% This file was created with JabRef 2.5. % Encoding: ISO8859_1 @ARTICLE{AlonsoSaez2008, author = {Laura Alonso-S\'aez and Olga S\'anchez and Josep M. Gasol and Vanessa Balagu\'e and Carlos Pedr\'os-Ali\'o}, title = {Winter-to-summer changes in the composition and single-cell activity of near-surface {A}rctic prokaryotes}, journal = {Environ Microbiol}, year = {2008}, volume = {10}, pages = {2444--2454}, abstract = {We collected surface samples in Franklin Bay (Western Arctic) from ice-covered to ice-free conditions, to determine seasonal changes in the identity and in situ activity of the prokaryotic assemblages. Catalysed reported fluorescence in situ hybridization was used to quantify the abundance of different groups, and combined with microautoradiography to determine the fraction of active cells taking up three substrates: glucose, amino acids and ATP. In surface waters, Archaea accounted for 16% of the total cell count in winter, but decreased to almost undetectable levels in summer, when Bacteria made up 97% of the total cell count. Alphaproteobacteria were the most abundant group followed by Bacteroidetes (average of 34% and 14% of total cell counts respectively). Some bacterial groups appearing in low abundances (< 10% of total cell counts), such as Betaproteobacteria, Roseobacter and Gammaproteobacteria, showed a high percentage of active cells. By contrast, more abundant groups, such as SAR11 or Bacteroidetes, had a lower percentage of active cells in the uptake of the substrates tested. Archaea showed low heterotrophic activity throughout the year. In comparison with temperate oceans, the percentage of active Bacteria in the uptake of the substrates was relatively high, even during the winter season.}, doi = {10.1111/j.1462-2920.2008.01674.x}, owner = {rec}, timestamp = {2008.07.24} } @ARTICLE{Boersheim1993, author = {K.Y. B\"orsheim}, title = {Native marine bacteriophages}, journal = {FEMS Microbiol Ecol}, year = {1993}, volume = {102}, pages = {141--159}, owner = {rec}, timestamp = {2009.07.27} } @ARTICLE{Baross1978a, author = {J.A. Baross and J. Liston and R.Y. Morita}, title = {Incidence of \emph{Vibrio parahaemolyticus} bacteriophages and other \emph{Vibrio} bacteriophages in marine samples}, journal = {Appl Environ Microbiol}, year = {1978}, volume = {36}, pages = {492--499}, owner = {rec}, timestamp = {2009.07.27} } @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{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{Chiura1997, author = {H. X. Chiura}, title = {Generalized gene transfer by virus-like particles from marine bacteria}, journal = {Aquat Microb Ecol}, year = {1997}, volume = {13}, pages = {75--83}, owner = {rec}, 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{CollinsDNA, author = {Collins, R. E. and Jody. W. Deming}, title = {Abundant dissolved genetic material in {A}rctic sea ice, {P}art {I}: {E}xtracellular {DNA}}, journal = {Polar Biol}, year = {submitted this issue}, owner = {rec}, timestamp = {2010.09.06} } @ARTICLE{Comeau2006, author = {Comeau, Andr\'e M. and Chan, Amy M. and Suttle, Curtis A.}, title = {Genetic richness of vibriophages isolated in a coastal environment}, journal = {Environ Microbiol}, year = {2006}, volume = {8}, pages = {1164--1176}, abstract = {The purpose of this study was to characterize Vibrio parahaemolyticus viruses (VpVs) isolated from different environments within and adjacent to the Strait of Georgia, and to examine the relative influences of distance and environment on host-range and genetic richness. Nearly all seawater enrichment cultures (29/31) generated isolates, implying that VpVs were widespread in the virioplankton, yet at low abundances (<1l22121). Viruses were not detected in sediments (n=99). Fourteen of the 16 viruses characterized were siphoviruses, with genome sizes ranging from 223C452013106kb, and half were capable of infecting other Vibrio species. The VpVs infected bacteria isolated from oysters and sediments fairly well (55% and 46% of the host-virus combinations, respectively), but were unable to infect many of the bacteria isolated from the water column (<13% of 112 combinations). When compared with VpVs from oysters, it was clear that the major determinant of phenotypic (host-range) and genetic richness (by the DP-RAPD assay) was not geography, but the source environment from which the VpVs originated. Therefore, the VpV population within the Strait of Georgia is a highly diverse mixture of phenotypes and genotypes.}, owner = {rec}, timestamp = {2009.08.22}, url = {http://dx.doi.org/10.1111/j.1462-2920.2006.01006.x} } @ARTICLE{Comiso2008, author = {Comiso,J. C. and C. L. Parkinson and R. Gersten and L. Stock}, title = {Accelerated decline in the {A}rctic sea ice cover}, journal = {Geophys Res Lett}, year = {2008}, volume = {35}, pages = {L01703}, doi = {10.1029/2007GL031972}, owner = {rec}, timestamp = {2010.09.06} } @ARTICLE{CoxWeeks1975, author = {Cox, G.F.N. and Weeks, W.F.}, title = {Brine drainage and initial salt entrapment in sodium chloride ice}, journal = {CRREL Research Report}, year = {1975}, volume = {345}, pages = {1--46}, owner = {rec}, timestamp = {2009.08.20} } @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{Friedman1986, author = {Alan L. Friedman and Randall S. Alberte}, title = {Biogenesis and Light Regulation of the Major Light Harvesting Chlorophyll-Protein of Diatoms}, journal = {Plant Physiol}, year = {1986}, volume = {80}, pages = {43--51}, owner = {rec}, timestamp = {2010.09.06} } @ARTICLE{Gantzer1994, author = {Christophe Gantzer and Fr\'ed\'eric Quignon and Louis Schwartzbrod}, title = {Poliovirus-1 adsorption onto and desorption from montmorillonite in seawater. {S}urvival of the adsorbed virus}, journal = {Environ Technol}, year = {1994}, volume = {15}, pages = {271--278}, owner = {rec}, timestamp = {2009.08.22} } @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{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{Gowing2003, author = {Gowing, M. M.}, title = {Large viruses and infected microeukaryotes in {R}oss {S}ea summer pack ice habitats}, journal = {Mar Biol}, year = {2003}, volume = {142}, pages = {1029--1040}, abstract = {A variety of Ross Sea summer pack ice habitats between 66 and 75°S were examined for viruses 𔒦 nm capsid diameter. Maximum abundances of these viruses likely to infect eukaryotes were 106-107 ml-1 brine in surface, interior, and bottom habitats and constituted up to 18% of the total (all sizes) viruses. There is abundant ultrastructural evidence for infection of a variety of microheterotrophs and some autotrophs. One station exhibited the classical characteristics of a lower latitude algal bloom with potential viral control. The blooming alga, Pyramimonas tychotreta Daugbjerg 2000, was infected, as were two abundant heterotrophs, Cryothecomonas spp. and an unidentified flagellate, that fed on P. tychotreta. Infections were observed in only one life history stage (multiflagellate cells) of P. tychotreta, suggesting a relationship among virus-induced lysis, life-history stages, physiology, and environmental factors regulating the life cycle. There is good evidence that diatoms are not a likely source of the large viruses, and viruses in general are not a major food source for ice microheterotrophs in summer.}, owner = {rec}, timestamp = {2009.08.22}, url = {http://dx.doi.org/10.1007/s00227-003-1015-x} } @ARTICLE{Gowing2004, author = {Gowing, Marcia M. and Garrison, David L. and Gibson, Angela H. and Krupp, Jonathan M. and Jeffries, Martin O. and Fritsen, Christian H.}, title = {{B}acterial and viral abundance in {R}oss {S}ea summer pack ice communities}, journal = {Mar Ecol Prog Ser}, year = {2004}, volume = {279}, pages = {3--12}, owner = {rec}, timestamp = {2007.06.17} } @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{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{Holmfeldt2007, author = {Holmfeldt, Karin and Middelboe, Mathias and Nybroe, Ole and Riemann, Lasse}, title = {Large Variabilities in Host Strain Susceptibility and Phage Host Range Govern Interactions between Lytic Marine Phages and Their \emph{Flavobacterium} Hosts}, journal = {Appl Environ Microbiol}, year = {2007}, volume = {73}, pages = {6730--6739}, abstract = {Phages are a main mortality factor for marine bacterioplankton and are thought to regulate bacterial community composition through host-specific infection and lysis. In the present study we demonstrate for a marine phage-host assemblage that interactions are complex and that specificity and efficiency of infection and lysis are highly variable among phages infectious to strains of the same bacterial species. Twenty-three Bacteroidetes strains and 46 phages from Swedish and Danish coastal waters were analyzed. Based on genotypic and phenotypic analyses, 21 of the isolates could be considered strains of Cellulophaga baltica (Flavobacteriaceae). Nevertheless, all bacterial strains showed unique phage susceptibility patterns and differed by up to 6 orders of magnitude in sensitivity to the same titer of phage. The isolated phages showed pronounced variations in genome size (8 to >242 kb) and host range (infecting 1 to 20 bacterial strains). Our data indicate that marine bacterioplankton are susceptible to multiple co-occurring phages and that sensitivity towards phage infection is strain specific and exists as a continuum between highly sensitive and resistant, implying an extremely complex web of phage-host interactions. Hence, effects of phages on bacterioplankton community composition and dynamics may go undetected in studies where strain identity is not resolvable, i.e., in studies based on the phylogenetic resolution provided by 16S rRNA gene or internal transcribed spacer sequences.}, doi = {10.1128/AEM.01399-07}, eprint = {http://aem.asm.org/cgi/reprint/73/21/6730.pdf}, owner = {rec}, timestamp = {2009.08.22}, url = {http://aem.asm.org/cgi/content/abstract/73/21/6730} } @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 ∼25 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{Jiang1998, author = {S. C. Jiang and J. H. Paul}, title = {{G}ene transfer by transduction in the marine environment}, journal = {Appl Environ Microbiol}, year = {1998}, volume = {64}, pages = {2780--2787}, abstract = {To determine the potential for bacteriophage-mediated gene transfer in the marine environment, we established transduction systems by using marine phage host isolates. Plasmid pQSR50, which contains transposon Tn5 and encodes kanamycin and streptomycin resistance, was used in plasmid transduction assays. Both marine bacterial isolates and concentrated natural bacterial communities were used as recipients in transduction studies. Transductants were detected by a gene probe complementary to the neomycin phosphotransferase (nptII) gene in Tn5. The transduction frequencies ranged from 1.33 x 10(-7) to 5.13 x 10(-9) transductants/PFU in studies performed with the bacterial isolates. With the mixed bacterial communities, putative transductants were detected in two of the six experiments performed. These putative transductants were confirmed and separated from indigenous antibiotic-resistant bacteria by colony hybridization probed with the nptII probe and by PCR amplification performed with two sets of primers specific for pQSR50. The frequencies of plasmid transduction in the mixed bacterial communities ranged from 1.58 x 10(-8) to 3.7 x 10(-8) transductants/PFU. Estimates of the transduction rate obtained by using a numerical model suggested that up to 1.3 x 10(14) transduction events per year could occur in the Tampa Bay Estuary. The results of this study suggest that transduction could be an important mechanism for horizontal gene transfer in the marine environment.}, keywords = {Bacteria; Bacteriophages; Blotting, Southern; DNA Transposable Elements; Drug Resistance, Microbial; Escherichia coli; Gene Transfer, Horizontal; Kanamycin Kinase; Kanamycin Resistance; Plasmids; Polymerase Chain Reaction; Seawater; Transduction, Genetic; Water Microbiology}, owner = {rec}, pmid = {9687430}, timestamp = {2007.06.17} } @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{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} } @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} } @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{Lawrence2003, author = {Lawrence, J. G. and Hendrickson, H.}, title = {{L}ateral gene transfer: {W}hen 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{Parry2007, author = {Laybourn-Parry, Johanna and Marshall, William and Madan, Nanette}, title = {Viral dynamics and patterns of lysogeny in saline {A}ntarctic lakes}, journal = {Polar Biol}, year = {2007}, volume = {30}, pages = {351--358}, abstract = {Abstract  Antarctic lakes are extreme ecosystems with microbially dominated food webs, in which viruses may be important in controlling community dynamics. A year long investigation of two Antarctic saline lakes (Ace and Pendant Lakes) revealed high concentrations of virus like particles (VLP) (0.20–1.26 Ã— 108 ml−1), high VLP: bacteria ratios (maximum 70.6) and a seasonal pattern of lysogeny differing from that seen at lower latitudes. Highest rates of lysogeny (up to 32% in Pendant Lake and 71% in Ace Lake) occurred in winter and spring, with low or no lysogeny in summer. Rates of virus production (range 0.176–0.823 Ã— 106 viruses ml−1 h−1) were comparable to lower latitude freshwater lakes. In Ace Lake VLP did not correlate with bacterial cell concentration or bacterial production but correlated positively with primary production, while in Pendant Lake VLP abundance correlated positively with both bacterial cell numbers and bacterial production but not with primary production. In terms of virus and bacterial dynamics the two saline Antarctic lakes studied appear distinct from other aquatic ecosystems investigated so far, in having very high viral to bacterial ratios (VBR) and a very high occurrence of lysogeny in winter.}, owner = {rec}, timestamp = {2009.08.21}, url = {http://dx.doi.org/10.1007/s00300-006-0191-9} } @ARTICLE{Madan2005, author = {Madan, Nanette J. and Marshall, William A. and Laybourn-Parry, Johanna}, title = {Virus and microbial loop dynamics over an annual cycle in three contrasting {A}ntarctic lakes}, journal = {Freshwater Biol}, year = {2005}, volume = {50}, pages = {1291--1300}, abstract = {1. Viral and microbial loop dynamics were investigated over an annual cycle in three contrasting saline Antarctic lakes 2013 Highway Lake (salinity 42030), Pendant Lake (salinity 192030) and Ace Lake, a meromictic system (with a mixolimnion salinity of 182030) in order to assess the importance of viruses in extreme, microbially dominated systems. 2. Virus like particles (VLP) showed no clear seasonal pattern, with high concentrations occurring in both winter and summer (range 0.89107±0.038 to 12.017107±1.28mL22121). VLP abundances reflected lake productivity based on chlorophyll a concentrations. Bacterial abundances and biomass did not correlate with VLP numbers except in Pendant Lake, the most productive of the three lakes studied. 3. Pendant Lake supported the highest bacterial biomass (range Highway: 18.44±1.35 to 59.43±2.80ng CmL22121; Ace: 14.42±2.69 to 68.39±2.95ng C mL22121; Pendant: 31.36±3.94 to 115.95±4.49ng C mL22121) so that virus to bacteria ratios (VBR) (range 30.48±7.96 to 96.67±8.21) were higher in Ace Lake (range 30.58±3.98 to 80.037±1.60) and Highway Lake (range 18.63±3.12 to 126.74±6.50). 4. Negative correlations occurred between VLP and cryptophytes (dominant phototrophic nanoflagellates), suggesting that they were not hosts to lytic viruses. Among the other protists only the heterotrophic nanoflagellates of Highway Lake (dominated by the marine choanoflagellate Diaphanoeca grandis) showed a positive correlation with VLP. 5. The VLP was negatively correlated with photosynthetically active radiation (PAR) and temperature, both of which increased with ice thinning and breakout, increasing viral decay. In winter VLP probably persisted in cold, dark water. 6. High VLP concentrations and high VBR (values at the upper end of those reported for marine and lacustrine systems) indicated that viruses, most of which were probably bacteriophage, are a major element within the microbial communities in extreme, saline lakes.}, owner = {rec}, timestamp = {2009.08.22}, url = {http://dx.doi.org/10.1111/j.1365-2427.2005.01399.x} } @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{Middelboe2002, author = {Mathias Middelboe and Torkel G. Nielsen and Peter K. Bj\o{}rnsen}, title = {Viral and bacterial production in the {N}orth {W}ater: in situ measurements, batch-culture experiments and characterization and distribution of a virus-host system}, journal = {Deep-Sea Res Pt II}, year = {2002}, volume = {49}, pages = {5063--5079}, abstract = {Growth and viral lysis of bacterioplankton at subzero temperatures were measured in the North Water polynya in July 1998. In situ measurements of bacterial carbon consumption in surface waters ranged from 15 to 63 [mu]g C l-1 d-1 in the eastern and 6 to 7 [mu]g C l-1 d-1 in the northern part of the polynya. Both bacterial abundance and activity appeared to increase in response to the decay of the phytoplankton bloom that developed in the North Water. Organic carbon was the limiting substrate for bacteria in the polynya since addition of glucose, but not inorganic nutrients, to batch cultures increased both the carrying capacity of the substrate and the growth rate of the bacteria. Bacterial growth rates ranged from 0.11 to 0.40 d-1, corresponding to bacterial generation times of 1.7-6.3 d. The in situ viral production rate was estimated both from the frequency of visibly infected cells and from the rate of viral production in batch cultures; it ranged from 0.04 to 0.52 d-1 and from 0.25 to 0.47 d-1, respectively. From 6% to 28% of bacterial production was found to be lost due to viral lysis. The average virus-bacteria ratio was 5.1±3.1, with the abundance of viruses being correlated positively with bacterial production. A Pseudoalteromonas sp. bacterial host and an infective virus were isolated from the polynya; characteristics and distribution of the virus-host system were examined. The Pseudoalteromonas sp. showed psychrotolerant growth and sustained significant production of viruses at 0°C. The virus-host system was found throughout the polynya. Overall the results suggested that a large amount of organic carbon released during the development and breakdown of the spring phytoplankton bloom was consumed by planktonic bacteria and that the microbial food web was an important and dynamic component of the planktonic food web in the North Water.}, doi = {DOI: 10.1016/S0967-0645(02)00178-9}, issn = {0967-0645}, owner = {rec}, timestamp = {2011.03.16}, url = {http://www.sciencedirect.com/science/article/B6VGC-46RKK3C-1/2/5852ee88901686bbb979a24c31018566} } @ARTICLE{Miller2001, author = {R.V. Miller}, title = {Environmental bacteriophage-host interactions: factors contribution to natural transduction}, journal = {Antonie van Leeuwenhoek}, year = {2001}, volume = {79}, pages = {141--147}, 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{Nagasaki2005, author = {Keizo Nagasaki and Yuji Tomaru and Yoshitake Takao and Kensho Nishida and Yoko Shirai and Hidekazu Suzuki and Tamotsu Nagumo}, title = {Previously unknown virus infects marine diatom}, journal = {Appl Environ Microbiol}, year = {2005}, volume = {71}, pages = {3528--3535}, abstract = {Diatoms are a major phytoplankton group that play important roles in maintaining oxygen levels in the atmosphere and sustaining the primary nutritional production of the aquatic environment. Among diatoms, the genus Chaetoceros is one of the most abundant and widespread. Temperature, climate, salinity, nutrients, and predators were regarded as important factors controlling the abundance and population dynamics of diatoms. Here we show that a viral infection can occur in the genus Chaetoceros and should therefore be considered as a potential mortality source. Chaetoceros salsugineum nuclear inclusion virus (CsNIV) is a 38-nm icosahedral virus that replicates within the nucleus of C. salsugineum. The latent period was estimated to be between 12 and 24 h, with a burst size of 325 infectious units per host cell. CsNIV has a genome structure unlike that of other viruses that have been described. It consists of a single molecule of covalently closed circular single-stranded DNA (ssDNA; 6,005 nucleotides), as well as a segment of linear ssDNA (997 nucleotides). The linear segment is complementary to a portion of the closed circle creating a partially double-stranded genome. Sequence analysis reveals a low but significant similarity to the replicase of circoviruses that have a covalently closed circular ssDNA genome. This new host-virus system will be useful for investigating the ecological relationships between bloom-forming diatoms and other viruses in the marine system. Our study supports the view that, given the diversity and abundance of plankton, the ocean is a treasury of undiscovered viruses.}, doi = {10.1128/AEM.71.7.3528-3535.2005}, institution = {Harmful Algal Bloom Division, National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Ohno, Saeki, Hiroshima 739-0452, Japan. nagasaki@affrc.go.jp}, keywords = {Animals; DNA Viruses, isolation /&/ purification/pathogenicity/ultrastructure; DNA, Viral, genetics/isolation /&/ purification; Diatoms, growth /&/ development/ultrastructure/virology; Microscopy, Electron, Scanning; Microscopy, Electron, Transmission; Phytoplankton, pathogenicity/virology; Seawater; Species Specificity; Virus Replication}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {71/7/3528}, pmid = {16000758}, timestamp = {2010.09.06}, url = {http://dx.doi.org/10.1128/AEM.71.7.3528-3535.2005} } @ARTICLE{Noble1997, author = {R. T. Noble and J. A. Fuhrman}, title = {Virus Decay and Its Causes in Coastal Waters}, journal = {Appl Environ Microbiol}, year = {1997}, volume = {63}, pages = {77--83}, abstract = {Recent evidence suggests that viruses play an influential role within the marine microbial food web. To understand this role, it is important to determine rates and mechanisms of virus removal and degradation. We used plaque assays to examine the decay of infectivity in lab-grown viruses seeded into natural seawater. The rates of loss of infectivity of native viruses from Santa Monica Bay and of nonnative viruses from the North Sea in the coastal seawater of Santa Monica Bay were determined. Viruses were seeded into fresh seawater that had been pretreated in various ways: filtration with a 0.2-(mu)m-pore-size filter to remove organisms, heat to denature enzymes, and dissolved organic matter enrichment to reconstitute enzyme activity. Seawater samples were then incubated in full sunlight, in the dark, or under glass to allow partitioning of causative agents of virus decay. Solar radiation always resulted in increased rates of loss of virus infectivity. Virus isolates which are native to Santa Monica Bay consistently degraded more slowly in full sunlight in untreated seawater (decay ranged from 4.1 to 7.2\% h(sup-1)) than nonnative marine bacteriophages which were isolated from the North Sea (decay ranged from 6.6 to 11.1\% h(sup-1)). All phages demonstrated susceptibility to degradation by heat-labile substances, as heat treatment reduced the decay rates to about 0.5 to 2.0\% h(sup-1) in the dark. Filtration reduced decay rates by various amounts, averaging 20\%. Heat-labile, high-molecular-weight dissolved material (>30 kDa, probably enzymes) appeared responsible for about 1/5 of the maximal decay. Solar radiation was responsible for about 1/3 to 2/3 of the maximal decay of nonnative viruses and about 1/4 to 1/3 of that of the native viruses, suggesting evolutionary adaptation to local light levels. Our results suggest that sunlight is an important contributing factor to virus decay but also point to the significance of particles and dissolved substances in seawater.}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {16535501}, timestamp = {2009.07.27} } @ARTICLE{Patel2007, author = {Anand Patel and Rachel T Noble and Joshua A Steele and Michael S Schwalbach and Ian Hewson and Jed A Fuhrman}, title = {Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with {SYBR} {G}reen {I}.}, journal = {Nat Protoc}, year = {2007}, volume = {2}, pages = {269--276}, abstract = {Viruses are the most abundant biological entities in aquatic environments, typically exceeding the abundance of bacteria by an order of magnitude. The reliable enumeration of virus-like particles in marine microbiological investigations is a key measurement parameter. Although the size of typical marine viruses (20-200 nm) is too small to permit the resolution of details by light microscopy, such viruses can be visualized by epifluorescence microscopy if stained brightly. This can be achieved using the sensitive DNA dye SYBR Green I (Molecular Probes-Invitrogen). The method relies on simple vacuum filtration to capture viruses on a 0.02-microm aluminum oxide filter, and subsequent staining and mounting to prepare slides. Virus-like particles are brightly stained and easily observed for enumeration, and prokaryotic cells can easily be counted on the same slides. The protocol provides an inexpensive, rapid (30 min) and reliable technique for obtaining counts of viruses and prokaryotes simultaneously.}, doi = {10.1038/nprot.2007.6}, institution = {Marine Environmental Biology Section, University of Southern California, 3616 Trousdale Parkway, AHF-107, Los Angeles, California 90089, USA. anandp@usc.edu}, keywords = {Bacteria, isolation /&/ purification; Colony Count, Microbial, methods; Filtration, methods; Microscopy, Fluorescence, methods; Organic Chemicals; Viruses, isolation /&/ purification/ultrastructure; Water Microbiology}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {nprot.2007.6}, pmid = {17406585}, timestamp = {2009.08.18}, url = {http://dx.doi.org/10.1038/nprot.2007.6} } @ARTICLE{Payet2008, author = {Payet, J\'er\^ome P. and Suttle, Curtis A.}, title = {Physical and biological correlates of virus dynamics in the southern {B}eaufort {S}ea and {A}mundsen {G}ulf}, journal = {J Mar Sys}, year = {2008}, volume = {74}, pages = {933--945}, abstract = {As part of the Canadian Arctic Shelf Exchange Study (CASES), we investigated the spatial and seasonal distributions of viruses in relation to biotic (bacteria, chlorophyll-a (chl a)) and abiotic variables (temperature, salinity and depth). Sampling occurred in the southern Beaufort Sea Shelf in the region of the Amundsen Gulf and Mackenzie Shelf, between November 2003 and August 2004. Bacterial and viral abundances estimated by epifluorescence microscopy (EFM) and flow cytometry (FC) were highly correlated (r2=0.89 and r2=0.87, respectively), although estimates by EFM were slightly higher (FC=1.08 times EFM+0.12 and FC=1.07 times EFM+0.43, respectively). Viral abundances ranged from 0.13 times 106 to 23 times 106ml-1, and in surface waters were ~2-fold higher during the spring bloom in May and June and ~1.5-fold higher during July and August, relative to winter abundances. These increases were coincident with a ~6-fold increase in chl a during spring and a ~4-fold increase in bacteria during summer. Surface viral abundances near the Mackenzie River were ~2-fold higher than in the Mackenzie Shelf and Amundsen Gulf regions during the peak summer discharge, concomitant with a ~5.5-fold increase in chl a (up to 2.4[mu]g l-1) and a ~2-fold increase in bacterial abundance (up to 22 times 105ml-1). Using FC, two subgroups of viruses and heterotrophic bacteria were defined. A low SYBR-green fluorescence virus subgroup (V2) representing ~71% of the total viral abundance, was linked to the abundance of high nucleic acid fluorescence (HNA) bacteria (a proxy for bacterial activity), which represented 42 to 72% of the bacteria in surface layers. A high SYBR-green fluorescence viral subgroup (V1) was more related to high chl a concentrations that occurred in surface waters during spring and at stations near the Mackenzie River plume during the summer discharge. These results suggest that V1 infect phytoplankton, while most V2 are bacteriophages. On the Beaufort Sea shelf, viral abundance displayed seasonal and spatial variations in conjunction with chl a concentration, bacterial abundance and composition, temperature, salinity and depth. The highly dynamic nature of viral abundance and its correlation with increases in chl a concentration and bacterial abundance implies that viruses are important agents of microbial mortality in Arctic shelf waters.}, booktitle = {Sea ice and life in a river-influenced arctic shelf ecosystem}, issn = {0924-7963}, keywords = {Canada, Beaufort Sea, Mackenzie Shelf, Amundsen Gulf, 69-72 deg N, 122-139 deg W, Marine viruses, Bacteria, Chlorophyll a, Arctic, Flow cytometry, Seasonal variation, Spatial variation}, owner = {rec}, timestamp = {2009.08.22} } @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}, owner = {rec}, timestamp = {2011.03.17}, 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{Replicon1995, author = {J. Replicon and A. Frankfater and R. V. Miller}, title = {A Continuous Culture Model To Examine Factors That Affect Transduction among \emph{Pseudomonas aeruginosa} Strains in Freshwater Environments}, journal = {Appl Environ Microbiol}, year = {1995}, volume = {61}, pages = {3359--3366}, abstract = {Transduction among Pseudomonas aeruginosa strains was observed in continuous cultures operated under environmentally relevant generation times, cell densities, and phage-to-bacterium ratios, suggesting its importance as a natural mechanism of gene transfer. Transduction was quantified by the transfer of the Tra(sup-) Mob(sup-) plasmid Rms149 from a plasmid-bearing strain to an F116 lysogen that served as both the recipient and source of transducing phages. In control experiments in which transduction was prevented, there was a reduction in the phenotype of the mock transductant over time. However, in experiments in which transduction was permitted, the proportion of transductants in the population increased over time. These data suggest that transduction can maintain a phenotype for an extended period of time in a population from which it would otherwise be lost. Changes in the numbers of transductants were analyzed by a two-part mathematical model, which consisted of terms for the selection of the transductant's phenotype and for the formation of new transductants. Transduction rates ranged from 10(sup-9) to 10(sup-6) per total viable cell count per ml per generation and increased with both the recipient concentration and the phage-to-bacterium ratio. These observations indicate an increased opportunity for transduction to occur when the interacting components are in greater abundance.}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {16535123}, timestamp = {2009.07.27} } @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 = {Aquatic Microbial Ecology}, 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.}, owner = {rec}, timestamp = {2006.12.30}, url = {http://www.int-res.com/abstracts/ame/v45/n2/p195-206/} } @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{Riedel2003, author = {A. Riedel and C. Michel and M. Poulin and S. Lessard}, title = {Taxonomy and Abundance of Microalgae and Protists at a First-Year Sea Ice Station near {R}esolute {B}ay, {N}unavut, Spring to Early Summer 2001}, journal = {Canadian Data Report of Hydrography and Ocean Sciences 159}, year = {2003}, owner = {rec}, timestamp = {2010.09.06} } @ARTICLE{Rozanska2009, author = {M. Rozanska and M. Gosselin and M. Poulin and J.M. Wiktor and C. Michel}, title = {Influence of environmental factors on the development of bottom ice protist communities during the winter--spring transition}, journal = {Mar Ecol Prog Ser}, year = {2009}, volume = {386}, pages = {43--59}, comment = {10.3354/meps08092}, owner = {rec}, timestamp = {2011.03.12}, url = {http://www.int-res.com/abstracts/meps/v386/p43-59/} } @ARTICLE{Sawstrom2008, author = {S\"awstr\"om, Christin and Lisle, John and Anesio, Alexandre and Priscu, John and Laybourn-Parry, Johanna}, title = {Bacteriophage in polar inland waters}, journal = {Extremophiles}, year = {2008}, volume = {12}, pages = {167--175}, abstract = {Abstract  Bacteriophages are found wherever microbial life is present and play a significant role in aquatic ecosystems. They mediate microbial abundance, production, respiration, diversity, genetic transfer, nutrient cycling and particle size distribution. Most studies of bacteriophage ecology have been undertaken at temperate latitudes. Data on bacteriophages in polar inland waters are scant but the indications are that they play an active and dynamic role in these microbially dominated polar ecosystems. This review summarises what is presently known about polar inland bacteriophages, ranging from subglacial Antarctic lakes to glacial ecosystems in the Arctic. The review examines interactions between bacteriophages and their hosts and the abiotic and biotic variables that influence these interactions in polar inland waters. In addition, we consider the proportion of the bacteria in Arctic and Antarctic lake and glacial waters that are lysogenic and visibly infected with viruses. We assess the relevance of bacteriophages in the microbial loop in the extreme environments of Antarctic and Arctic inland waters with an emphasis on carbon cycling.}, owner = {rec}, timestamp = {2009.08.21}, url = {http://dx.doi.org/10.1007/s00792-007-0134-6} } @ARTICLE{Saye1987, author = {D. J. Saye and O. Ogunseitan and G. S. Sayler and R. V. Miller}, title = {Potential for transduction of plasmids in a natural freshwater environment: effect of plasmid donor concentration and a natural microbial community on transduction in \emph{Pseudomonas aeruginosa}.}, journal = {Appl Environ Microbiol}, year = {1987}, volume = {53}, pages = {987--995}, abstract = {Transduction of Pseudomonas aeruginosa plasmid Rms149 by the generalized transducing bacteriophage phi DS1 was shown to occur during a 9-day incubation of environmental test chambers in a freshwater reservoir. Plasmid DNA was transferred from a nonlysogenic plasmid donor to a phi DS1 lysogen of P. aeruginosa that served both as the source of the transducing phage and as the recipient of the plasmid DNA. When the concentration of donors introduced into the chambers was varied while the recipient concentration in each chamber was at a level equivalent to natural concentrations of P. aeruginosa, the concentration of plasmid-containing donor cells introduced was shown to affect the frequency of transduction significantly. Transduction was observed both in the absence and in the presence of the natural microbial community. The presence of the natural community resulted in a rapid decrease in the numbers of the introduced donors and recipients and a decrease in the number of transductants recovered. These results demonstrate the potential for naturally occurring transduction in aquatic environments and indicate that donor load may be an important parameter in assessing this potential.}, keywords = {Bacteriophages; DNA, Bacterial, genetics; Fresh Water; Plasmids; Pseudomonas aeruginosa, genetics; Transduction, Genetic; Water Microbiology}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {3111371}, timestamp = {2009.07.27} } @ARTICLE{Shirai2008, author = {Yoko Shirai and Yuji Tomaru and Yoshitake Takao and Hidekazu Suzuki and Tamotsu Nagumo and Keizo Nagasaki}, title = {Isolation and characterization of a single-stranded {RNA} virus infecting the marine planktonic diatom \emph{Chaetoceros tenuissimus} {M}eunier}, journal = {Appl Environ Microbiol}, year = {2008}, volume = {74}, pages = {4022--4027}, abstract = {Diatoms are important components of the biological community and food web in the aquatic environment. Here, we report the characteristics of a single-stranded RNA (ssRNA) virus (CtenRNAV01) that infects the marine diatom Chaetoceros tenuissimus Meunier (Bacillariophyceae). The ca. 31-nm virus particle is icosahedral and lacks a tail. CtenRNAV01 forms crystalline arrays occupying most of the infected host's cytoplasm. By growth experiments, the lytic cycle and the burst size were estimated to be <24 h and approximately 1 x 10(4) infectious units per host cell, respectively. Stationary-phase C. tenuissimus cultures were shown to be more sensitive to CtenRNAV01 than logarithmic-phase cultures. The most noticeable feature of this virus is its exceptionally high yields of approximately 10(10) infectious units ml(-1); this is much higher than those of any other algal viruses previously characterized. CtenRNAV01 has two molecules of ssRNA of approximately 8.9 and 4.3 kb and three major proteins (33.5, 31.5, and 30.0 kDa). Sequencing of the total viral genome has produced only one large contig [9,431 bases excluding the poly(A) tail], suggesting considerable overlapping between the two RNA molecules. The monophyly of CtenRNAV01 compared to another diatom-infecting virus, Rhizosolenia setigera RNA virus, was strongly supported in a maximum likelihood phylogenetic tree constructed based on the concatenated amino acid sequences of the RNA-dependent RNA polymerase domains. Although further analysis is required to determine the detailed classification and nomenclature of this virus, these data strongly suggest the existence of a diatom-infecting ssRNA virus group in natural waters.}, doi = {10.1128/AEM.00509-08}, institution = {National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan.}, keywords = {Animals; Diatoms, ultrastructure/virology; Microscopy, Electron, Transmission; Molecular Sequence Data; Phylogeny; Phytoplankton, ultrastructure/virology; RNA Viruses, classification/genetics/isolation /&/ purification; RNA, Viral, genetics/isolation /&/ purification; Seawater, microbiology; Sequence Analysis, DNA; Species Specificity}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pii = {AEM.00509-08}, pmid = {18469125}, timestamp = {2010.09.06}, url = {http://dx.doi.org/10.1128/AEM.00509-08} } @ARTICLE{Steward1996, author = {Steward, G.F. and Smith, D.C. and Azam, F.}, title = {Abundance and production of bacteria and viruses in the {B}ering and {C}hukchi {S}eas}, journal = {Mar Ecol Prog Ser}, year = {1996}, volume = {131}, pages = {287--300}, owner = {rec}, timestamp = {2009.08.21} } @ARTICLE{Suttle1992, author = {Curtis A Suttle and Feng Chen}, title = {Mechanisms and Rates of Decay of Marine Viruses in Seawater}, journal = {Appl Environ Microbiol}, year = {1992}, volume = {58}, pages = {3721--3729}, abstract = {Loss rates and loss processes for viruses in coastal seawater from the Gulf of Mexico were estimated with three different marine bacteriophages. Decay rates in the absence of sunlight ranged from 0.009 to 0.028 h, with different viruses decaying at different rates. In part, decay was attributed to adsorption by heat-labile particles, since viruses did not decay or decayed very slowly in seawater filtered through a 0.2-mum-pore-size filter (0.2-mum-filtered seawater) and in autoclaved or ultracentrifuged seawater but continued to decay in cyanide-treated seawater. Cyanide did cause decay rates to decrease, however, indicating that biological processes were also involved. The observations that decay rates were often greatly reduced in 0.8- or 1.0-mum-filtered seawater, whereas bacterial numbers were not, suggested that most bacteria were not responsible for the decay. Decay rates were also reduced in 3-mum-filtered or cycloheximide-treated seawater but not in 8-mum-filtered seawater, implying that flagellates consumed viruses. Viruses added to flagellate cultures decayed at 0.15 h, corresponding to 3.3 viruses ingested flagellate h. Infectivity was very sensitive to solar radiation and, in full sunlight, decay rates were 0.4 to 0.8 h. Even when UV-B radiation was blocked, rates were as high as 0.17 h. Calculations suggest that in clear oceanic waters exposed to full sunlight, most of the virus decay, averaged over a depth of 200 m, would be attributable to solar radiation. When decay rates were averaged over 24 h for a 10-m coastal water column, loss rates of infectivity attributable to sunlight were similar to those resulting from all other processes combined. Consequently, there should be a strong diel signal in the concentration of infectious viruses. In addition, since sunlight destroys infectivity more quickly than virus particles, a large proportion of the viruses in seawater is probably not infective.}, institution = {Marine Science Institute, The University of Texas at Austin, P.O. Box 1267, Port Aransas, Texas 78373-1267.}, language = {eng}, medline-pst = {ppublish}, owner = {rec}, pmid = {16348812}, timestamp = {2009.08.22} } @ARTICLE{Wells2006-9a, author = {Wells, L. E. and Deming, J. W.}, title = {{C}haracterization of a cold-active bacteriophage on two psychrophilic marine hosts}, journal = {Aquat Microb Ecol}, year = {2006}, volume = {45}, pages = {15--29}, owner = {rec}, timestamp = {2007.01.27} } @ARTICLE{Wells2006-decay, author = {Wells, L. E. and Deming, J. W.}, title = {{E}ffects of temperature, salinity and clay particles on inactivation and decay of cold-active marine {B}acteriophage 9{A}}, journal = {Aquat Microb Ecol}, year = {2006}, volume = {45}, pages = {31--39}, abstract = {The effects of temperature, salinity and clay particles on the inactivation and decay of the cold-active Bacteriophage 9A, isolated from particle-rich Arctic seawater, were examined using a plating technique to evaluate infectivity (inactivation) and epifluorescence microscopy to measure phage concentrations (decay). Phage 9A was rapidly inactivated over a temperature test range of 25 to 55 degrees C in marine broth (salinity of 36 psu), with half-lives ranging from < 10 min at 25 degrees C to similar to 1 min at 32.5 degrees C and too rapid to measure at >= 35 degrees C, making it among the most thermolabile phages. When salinity was varied at 30 degrees C, the inactivation rates in brackish (21 psu) and briny (161 psu) broth were indistinguishable from that in marine broth (p > 0.20). At the environmentally relevant temperature of -1 degrees C, however, loss of infectivity in briny broth was 3 to 4 times greater than in marine or brackish broth. As commonly observed, viral decay determined microscopically often substantially underestimated loss of infectivity: at 30 degrees C, loss of infectivity exceeded the viral decay rate by approximately 1000-fold, while at -1 degrees C, microscopic counts did not detect any of the losses observed by plaque assay. Under conditions comparable to a winter sea-ice brine inclusion (-12 degrees C and 161 psu), however, plating and microscopy were in substantive agreement, indicating relatively minor losses of 16 to 34% losses over a 5 wk period. Illite, kaolinite or montmorillonite clays had no statistically significant effect on phage inactivation as a function of temperature or salinity, although rates tended to be slower in the presence of the clays. In general, our results emphasize the importance of working with cold-active phages under environmentally-relevant conditions of temperature and salinity. They also imply decay processes that involve viral proteins rather than nucleic acids; as a result, affected viruses may be recalcitrant to reactivation by known host-based repair mechanisms.}, af = {Wells, Llyd E.EOLEOLDeming, Jody W.}, c1 = {Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.}, citedreferences = {BITTON G, 1974, WATER RES, V8, P227 ; CARLSON GF, 1968, J WATER POLLUT CONTR, V40, R89 ; CARSON MA, 1998, ARCTIC, V51, P116 ; CHEN PK, 1966, J BACTERIOL, V91, P1136 ; DELISLE AL, 1972, ANTON LEEUW INT J G, V38, P1 ; EMEIS K, 1985, MITT GEOLPALAONT I U, V58, P593 ; FELLER G, 2003, NAT REV MICROBIOL, V1, P200 ; GANTZER C, 1994, ENVIRON TECHNOL, V15, P271 ; GIANFREDA L, 1991, MOL CELL BIOCHEM, V100, P97 ; GOWING MM, 2002, MAR ECOL-PROG SER, V241, P1 ; GUIXABOIXEREU N, 2002, DEEP-SEA RES PT II, V49, P827 ; HARA S, 1996, MAR ECOL-PROG SER, V145, P269 ; HEWSON I, 2003, MICROBIAL ECOL, V46, P337 ; HILL PR, 1989, J SEDIMENT PETROL, V59, P455 ; HURST CJ, 1989, CAN J MICROBIOL, V35, P474 ; HUSTON AL, 2004, APPL ENVIRON MICROB, V70, P3321 ; KAPUSCINSKI RB, 1980, WATER RES, V14, P363 ; KULPA CF, 1971, CAN J MICROBIOL, V17, P157 ; LABELLE RL, 1979, APPL ENVIRON MICROB, V38, P93 ; LABELLE RL, 1980, APPL ENVIRON MICROB, V39, P749 ; LAWRENCE JE, 2002, LIMNOL OCEANOGR, V47, P545 ; MACDONALD RW, 1998, MAR GEOL, V144, P255 ; MARANGER R, 1994, MAR ECOL-PROG SER, V111, P121 ; MEYERREIL LA, 1991, MICROBIAL ENZYMES AQ, P84 ; MIDDELBOE M, 2002, DEEP-SEA RES PT II, V49, P5063 ; MOWATT TC, 1987, MITT GEOL PALI U HAM, V64, P269 ; NOBLE RT, 1997, APPL ENVIRON MICROB, V63, P77 ; NOBLE RT, 1998, AQUAT MICROB ECOL, V14, P113 ; OLSEN RH, 1968, J VIROL, V2, P357 ; ORTMANN AC, 2005, DEEP-SEA RES PT I, V52, P1515 ; QUIGNON F, 1995, WATER SCI TECHNOL, V31, P177 ; SCHAIBERGER GE, 1982, WATER RES, V16, P1425 ; SMITH EM, 1978, APPL ENVIRON MICROB, V35, P685 ; SPENCER R, 1955, NATURE, V175, P690 ; SPENCER R, 1963, S MARINE MICROBIOLOG, P350 ; STEWARD GF, 1996, MAR ECOL-PROG SER, V131, P287 ; STOTZKY G, 1981, VIRUSES WASTEWATER T, P199 ; SUTTLE CA, 1992, APPL ENVIRON MICROB, V58, P3721 ; WEINBAUER MG, 1999, AQUAT MICROB ECOL, V17, P111 ; WEINBAUER MG, 2003, LIMNOL OCEANOGR, V48, P1457 ; WELLS LE, 2006, AQUAT MICROB ECOL, V43, P209 ; WELLS LE, 2006, AQUAT MICROB ECOL, V45, P15 ; WELLS LE, 2006, ENVIRON MICROBIOL, V8, P1115 ; WELLS LE, 2006, LIMNOL OCEANOGR, V51, P47 ; WELLS LE, 2006, THESIS U WASHINGTON ; WHITMAN PA, 1971, APPL MICROBIOL, V22, P463 ; WIEBE WJ, 1968, MAR BIOL, V1, P244 ; WILHELM SW, 1998, AQUAT MICROB ECOL, V14, P215 ; WILHELM SW, 1998, LIMNOL OCEANOGR, V43, P586 ; WOMMACK KE, 1996, APPL ENVIRON MICROB, V62, P1336}, de = {virus; phage 9A; Colwellia psychrerythraea; 34H; temperature; salinity;EOLEOLclay; illite; Mackenzie Shelf}, em = {chimera.llyr@gmail.com}, ga = {107AD}, j9 = {AQUAT MICROB ECOL}, ji = {Aquat. Microb. Ecol.}, keywords = {ESTUARINE SEDIMENT; VIRUS INACTIVATION; COASTAL WATERS; BEAUFORT SHELF; FRANKLIN BAY; DNA-DAMAGE; SEA-ICE; DEEP; ENTEROVIRUSES; SURVIVAL}, la = {English}, nr = {50}, owner = {rec}, pa = {NORDBUNTE 23, D-21385 OLDENDORF LUHE, GERMANY}, pg = {9}, pi = {OLDENDORF LUHE}, publisher = {Inter-Research}, rp = {Wells, LE, Sterling Coll, Ctr No Studies, POB 72, Craftsbury Common, VTEOLEOL05827 USA.}, sc = {Ecology; Marine & Freshwater Biology}, sn = {0948-3055}, tc = {1}, timestamp = {2007.06.17}, ut = {ISI:000242142200003} } @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{Wen2004, author = {Wen, Kevin and Ortmann, Alice C. and Suttle, Curtis A.}, title = {Accurate Estimation of Viral Abundance by Epifluorescence Microscopy}, journal = {Appl Environ Microbiol}, year = {2004}, volume = {70}, pages = {3862--3867}, abstract = {Virus enumeration by epifluorescence microscopy (EFM) is routinely done on preserved, refrigerated samples. Concerns about obtaining accurate and reproducible estimates led us to examine procedures for counting viruses by EFM. Our results indicate that aldehyde fixation results in rapid decreases in viral abundance. By 1 h postfixation, the abundance dropped by 16.4% {+/-} 5.2% (n = 6), and by 4 h, the abundance was 20 to 35% lower. The average loss rates for glutaraldehyde- and formaldehyde-fixed samples over the first 2 h were 0.12 and 0.13 h-1, respectively. By 16 days, viral abundance had decreased by 72% (standard deviation, 6%; n = 6). Aldehyde fixation of samples followed by storage at 4{degrees}C, for even a few hours, resulted in large underestimates of viral abundance. The viral loss rates were not constant, and in glutaraldehyde- and formaldehyde-fixed samples they decreased from 0.13 and 0.17 h-1 during the first hour to 0.01 h-1 between 24 and 48 h. Although decay rates changed over time, the abundance was predicted by using separate models to describe decay over the first 8 h and decay beyond 8 h. Accurate estimates of abundance were easily made with unfixed samples stained with Yo-Pro-1, SYBR Green I, or SYBR Gold, and slides could be stored at -20{degrees}C for at least 2 weeks or, for Yo-Pro-1, at least 1 year. If essential, samples can be fixed and flash frozen in liquid nitrogen upon collection and stored at -86{degrees}C. Determinations performed with fixed samples result in large underestimates of abundance unless slides are made immediately or samples are flash frozen. If protocols outlined in this paper are followed, EFM yields accurate estimates of viral abundance.}, doi = {10.1128/AEM.70.7.3862-3867.2004}, eprint = {http://aem.asm.org/cgi/reprint/70/7/3862.pdf}, owner = {rec}, timestamp = {2011.03.11}, url = {http://aem.asm.org/cgi/content/abstract/70/7/3862} } @ARTICLE{Wilhelm2002, author = {Wilhelm, S.W. and Brigden, S.M. and Suttle, C.A.}, 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}, affiliation = {Department of Microbiology, The University of Tennessee, Knoxville, TN, USA US}, issn = {0095-3628}, issue = {1}, keyword = {Earth and Environmental Science}, owner = {rec}, publisher = {Springer New York}, timestamp = {2011.03.16}, url = {http://dx.doi.org/10.1007/s00248-001-1021-9} } @ARTICLE{Winget2005, author = {Winget, Danielle M. and Williamson, Kurt E. and Helton, Rebekah R. and Wommack, K. Eric}, title = {Tangential flow diafiltration: an improved technique for estimation of virioplankton production}, journal = {Aquat Microb Ecol}, year = {2005}, volume = {41}, pages = {221--232}, comment = {10.3354/ame041221}, owner = {rec}, timestamp = {2011.03.16}, url = {http://www.int-res.com/abstracts/ame/v41/n3/p221-232/} } @ARTICLE{Winter2004, author = {Winter, Christian and Herndl, Gerhard J. and Weinbauer, Markus G.}, title = {Diel cycles in viral infection of bacterioplankton in the {N}orth {S}ea}, journal = {Aquat Microb Ecol}, year = {2004}, volume = {35}, pages = {207--216}, comment = {10.3354/ame035207}, owner = {rec}, timestamp = {2011.03.16}, url = {http://www.int-res.com/abstracts/ame/v35/n3/p207-216/} } @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{Wommack2000, author = {K. E. Wommack and R. R. Colwell}, title = {{V}irioplankton: viruses in aquatic ecosystems}, journal = {Microbiol Mol Biol Rev}, year = {2000}, volume = {64}, pages = {69--114}, abstract = {The discovery that viruses may be the most abundant organisms in natural waters, surpassing the number of bacteria by an order of magnitude, has inspired a resurgence of interest in viruses in the aquatic environment. Surprisingly little was known of the interaction of viruses and their hosts in nature. In the decade since the reports of extraordinarily large virus populations were published, enumeration of viruses in aquatic environments has demonstrated that the virioplankton are dynamic components of the plankton, changing dramatically in number with geographical location and season. The evidence to date suggests that virioplankton communities are composed principally of bacteriophages and, to a lesser extent, eukaryotic algal viruses. The influence of viral infection and lysis on bacterial and phytoplankton host communities was measurable after new methods were developed and prior knowledge of bacteriophage biology was incorporated into concepts of parasite and host community interactions. The new methods have yielded data showing that viral infection can have a significant impact on bacteria and unicellular algae populations and supporting the hypothesis that viruses play a significant role in microbial food webs. Besides predation limiting bacteria and phytoplankton populations, the specific nature of virus-host interaction raises the intriguing possibility that viral infection influences the structure and diversity of aquatic microbial communities. Novel applications of molecular genetic techniques have provided good evidence that viral infection can significantly influence the composition and diversity of aquatic microbial communities.}, keywords = {Animals; Bacteria; Bacteriophages; Chlorophyll; Ecosystem; Gene Transfer Techniques; Models, Biological; Plankton; Viral Physiology; Virus Replication; Water Microbiology}, owner = {rec}, pmid = {10704475}, timestamp = {2007.06.17} } @ARTICLE{Yager2001, author = {Patricia L. Yager and Tara L. Connelly and Behzad Mortazavi and K. Eric Wommack and Nasreen Bano and James E. Bauer and Stephen Opsahl and James T. Hollibaugh}, title = {Dynamic Bacterial and Viral Response to an Algal Bloom at Subzero Temperatures}, journal = {Limnol Oceanogr}, year = {2001}, volume = {46}, pages = {790--801}, owner = {rec}, timestamp = {2009.08.21} } @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:}