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On the Eco-Evolutionary Relationships of Fresh and Salt Water Bacteria and the Role of Gene Transfer in Their Adaptation

  • David A Walsh
  • Josine Lafontaine
  • Hans-Peter Grossart
Chapter

Abstract

Bacteria are ubiquitous and important members of aquatic ecosystems ranging from inland lakes to the open ocean. Since the advent of molecular approaches for investigating bacteria community composition (BCC), the biogeography of aquatic bacteria has been investigated across a wide variety of environments. In addition to illuminating important aspects of microbial ecology, these studies have unveiled the evolutionary relationships between freshwater and marine bacteria. It is now clear that marine and freshwater ecosystems are inhabited by evolutionarily distinct bacterial lineages, suggesting that environmental transitions across the marine–freshwater boundary have occurred rarely during the evolution of bacteria. In this chapter, we consider successful freshwater–marine transitions as a form of evolutionary innovation in bacteria. Here, we discuss recent genomic insights into the evolution of marine and freshwater bacteria, and the metabolic and physiological traits of aquatic bacteria that may either restrict or facilitate cross-colonization of freshwater and marine habitats. In doing so, we will also highlight the potential role that lateral gene transfer (LGT) has played in marine–freshwater transitions over the course of bacterial evolution.

Keywords

Aquatic microbial ecology Salinity barrier Comparative genomics Metagenomics Evolutionary transitions Microbial evolution Ecological diversification Invasion 

Notes

Acknowledgments

This work was supported by grants from the Canada Research Chair (CRC:950-221184) Program, the Natural Sciences and Engineering Research Council (NSERC:402214-2011) of Canada, and the Fond Quebecois de la Recherche sure la Nature et les Technologies (FQRNT: 2012-RS-144365).

References

  1. 1.
    Allgaier M, Grossart HP (2006a) Diversity and seasonal dynamics of Actinobacteria populations in four lakes in northeastern Germany. Appl Environ Microbiol 72:3489–3497CrossRefGoogle Scholar
  2. 2.
    Allgaier M, Grossart HP (2006b) Seasonal dynamics and phylogenetic diversity of free-living and particle-associated bacterial communities in four lakes in northeastern Germany. Aquat Microbial Ecol 45:115–128CrossRefGoogle Scholar
  3. 3.
    Aminov RI (2011) Horizontal gene exchange in environmental microbiota. Front Microbiol 2:158PubMedCrossRefGoogle Scholar
  4. 4.
    Angles ML, Marshall KC, Goodman AE (1993) Plasmid transfer between marine bacteria in the aqueous phase and biofilms in reactor microcosms. Appl Environ Microbiol 59:843–850PubMedGoogle Scholar
  5. 5.
    Arnds J, Knittel K, Buck U, Winkel M, Amann R (2010) Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake. Syst Appl Microbiol 33:139–148PubMedCrossRefGoogle Scholar
  6. 6.
    Bahr M, Hobbie JE, Sogin ML (1996) Bacterial diversity in an arctic lake: a freshwater SAR 11 cluster. Aquat Microbial Ecol 11:271–277CrossRefGoogle Scholar
  7. 7.
    Barberán A, Casamayor E (2010) Global phylogenetic community structure and β-diversity patterns in surface bacterioplankton metacommunities. Aquat Microbial Ecol 59:1–10CrossRefGoogle Scholar
  8. 8.
    Bauer M, Kube M, Teeling H, Richter M, Lombardot T, Allers E, Wurdemann CA, Quast C, Kuhl H, Knaust F, Woebken D, Bischof K, Mussmann M, Choudhuri JV, Meyer F, Reinhardt R, Amann RI, Glockner FO (2006) Whole genome analysis of the marine Bacteroidetes’Gramella forsetii’ reveals adaptations to degradation of polymeric organic matter. Environ Microbiol 8:2201–2213PubMedCrossRefGoogle Scholar
  9. 9.
    Berggren M, Ström L, Laudon H, Karlsson J, Jonsson A, Giesler R, Bergström AK, Jansson M (2010) Lake secondary production fueled by rapid transfer of low molecular weight organic carbon from terrestrial sources to aquatic consumers. Ecol Lett 13:870–880PubMedCrossRefGoogle Scholar
  10. 10.
    Boucher Y, Cordero OX, Takemura A, Hunt DE, Schliep K, Bapteste E, Lopez P, Tarr CL, Polz MF (2011) Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. MBio 2(2)Google Scholar
  11. 11.
    Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau MER, Nesbø CL, Case RJ, Doolittle WF (2003) Lateral gene transfer and the origins of prokaryotic groups. Ann Rev Genet 37:283–328PubMedCrossRefGoogle Scholar
  12. 12.
    Bouvier TC, del Giorgio PA (2002) Compositional changes in free-living bacterial communities along a salinity gradient in two temperate estuaries. Limnol Oceanogr 453–470Google Scholar
  13. 13.
    Brown MV, Lauro FM, DeMaere MZ et al (2012) Global biogeography of SAR11 marine bacteria. Mol Syst 8:595Google Scholar
  14. 14.
    Buchan A, Gonzalez JM, Moran MA (2005) Overview of the marine roseobacter lineage. Appl Environ Microbiol 71:5665–5677PubMedCrossRefGoogle Scholar
  15. 15.
    Buck U, Grossart HP, Amann R, Pernthaler J (2009) Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake. Environ Microbiol 11:1854–1865PubMedCrossRefGoogle Scholar
  16. 16.
    Burd AB, Jackson GA (2009) Particle aggregation. Ann Rev Mar Sci 1:65–90PubMedCrossRefGoogle Scholar
  17. 17.
    Chan LK, Newton RJ, Sharma S, Smith CB, Rayapati P, Limardo AJ, Meile C, Moran MA (2012) Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium. Front Microbiol 3:159PubMedCrossRefGoogle Scholar
  18. 18.
    Cho JC, Giovannoni SJ (2004) Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl Environ Microbiol 70:432–440PubMedCrossRefGoogle Scholar
  19. 19.
    Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavrommatis K, Lucas S, Glavina T, Del R, Nolan M, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Kuske C, Bruce D, Goodwin L, Ovchinikova G, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A (2009) Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Stand Genomic Sci 1:308–316PubMedCrossRefGoogle Scholar
  20. 20.
    Crawford JW, Harris JA, Ritz K, Young IM (2005) Towards an evolutionary ecology of life in soil. Trends Ecol Evol 20:81–87PubMedCrossRefGoogle Scholar
  21. 21.
    DeLong EF, Franks DG, Alldredge AL (1993) Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol Oceanogr 924–934Google Scholar
  22. 22.
    Drapeau GR, Matula TI, MacLeod RA (1966) Nutrition and metabolism of marine bacteria XV. Relation of Na+-activated transport to the Na+ requirement of a marine pseudomonad for growth. J Bacteriol 92:63–71PubMedGoogle Scholar
  23. 23.
    Eiler A, Bertilsson S (2007) Flavobacteria blooms in four eutrophic lakes: linking population dynamics of freshwater bacterioplankton to resource availability. Appl Environ Microbiol 73:3511–3518PubMedCrossRefGoogle Scholar
  24. 24.
    Empadinhas N, da Costa MS (2008) Osmoadaptation mechanisms in prokaryotes: distribution of compatible solutes. Int Microbiol 11:151–161PubMedGoogle Scholar
  25. 25.
    Fagerbakke KM, Norland S, Heldal M (1999) The inorganic ion content of native aquatic bacteria. Can J Microbiol 45:304–311PubMedCrossRefGoogle Scholar
  26. 26.
    Fortunato C, Herfort L, Zuber P, Baptista A, Crump B (2011) Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME J 6:554–563PubMedCrossRefGoogle Scholar
  27. 27.
    Freitas S, Hatosy S, Fuhrman JA, Huse SM, Welch DB, Sogin ML, Martiny AC (2012) Global distribution and diversity of marine Verrucomicrobia. ISME J 6:1499–1505PubMedCrossRefGoogle Scholar
  28. 28.
    Fujiwara-Nagata E, Kogure K, Kita-Tsukamoto K, Wada M, Eguchi M (2006) Characteristics of Na+-dependent respiratory chain in Vibrio anguillarum, a fish pathogen, in comparison with other marine Vibrios. FEMS Microbiol Ecol 44:225–230CrossRefGoogle Scholar
  29. 29.
    Galand PE, Casamayor EO, Kirchman DL, Lovejoy C (2009) Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci U S A 106:22427–22432PubMedCrossRefGoogle Scholar
  30. 30.
    Garcia SL, McMahon KD, Martinez-Garcia M, Srivastava A, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F (2012) Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. ISME J 7(1):137–147Google Scholar
  31. 31.
    Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R, Cristina Souza de Oliveira T, Wagner Garcia J, Pellon de Miranda F, Henrique-Silva F (2011) Metagenomics of the water column in the pristine upper course of the Amazon river. PLoS One 6:e23785PubMedCrossRefGoogle Scholar
  32. 32.
    Giovannoni S, Stingl U (2005) Molecular diversity and ecology of microbial plankton. Nature 437:343–348PubMedCrossRefGoogle Scholar
  33. 33.
    Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D, Bibbs L, Eads J, Richardson TH, Noordewier M, Rappe MS, Short JM, Carrington JC, Mathur EJ (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242–1245PubMedCrossRefGoogle Scholar
  34. 34.
    Glöckner FO, Fuchs BM, Amann R (1999) Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65:3721–3726PubMedGoogle Scholar
  35. 35.
    Glockner FO, Kube M, Bauer M, Teeling H, Lombardot T, Ludwig W, Gade D, Beck A, Borzym K, Heitmann K, Rabus R, Schlesner H, Amann R, Reinhardt R (2003) Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proc Natl Acad Sci U S A 100:8298–8303PubMedCrossRefGoogle Scholar
  36. 36.
    Gomez-Consarnau L, Lindh MV, Gasol JM, Pinhassi J (2012) Structuring of bacterioplankton communities by specific dissolved organic carbon compounds. Environ Microbiol 14:2361–2378PubMedCrossRefGoogle Scholar
  37. 37.
    Gómez-Pereira PR, Fuchs BM, Alonso C, Oliver MJ, van Beusekom JEE, Amann R (2010) Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean. ISME J 4:472–487PubMedCrossRefGoogle Scholar
  38. 38.
    Gómez-Pereira PR, Schüler M, Fuchs BM, Bennke C, Teeling H, Waldmann J, Richter M, Barbe V, Bataille E, Glöckner FO (2011) Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environ Microbiol 14:52–66PubMedCrossRefGoogle Scholar
  39. 39.
    Gonzalez JM, Fernandez-Gomez B, Fernandez-Guerra A, Gomez-Consarnau L, Sanchez O, Coll-Llado M, Del Campo J, Escudero L, Rodriguez-Martinez R, Alonso-Saez L, Latasa M, Paulsen I, Nedashkovskaya O, Lekunberri I, Pinhassi J, Pedros-Alio C (2008) Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). Proc Natl Acad Sci U S A 105:8724–8729PubMedCrossRefGoogle Scholar
  40. 40.
    Grossart HP (2010) Ecological consequences of bacterioplankton lifestyles: changes in concepts are needed. Environ Microbiol Rep 2:706–714PubMedCrossRefGoogle Scholar
  41. 41.
    Grossart HP, Simon M (2007) Interactions of planktonic algae and bacteria: effects on algal growth and organic matter dynamics. Aquat Microbial Ecol 47:163CrossRefGoogle Scholar
  42. 42.
    Hahn MW, Scheuerl T, Jezberova J, Koll U, Jezbera J, Simek K, Vannini C, Petroni G, Wu QL (2012) The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living polynucleobacter population. PLoS One 7:e32772PubMedCrossRefGoogle Scholar
  43. 43.
    Hedges JI, Keil RG, Benner R (1997) What happens to terrestrial organic matter in the ocean? Organ Geochem 27:195–212CrossRefGoogle Scholar
  44. 44.
    Heldal M, Norland S, Erichsen ES, Sandaa RA, Larsen A, Thingstad F, Bratbak G (2012) Mg2+ as an indicator of nutritional status in marine bacteria. ISME J 6:524–530PubMedCrossRefGoogle Scholar
  45. 45.
    Herlemann DPR, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, Andersson AF (2011) Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J 5:1571–1579PubMedCrossRefGoogle Scholar
  46. 46.
    Hobbie JE (1988) A comparison of the ecology of planktonic bacteria in fresh and salt water. Limnol Oceanogr 750–764Google Scholar
  47. 47.
    Imae Y, Atsumi T (1989) Na+-driven bacterial flagellar motors. J Bioenerget Biomembran 21:705–716CrossRefGoogle Scholar
  48. 48.
    Jezbera J, Jezberová J, Koll U (2012) Contrasting trends in distribution of four major planktonic betaproteobacterial groups along a pH gradient of epilimnia of 72 freshwater habitats. FEMS Microbiol Ecol 81(2):467–479Google Scholar
  49. 49.
    Jiang W, Hermolin J, Fillingame RH (2001) The preferred stoichiometry of c subunits in the rotary motor sector of Escherichia coli ATP synthase is 10. Proc Natl Acad Sci U S A 98:4966–4971PubMedCrossRefGoogle Scholar
  50. 50.
    Joint I, Doney SC, Karl DM (2010) Will ocean acidification affect marine microbes? ISME J 5:1–7PubMedCrossRefGoogle Scholar
  51. 51.
    Kan J, Evans SE, Chen F, Suzuki MT (2008) Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay. Aquat Microbial Ecol 51:55CrossRefGoogle Scholar
  52. 52.
    Kent AD, Jones SE, Lauster GH, Graham JM, Newton RJ, McMahon KD (2006) Experimental manipulations of microbial food web interactions in a humic lake: shifting biological drivers of bacterial community structure. Environ Microbiol 8:1448–1459PubMedCrossRefGoogle Scholar
  53. 53.
    Kimura H, Young CR, Martinez A, DeLong EF (2011) Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium. ISME J 5:1641–1651PubMedCrossRefGoogle Scholar
  54. 54.
    Kirchman DL, Dittel AI, Malmstrom RR, Cottrell MT (2005) Biogeography of major bacterial groups in the Delaware Estuary. Limnol Oceanogr 1697–1706Google Scholar
  55. 55.
    Kirchman DL, Mitchell R (2008) Microbial ecology of the oceans. Wiley Online LibraryGoogle Scholar
  56. 56.
    Kogure K (1998) Bioenergetics of marine bacteria. Curr Opin Biotechnol 9:278–282PubMedCrossRefGoogle Scholar
  57. 57.
    Konings WN (2006) Microbial transport: adaptations to natural environments. Antonie Van Leeuwenhoek 90:325–342PubMedCrossRefGoogle Scholar
  58. 58.
    Kronberg L (1999) Content of humic substances in freshwater: Limnology of humic waters, vol. 9–10. Leiden, The NetherlandsGoogle Scholar
  59. 59.
    Krulwich TA (1995) Alkaliphiles: ’basic’ molecular problems of pH tolerance and bioenergetics. Mol Microbiol 15:403–410PubMedCrossRefGoogle Scholar
  60. 60.
    Kujawinski EB (2011) The impact of microbial metabolism on marine dissolved organic matter. Ann Rev Mar Sci 3:567–599PubMedCrossRefGoogle Scholar
  61. 61.
    Labutti K, Sikorski J, Schneider S, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Tindall BJ, Rohde M, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A (2010) Complete genome sequence of Planctomyces limnophilus type strain (Mu 290). Stand Genomic Sci 3:47–56PubMedCrossRefGoogle Scholar
  62. 62.
    Lavik G, Stuhrmann T, Bruchert V, Van der Plas A, Mohrholz V, Lam P, Mussmann M, Fuchs BM, Amann R, Lass U, Kuypers MMM (2009) Detoxification of sulphidic African shelf waters by blooming chemolithotrophs. Nature 457:581–586PubMedCrossRefGoogle Scholar
  63. 63.
    Lee CE, Bell MA (1999) Causes and consequences of recent freshwater invasions by saltwater animals. Trends Ecol Evol 14:284–288PubMedCrossRefGoogle Scholar
  64. 64.
    Lee KC, Webb RI, Janssen PH, Sangwan P, Romeo T, Staley JT, Fuerst JA (2009) Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes. BMC Microbiol 9:5PubMedCrossRefGoogle Scholar
  65. 65.
    Logan BE, Grossart HP, Simon M (1994) Direct observation of phytoplankton, TEP and aggregates on polycarbonate filters using brightfield microscopy. J Plankton Res 16:1811–1815CrossRefGoogle Scholar
  66. 66.
    Logares R, Bråte J, Heinrich F, Shalchian-Tabrizi K, Bertilsson S (2010) Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11). Mol Biol Evol 27:347–357PubMedCrossRefGoogle Scholar
  67. 67.
    Lorenz MG, Aardema BW, Wackernagel W (1988) Highly efficient genetic transformation of Bacillus subtilis attached to sand grains. J Gen Microbiol 134:107–112PubMedGoogle Scholar
  68. 68.
    Lorenz MG, Wackernagel W (1990) Natural genetic transformation of Pseudomonas stutzeri by sand-adsorbed DNA. Arch Microbiol 154:380–385PubMedCrossRefGoogle Scholar
  69. 69.
    Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proc Natl Acad Sci U S A 104:11436–11440PubMedCrossRefGoogle Scholar
  70. 70.
    Maberly SC (2008) Diel, episodic and seasonal changes in pH and concentrations of inorganic carbon in a productive lake. Freshwater Biol 35:579–598CrossRefGoogle Scholar
  71. 71.
    MacLeod RA (1965) The question of the existence of specific marine bacteria. Bacteriol Rev 29:9Google Scholar
  72. 72.
    Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PS, Reitenga KG, Xie G, Poulton NJ, Lluesma Gomez M, Masland DE, Thompson B, Bellows WK, Ziervogel K, Lo CC, Ahmed S, Gleasner CD, Detter CJ, Stepanauskas R (2012) Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS One 7:e35314PubMedCrossRefGoogle Scholar
  73. 73.
    Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102–112PubMedCrossRefGoogle Scholar
  74. 74.
    McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B, Rhodes RG, Goltsman E, Wang W, Xu J, Hunnicutt DW, Staroscik AM, Hoover TR, Cheng YQ, Stein JL (2009) Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol 75:6864–6875PubMedCrossRefGoogle Scholar
  75. 75.
    Moliner C, Fournier PE, Raoult D (2010) Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution. FEMS Microbiol Rev 34:281–294PubMedCrossRefGoogle Scholar
  76. 76.
    Morris RM, Rappé MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ (2002) SAR 11 clade dominates ocean surface bacterioplankton communities. Nature 420:806–810PubMedCrossRefGoogle Scholar
  77. 77.
    Mou X, Sun S, Edwards RA, Hodson RE, Moran MA (2008) Bacterial carbon processing by generalist species in the coastal ocean. Nature 451:708–711PubMedCrossRefGoogle Scholar
  78. 78.
    Mulkidjanian AY, Dibrov P, Galperin MY (2008) The past and present of sodium energetics: may the sodium-motive force be with you. Biochim Biophys Acta 1777:985–992PubMedCrossRefGoogle Scholar
  79. 79.
    Naughton LM, Blumerman SL, Carlberg M, Boyd EF (2009) Osmoadaptation among Vibrio species and unique genomic features and physiological responses of Vibrio parahaemolyticus. Appl Environ Microbiol 75:2802–2810PubMedCrossRefGoogle Scholar
  80. 80.
    Newton RJ, Griffin LE, Bowles KM, Meile C, Gifford S, Givens CE, Howard EC, King E, Oakley CA, Reisch CR (2010) Genome characteristics of a generalist marine bacterial lineage. ISME J 4:784–798PubMedCrossRefGoogle Scholar
  81. 81.
    Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S (2011) A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 75:14–49PubMedCrossRefGoogle Scholar
  82. 82.
    Newton RJ, Jones SE, Helmus MR, McMahon KD (2007) Phylogenetic ecology of the freshwater Actinobacteria acI lineage. Appl Environ Microbiol 73:7169–7176PubMedCrossRefGoogle Scholar
  83. 83.
    Newton RJ, McMahon KD (2011) Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake. Environ Microbiol 13:887–899Google Scholar
  84. 84.
    Nishimura Y, Kim C, Nagata T (2005) Vertical and seasonal variations of bacterioplankton subgroups with different nucleic Acid contents: possible regulation by phosphorus. Appl Environ Microbiol 71:5828–5836PubMedCrossRefGoogle Scholar
  85. 85.
    Nold S, Zwart G (1998) Patterns and governing forces in aquatic microbial communities. Aquat Ecol 32:17–35CrossRefGoogle Scholar
  86. 86.
    Oh HM, Giovannoni SJ, Lee K, Ferriera S, Johnson J, Cho JC (2009) Complete genome sequence of Robiginitalea biformata HTCC2501. J Bacteriol 191:7144–7145PubMedCrossRefGoogle Scholar
  87. 87.
    Oh HM, Kang I, Ferriera S, Giovannoni SJ, Cho JC (2010) Complete genome sequence of Croceibacter atlanticus HTCC2559T. J Bacteriol 192:4796–4797PubMedCrossRefGoogle Scholar
  88. 88.
    Oh S, Caro-Quintero A, Tsementzi D, DeLeon-Rodriguez N, Luo C, Poretsky R, Konstantinidis KT (2011) Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl Environ Microbiol 77:6000–6011PubMedCrossRefGoogle Scholar
  89. 89.
    Oren A (2001) The bioenergetic basis for the decrease in metabolic diversity at increasing salt concentrations: implications for the functioning of salt lake ecosystems. Hydrobiologia 466:61–72CrossRefGoogle Scholar
  90. 90.
    Oren A (2008) Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst 4:13CrossRefGoogle Scholar
  91. 91.
    Penn K, Jensen PR (2012) Comparative genomics reveals evidence of marine adaptation in Salinispora species. BMC Genomics 13:86PubMedCrossRefGoogle Scholar
  92. 92.
    Pernthaler J, Posch T, Simek K, Vrba J, Pernthaler A, Glöckner FO, Nübel U, Psenner R, Amann R (2001) Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture. Appl Environ Microbiol 67:2145–2155PubMedCrossRefGoogle Scholar
  93. 93.
    Polz MF, Hunt DE, Preheim SP, Weinreich DM, Polz MF, Hunt DE, Preheim SP, Weinreich DM (2006) Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philo Trans R Soc B: Biol Sci 361:2009–2021CrossRefGoogle Scholar
  94. 94.
    Rappe MS, Vergin K, Giovannoni SJ (2000) Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol Ecol 33:219–232PubMedCrossRefGoogle Scholar
  95. 95.
    Riemann L, Grossart HP (2008) Elevated lytic phage production as a consequence of particle colonization by a marine Flavobacterium (Cellulophaga sp.). Microbiol Ecol 56:505–512CrossRefGoogle Scholar
  96. 96.
    Sarmento H, Gasol JM (2012) Use of phytoplankton-derived dissolved organic carbon by different types of bacterioplankton. Environ Microbiol 14:2348–2360PubMedCrossRefGoogle Scholar
  97. 97.
    Schwalbach MS, Tripp HJ, Steindler L, Smith DP, Giovannoni SJ (2010) The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity. Environ Microbiol 12:490–500PubMedCrossRefGoogle Scholar
  98. 98.
    Semenov AM (1991) Physiological bases of oligotrophy of microorganisms and the concept of microbial community. Microbial Ecol 22:239–247CrossRefGoogle Scholar
  99. 99.
    Shea K, Chesson P (2002) Community ecology theory as a framework for biological invasions. Trends Ecol Evol 17:170–176CrossRefGoogle Scholar
  100. 100.
    Simon M, Grossart HP, Schweitzer B, Ploug H (2002) Microbial ecology of organic aggregates in aquatic ecosystems. Aquat Microbial Ecol 28:175–211CrossRefGoogle Scholar
  101. 101.
    Skippington E, Ragan MA (2011) Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol Rev 35:707–735PubMedCrossRefGoogle Scholar
  102. 102.
    Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241–244PubMedCrossRefGoogle Scholar
  103. 103.
    Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103:12115–12120PubMedCrossRefGoogle Scholar
  104. 104.
    Steindler L, Schwalbach MS, Smith DP, Chan F, Giovannoni SJ (2011) Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration. PLoS One 6:e19725.PubMedCrossRefGoogle Scholar
  105. 105.
    Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, Kassabgy M, Huang S, Mann AJ, Waldmann J, Weber M, Klindworth A, Otto A, Lange J, Bernhardt J, Reinsch C, Hecker M, Peplies J, Bockelmann FD, Callies U, Gerdts G, Wichels A, Wiltshire KH, Glockner FO, Schweder T, Amann R (2012) Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336:608–611PubMedCrossRefGoogle Scholar
  106. 106.
    Tokuda H, Asano M, Shimamura Y, Unemoto T, Sugiyama S, Imae Y (1988) Roles of the respiratory Na+ pump in bioenergetics of Vibrio alginolyticus. J Biochem 103:650–655PubMedGoogle Scholar
  107. 107.
    Tokuda H, Nakamura T, Unemoto T (1981) Potassium ion is required for the generation of pH-dependent membrane potential and delta pH by the marine bacterium Vibrio alginolyticus. Biochemistry 20:4198–4203PubMedCrossRefGoogle Scholar
  108. 108.
    Tokuda H, Unemoto T (1982) Characterization of the respiration-dependent Na+ pump in the marine bacterium Vibrio alginolyticus. J Biol Chem 257:10007–10014PubMedGoogle Scholar
  109. 109.
    Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5:e1000344PubMedCrossRefGoogle Scholar
  110. 110.
    Unemoto T, Akagawa A, Mizugaki M, Hayashi M (1992) Distribution of Na+-dependent respiration and a respiration-driven electrogenic Na+ pump in moderately halophilic bacteria. J General Microbiol 138:1999–2005CrossRefGoogle Scholar
  111. 111.
    Ward N, Rainey FA, Stackebrandt E, Schlesner H (1995) Unraveling the extent of diversity within the order Planctomycetales. Appl Environ Microbiol 61:2270–2275PubMedGoogle Scholar
  112. 112.
    Wetzel R (2001) Limnology, 3 E. Lake and River Ecosystems, vol 850. Academic Press, San Diego, CAGoogle Scholar
  113. 113.
    Wiedenbeck J, Cohan FM (2011) Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35:957–976PubMedCrossRefGoogle Scholar
  114. 114.
    Woebken D, Teeling H, Wecker P, Dumitriu A, Kostadinov I, Delong EF, Amann R, Glockner FO (2007) Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME J 1:419–435PubMedCrossRefGoogle Scholar
  115. 115.
    Yannarell AC, Triplett EW (2005) Geographic and environmental sources of variation in lake bacterial community composition. Appl Environ Microbiol 71:227–239PubMedCrossRefGoogle Scholar
  116. 116.
    Zeng Y, Kasalicky V, Simek K, Koblizek M (2012) Genome sequences of two freshwater betaproteobacterial isolates, limnohabitans species strains rim28 and rim47, indicate their capabilities as both photoautotrophs and ammonia oxidizers. J Bacteriol 194:6302–6303PubMedCrossRefGoogle Scholar
  117. 117.
    Zhao JS, Deng Y, Manno D, Hawari J (2010) Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation. PloS One 5:e9109PubMedCrossRefGoogle Scholar
  118. 118.
    Zwart G, Crump BC, Kamst-van Agterveld MP, Hagen F, Han SK (2002) Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microbial Ecol 28:141–155CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • David A Walsh
    • 1
    • 2
  • Josine Lafontaine
    • 1
  • Hans-Peter Grossart
    • 3
    • 4
  1. 1.Department of BiologyConcordia UniversityMontrealCanada
  2. 2.Integrated Microbial Biodiversity ProgramCanadian Institute for Advanced ResearchTorontoCanada
  3. 3.Department Limnology of Stratified LakesLeibniz-Institute of Freshwater Ecology and Inland FisheriesStechlinGermany
  4. 4.Institute of Biochemistry and BiologyPotsdam UniversityPotsdamGermany

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