, P65 ; DORWARD DW, 1989, J BACTERIOL, V171, P2499 ; DUGDALE RC, 1967, LIMNOL OCEANOGR, V12, P196 ; FAGANELI J, 1991, THALASSIA JUGOSL, V23, P51 ; FENCHEL T, 1982, MAR ECOL-PROG SER, V9, P35 ; FENCHEL T, 1984, FLOWS ENERGY MAT MAR, P301 ; FUHRMAN JA, 1982, MAR BIOL, V66, P109 ; GRASSHOFF K, 1976, METHODS SEAWATER ANA ; HAGSTROM A, 1984, MAR ECOL-PROG SER, V18, P41 ; HAGSTROM A, 1988, MAR ECOL-PROG SER, V49, P171 ; HECKY RE, 1988, LIMNOL OCEANOGR, V33, P796 ; HELDAL M, 1991, MAR ECOL-PROG SER, V72, P205 ; JOHANNES RE, 1965, LIMNOL OCEANOGR, V10, P434 ; JURGENS K, 1990, MAR ECOL-PROG SER, V59, P271 ; KARL DM, 1989, LIMNOL OCEANOGR, V34, P543 ; LANCELOT C, 1984, LIMNOL OCEANOGR, V29, P721 ; MANIATIS T, 1982, MOL CLONING ; MURPHY J, 1962, ANAL CHIM ACTA, V27, P31 ; PAUL JH, 1984, LIMNOL OCEANOGR, V29, P1091 ; PAUL JH, 1988, APPL ENVIRON MICROB, V54, P718 ; PAUL JH, 1989, APPL ENVIRON MICROB, V55, P1823 ; PAUL JH, 1990, APPL ENVIRON MICROB, V56, P2957 ; PAUL JH, 1991, APPL ENVIRON MICROB, V57, P2197 ; PORTER KG, 1980, LIMNOL OCEANOGR, V25, P943 ; POUTANEN EL, 1983, ESTUAR COAST SHELF S, V17, P189 ; PROCTOR LM, 1990, NATURE, V343, P60 ; REHNSTAM AS, UNPUB ; REIMANN B, 1987, LIMNOL OCEANOGR, V32, P471 ; SHERR BF, 1988, APPL ENVIRON MICROB, V54, P1091 ; SMITH SV, 1984, LIMNOL OCEANOGR, V29, P1149 ; VIEIRA J, 1982, GENE, V19, P259 ; WIKNER J, 1988, MAR ECOL-PROG SER, V50, P137 ; WIKNER J, 1990, LIMNOL OCEANOGR, V35, P313 ; WIKNER J, 1991, LIMNOL OCENOGR, V36, P1316 ; WILLIAMS PJL, 1981, KIELER MEERESFORSCH, V5, P1}, ga = {JW473}, j9 = {APPL ENVIRON MICROBIOL}, ji = {Appl. Environ. Microbiol.}, keywords = {MICROFLAGELLATE FOOD-CHAIN; DISSOLVED DNA; AQUATIC ENVIRONMENTS; PLANKTONIC BACTERIA; MOLECULAR-WEIGHT; FRESH-WATER; VIRUSES; SEA; CYANOBACTERIA; PHYTOPLANKTON}, la = {English}, nr = {51}, owner = {rec}, pa = {1325 MASSACHUSETTS AVENUE, NW, WASHINGTON, DC 20005-4171}, pg = {7}, pi = {WASHINGTON}, publisher = {Amer Soc Microbiology}, sc = {Biotechnology & Applied Microbiology; Microbiology}, sn = {0099-2240}, tc = {53}, timestamp = {2007.06.17}, ut = {ISI:A1992JW47300042} } @ARTICLE{Wells2006-model, author = {Wells, L. E. and Deming, J. W.}, title = {{M}odelled and measured dynamics of viruses in {A}rctic winter sea-ice brines}, journal = {Environ Microbiol}, year = {2006}, volume = {8}, pages = {1115--1121}, abstract = {We describe a model based on diffusion theory and the temperature-dependent mechanism of brine concentration in sea ice to argue that, if viruses partition with bacteria into sea-ice brine inclusions, contact rates between the two can be higher in winter sea ice than in seawater, increasing the probability of infection and possible virus production. To examine this hypothesis, we determined viral and bacterial concentrations in select winter sea-ice horizons using epifluorescence microscopy. Viral concentrations ranged from 1.6 to 82 x 10(6) Ml(-1) of brine volume of the ice, with highest values in brines from coldest (-24 to -31 degrees C) ice horizons. Calculated virus-bacteria contact rates in underlying -1 degrees C seawater were similar to those in brines of -11 degrees C ice but up to 600 times lower than those in ice brines at or below -24 degrees C. We then incubated native bacterial and viral assemblages from winter sea ice for 8 days in brine at a temperature (-12 degrees C) and salinity (similar to 160 psu) near expected in situ values, monitoring their concentrations microscopically. While different cores yielded different results, consistent with known spatial heterogeneity in sea ice, these experiments provided unambiguous evidence for viral persistence and production, as well as for bacterial growth, in -12 degrees C brine.}, c1 = {Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.}, citedreferences = {BORRISS M, 2003, EXTREMOPHILES, V7, P377 ; COX GFN, 1975, CRREL RES REP, V345, P1 ; COX GFN, 1983, J GLACIOL, V29, P306 ; DELISLE AL, 1972, ANTON LEEUW INT J G, V38, P9 ; EICKEN H, 1991, J GEOPHYS RES-OCEANS, V96, P10603 ; GOWING MM, 2002, MAR ECOL-PROG SER, V241, P1 ; GOWING MM, 2003, MAR BIOL, V142, P1029 ; GOWING MM, 2004, MAR ECOL-PROG SER, V279, P3 ; GUIXABOIXAREU N, 1996, AQUAT MICROB ECOL, V11, P215 ; HELMKE E, 1995, MAR ECOL-PROG SER, V117, P269 ; JUNGE K, 2001, ANN GLACIOL, V33, P304 ; JUNGE K, 2002, MICROBIAL ECOL, V43, P315 ; JUNGE K, 2004, APPL ENVIRON MICROB, V70, P550 ; MARANGER R, 1994, MAR ECOL-PROG SER, V111, P121 ; MIDDELBOE M, 2002, DEEP-SEA RES, V2, P5063 ; MIDDELBOE M, 2003, AQUAT MICROB ECOL, V33, P1 ; MURRAY AG, 1992, MAR ECOL-PROG SER, V89, P103 ; NOBLE RT, 1997, APPL ENVIRON MICROB, V63, P77 ; NOBLE RT, 1998, AQUAT MICROB ECOL, V14, P113 ; PRICE PB, 2004, P NATL ACAD SCI USA, V101, P4631 ; STEWARD GF, 1996, MAR ECOL-PROG SER, V131, P287 ; WEINBAUER MG, 2002, AQUAT MICROB ECOL, V27, P103 ; WELLS LE, 2006, LIMNOL OCEANOGR, V51, P47 ; WEN K, 2004, APPL ENVIRON MICROB, V70, P3862 ; WILHELM SW, 2002, MICROBIAL ECOL, V43, P168 ; WOMMACK KE, 2000, MICROBIOL MOL BIOL R, V64, P69}, em = {chimera1@ocean.washington.edu}, ga = {048LV}, j9 = {ENVIRON MICROBIOL}, ji = {Environ. Microbiol.}, keywords = {VIRAL ABUNDANCE; COASTAL WATERS; WEDDELL SEA; BACTERIA; TEMPERATURE; COMMUNITIES; MICROSCOPY; HABITATS; SAMPLES}, la = {English}, nr = {26}, owner = {rec}, pa = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND}, pg = {7}, pi = {OXFORD}, publisher = {Blackwell Publishing}, rp = {Wells, LE, Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.}, sc = {Microbiology}, sn = {1462-2912}, tc = {4}, timestamp = {2007.06.17}, ut = {ISI:000237949500017} } @ARTICLE{Wiebe1993, author = {Wiebe, W. J. and Sheldon, W. M. and Pomeroy, L. R.}, title = {{E}vidence for an enhanced substrate requirement by marine mesophilic bacterial isolates at minimal growth temperatures}, journal = {Microb Ecol}, year = {1993}, volume = {25}, pages = {151--159}, abstract = {Bacterial isolates from the subtropical southeastern continental shelf were cultured in a matrix of temperature and substrate concentrations encompassing a range of temperature and substrate concentrations equal to and exceeding natural ones. At the annual minimum temperature, marine heterotrophic bacterial isolates required higher concentrations of dissolved substrates for active growth than are usually found in seawater. We show this to result from a nonlinear interaction of the combined effects of temperature and substrate concentration on bacterial growth and respiratory rate. As a result, bacterial and protozoan utilization of phytoplankton production during winter and early spring is low, permitting greater energy flow to zooplankton and benthic animals, while in late spring, summer, and fall, the microbial loop dominates energy flux and organic carbon utilization. Escherichia coli shows a similar nonlinear response to temperature at minimal substrate concentrations, albeit at a higher range of concentrations than were utilized by the marine isolates. Thus, bacteria from subtropical regions are shown to have a differential growth response near the minimum temperature for growth, depending on the concentration of available substrates.}, owner = {rec}, timestamp = {2006.12.11}, ut = {ISI:A1993LB41200004} } @ARTICLE{Wiebe1992, author = {W. J. Wiebe and W. M. Sheldon and L. R. Pomeroy}, title = {Bacterial growth in the cold: evidence for an enhanced substrate requirement}, journal = {Appl Environ Microbiol}, year = {1992}, volume = {58}, pages = {359--364}, abstract = {Growth responses and biovolume changes for four facultatively psychrophilic bacterial isolates from Conception Bay, Newfoundland, and the Arctic Ocean were examined at temperatures from - 1.5 to 35 degrees C, with substrate concentrations of 0.15, 1.5, and 1,500 mg of proteose peptone-yeast extract per liter. For two cultures, growth in 0.1, 1.0, and 1,000 mg of proline per liter was also examined. At 10 to 15 degrees C and above, growth rates showed no marked effect of substrate concentration, while at - 1.5 and 0 degrees C, there was an increasing requirement for organic nutrients, with generation times in low-nutrient media that were two to three times longer than in high-nutrient media. Biovolume showed a clear dependence on substrate concentration and quality; the largest cells were in the highest-nutrient media. Biovolume was also affected by temperature; the largest cells were found at the lowest temperatures. These data have implications for both food web structure and carbon flow in cold waters and for the effects of global climate change, since the change in growth rate is most dramatic at the lowest temperatures.}, institution = {Departments of Microbiology and Zoology and Institute of Ecology, University of Georgia, Athens, Georgia 30602.}, owner = {rec}, pmid = {16348634}, timestamp = {2008.07.22} } @ARTICLE{Wilhelm2002, author = {S. W. Wilhelm and S. M. Brigden and C. A. Suttle}, title = {{A} dilution technique for the direct measurement of viral production: a comparison in stratified and tidally mixed coastal waters.}, journal = {Microb Ecol}, year = {2002}, volume = {43}, pages = {168--173}, abstract = {The abundance of heterotrophic bacteria and viruses, as well as rates of viral production and virus-mediated mortality, were measured in Discovery Passage and the Strait of Georgia (British Columbia, Canada) along a gradient of tidal mixing ranging from well mixed to stratified. The abundances of bacteria and viruses were approximately 10(6) and 10(7) mL(-1), respectively, independent of mixing regime. Viral production estimates, monitored by a dilution technique, demonstrated that new viruses were produced at rates of 10(6) and 10(7) mL(-1)h(-1) across the different mixing regimes. Using an estimated burst size of 50 viruses per lytic event, ca. 19 to 27\% of the standing stock of bacteria at the stratified stations and 46 to 137\% at the deep-mixed stations were removed by viruses. The results suggest that mixing of stratified waters during tidal exchange enhances virus-mediated bacterial lysis. Consequently, viral lysis recycled a greater proportion of the organic carbon required for bacterial growth under non-steady-state compared to steady-state conditions.}, doi = {10.1007/s00248-001-1021-9}, keywords = {Bacteria; Population Dynamics; Viruses; Water Microbiology; Water Movements}, owner = {rec}, pmid = {11984638}, timestamp = {2007.06.17}, url = {http://dx.doi.org/10.1007/s00248-001-1021-9} } @ARTICLE{Woese2002, author = {Woese, C. R.}, title = {{O}n the evolution of cells}, journal = {PNAS}, year = {2002}, volume = {99}, pages = {8742--8747}, abstract = {A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given.}, c1 = {Univ Illinois, Dept Microbiol, Chem & Life Sci Lab, Urbana, IL 61801 USA.}, citedreferences = {BARBIERI M, 2001, ORGANIC CODES ; BRENNER S, 1998, SCIENCE, V282, P1411 ; BROSIUS J, 2001, TRENDS BIOCHEM SCI, V26, P653 ; BROWN JR, 1997, MICROBIOL MOL BIOL R, V61, P456 ; BROWN JR, 2001, NAT GENET, V28, P281 ; BURKHARDT F, 1990, CORRESPONDENCE C DAR, V6, P1856 ; CECH TR, 2000, SCIENCE, V289, P878 ; DARWIN C, 1859, ORIGIN SPECIES, P484 ; GOODWIN B, 1996, LEOPARD CHANGED ITS ; GRAHAM DE, 2000, P NATL ACAD SCI USA, V97, P3304 ; HAROLD FM, 1995, MICROBIOL-UK, V141, P2765 ; HARTMAN H, 1984, SPECULAT SCI TECHNOL, V7, P77 ; HARTMAN H, 2001, P NATL ACAD SCI USA, V99, P1420 ; HUTTENHOFER A, 2001, EMBO J, V20, P2943 ; KANDLER O, 1994, J BIOL PHYS, V20, P165 ; LANGER D, 1995, P NATL ACAD SCI USA, V92, P5768 ; MARGULIS L, 1970, ORIGIN EUCARYOTIC CE ; MARTIN W, 1998, NATURE, V392, P37 ; MOREIRA D, 1998, J MOL EVOL, V47, P517 ; NESBO CL, 2001, J MOL EVOL, V53, P340 ; NISSEN P, 2000, SCIENCE, V289, P920 ; OLSEN GJ, 1996, TRENDS GENET, V12, P377 ; PENNISI E, 1998, SCIENCE, V280, P672 ; PENNISI E, 1999, SCIENCE, V284, P1305 ; SOGIN ML, 1991, CURR OPIN GENE DEV, V1, P457 ; WHITEHEAD AN, 1929, PROCESS REALITY ; WOESE C, 1998, P NATL ACAD SCI USA, V95, P6854 ; WOESE CR, 1965, P NATL ACAD SCI USA, V54, P1546 ; WOESE CR, 1967, GENETIC CODE MOL BAS ; WOESE CR, 1970, SOC GEN MICROBIOL S, V20, P39 ; WOESE CR, 1972, EXOBIOLOGY, P301 ; WOESE CR, 1977, J MOL EVOL, V10, P1 ; WOESE CR, 1982, ZENTRALBL BAKTERIO C, V3, P1 ; WOESE CR, 1983, EVOLUTION MOL MEN, P209 ; WOESE CR, 1987, MICROBIOL REV, V51, P221 ; WOESE CR, 2000, MICROBIOL MOL BIOL R, V64, P202 ; WOESE CR, 2000, P NATL ACAD SCI USA, V97, P8392 ; WOESE CR, 2001, RNA, V7, P1055 ; ZILLIG W, 1989, ENDOCYT CELL RES, V6, P1}, ga = {567GZ}, j9 = {PROC NAT ACAD SCI USA}, ji = {Proc. Natl. Acad. Sci. U. S. A.}, keywords = {ARCHAEA; TREE; HYPOTHESIS; EUKARYOTES; RIBOSOME; ORIGIN; GENOME; RNAS; LIFE}, la = {English}, nr = {39}, owner = {rec}, pa = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA}, pg = {6}, pi = {WASHINGTON}, publisher = {Natl Acad Sciences}, rp = {Woese, CR, Univ Illinois, Dept Microbiol, Chem & Life Sci Lab, 601 SEOLEOLGoodwin Ave,B103, Urbana, IL 61801 USA.}, sc = {Multidisciplinary Sciences}, sn = {0027-8424}, tc = {108}, timestamp = {2007.06.17}, ut = {ISI:000176478200051} } @ARTICLE{Yager1999, author = {P.L. Yager and J.W. Deming}, title = {Pelagic microbial activity in an {A}rctic polynya: Testing for temperature and substrate interactions using a kinetic approach}, journal = {Limnol Oceanogr}, year = {1999}, volume = {44}, pages = {1882--1893}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Yamanaka1997, author = {Yamanaka, Koichi and Araki, Jun and Takano, Mitsuo and Sekiguchi, Junichi}, title = {Characterization of \emph{Bacillus subtilis} mutants resistant to cold shock-induced autolysis}, journal = {FEMS Microbiol Lett}, year = {1997}, volume = {150}, pages = {269--275}, abstract = {Bacillus subtilis vegetative cells undergo autolysis when exposed to cold shock treatment. A mutant (CA1) resistant to cold shock was isolated, and its DNA was used for the transformation of B. subtilis 168AR. The transformant (TR1) and CA1 had almost completely lost major vegetative autolysins (CwlB and CwlG) and motility, and showed a filamentous cell morphology during the exponential phase. Expression of the sigD-lacZ fusion was reduced in TR1. But the introduction of a SigD overproducing plasmid, pHYSigD, into TR1 led to a considerable increase in the amount of autolysin, a normal cell morphology (short rod), and the cold shock-sensitive phenotype. However, motility was not restored in the transformant. The roles of pleiotropic genes in cold shock-induced autolysis are discussed.}, owner = {rec}, timestamp = {2009.08.21}, url = {http://dx.doi.org/10.1111/j.1574-6968.1997.tb10380.x} } @ARTICLE{Yin1997, author = {X. Yin and G. Stotzky}, title = {Gene transfer among bacteria in natural environments.}, journal = {Adv Appl Microbiol}, year = {1997}, volume = {45}, pages = {153--212}, institution = {SRA Technologies, Inc., Rockville, Maryland 20850, USA.}, keywords = {Animals; Bacteria, genetics; Conjugation, Genetic; Environmental Microbiology; Intestines, microbiology; Transduction, Genetic; Transformation, Bacterial}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {9342828}, timestamp = {2009.07.27} } @ARTICLE{Zaneveld2008a, author = {Jesse R Zaneveld and Diana R Nemergut and Rob Knight}, title = {Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of {HGT} patterns.}, journal = {Microbiology}, year = {2008}, volume = {154}, pages = {1--15}, abstract = {Detecting patterns of horizontal gene transfer (HGT) in genomic sequences is an important problem, with implications for evolution, ecology, biotechnology and medicine. Extensive genetic, biochemical and genomic studies have provided a good understanding of sequence features that are associated with many (though not all) known mobile elements and mechanisms of gene transfer. This information, however, is not currently incorporated into automated methods for gene transfer detection in genomic data. In this review, we argue that automated annotation of sequence features associated with gene transfer mechanisms could be used both to build more sensitive, mechanism-specific compositional models for the detection of some types of HGT in genomic data, and to ask new questions about the classes of genes most frequently transferred by each mechanism. We then summarize the genes and sequence features associated with different mechanisms of horizontal transfer, emphasizing those that are most useful for distinguishing types of transfer when examining genomic data, and noting those classes of transfers that cannot be distinguished in genomic data using existing techniques. Finally, we describe software, databases and algorithms for identifying particular classes of mobile elements, and outline prospects for better detection of HGT based on specific mechanisms of transfer.}, doi = {10.1099/mic.0.2007/011833-0}, institution = {Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.}, keywords = {Computational Biology, methods; Gene Transfer, Horizontal, genetics; Genomics, methods; Interspersed Repetitive Sequences}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {154/1/1}, pmid = {18174121}, timestamp = {2009.07.27}, url = {http://dx.doi.org/10.1099/mic.0.2007/011833-0} } @ARTICLE{Zhao2009, author = {Yanlin Zhao and Kui Wang and Charles Budinoff and Alison Buchan and Andrew Lang and Nianzhi Jiao and Feng Chen}, title = {Gene transfer agent ({GTA}) genes reveal diverse and dynamic \emph{Roseobacter} and \emph{Rhodobacter} populations in the {C}hesapeake {B}ay}, journal = {ISME J}, year = {2009}, volume = {3}, pages = {364--373}, abstract = {Within the bacterial class Alphaproteobacteria, the order Rhodobacterales contains the Roseobacter and Rhodobacter clades. Roseobacters are abundant and play important biogeochemical roles in marine environments. Roseobacter and Rhodobacter genomes contain a conserved gene transfer agent (GTA) gene cluster, and GTA-mediated gene transfer has been observed in these groups of bacteria. In this study, we investigated the genetic diversity of these two groups in Chesapeake Bay surface waters using a specific PCR primer set targeting the conserved Rhodobacterales GTA major capsid protein gene (g5). The g5 gene was successfully amplified from 26 Rhodobacterales isolates and the bay microbial communities using this primer set. Four g5 clone libraries were constructed from microbial assemblages representing different regions and seasons of the bay and yielded diverse sequences. In total, 12 distinct g5 clusters could be identified among 158 Chesapeake Bay clones, 11 fall within the Roseobacter clade, and one falls in the Rhodobacter clade. The vast majority of the clusters (10 out of 12) lack cultivated representatives. The composition of g5 sequences varied dramatically along the bay during the wintertime, and a distinct Roseobacter population composition between winter and summer was observed. The congruence between g5 and 16S rRNA gene phylogenies indicates that g5 may serve as a useful genetic marker to investigate diversity and abundance of Roseobacter and Rhodobacter in natural environments. The presence of the g5 gene in the natural populations of Roseobacter and Rhodobacter implies that genetic exchange through GTA transduction could be an important mechanism for maintaining the metabolic flexibility of these groups of bacteria.}, doi = {10.1038/ismej.2008.115}, institution = {Center of Marine Biotechnology, University of Maryland Biotechnology Institute, 701 E Pratt Street, Baltimore, MD 21202, USA.}, keywords = {Bacteriophages, genetics; Biodiversity; Capsid Proteins, genetics; Cloning, Molecular; Cluster Analysis; DNA, Bacterial, chemistry/genetics; DNA, Ribosomal, chemistry/genetics; DNA, Viral, chemistry/genetics; Gene Library; Maryland; Molecular Sequence Data; Phylogeny; Polymerase Chain Reaction; RNA, Ribosomal, 16S, genetics; Rhodobacter, classification/genetics/virology; Roseobacter, classification/genetics/virology; Seasons; Sequence Analysis, DNA; Sequence Homology; Water Microbiology}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {ismej2008115}, pmid = {19020557}, timestamp = {2009.08.22}, url = {http://dx.doi.org/10.1038/ismej.2008.115} } @ARTICLE{Zinder1952, author = {Zinder, Norton D. and Lederberg, Joshua}, title = {{G}enetic exchange in \emph{Salmonella}}, journal = {J Bacteriol}, year = {1952}, volume = {64}, pages = {679--699}, owner = {rec}, timestamp = {2007.06.17} } @comment{jabref-meta: selector_publisher:} @comment{jabref-meta: selector_author:} @comment{jabref-meta: selector_journal:} @comment{jabref-meta: selector_keywords:}