Skip to main content
SpringerLink
Log in
Book cover

The Prokaryotes pp 3–30Cite as

Structure and Function of Microbial Communities

  • Reference work entry

Abstract

Much of our current understanding of microbiology derives from laboratory-based studies of pure cultures, largely motivated by societal needs of improved understanding of the complex physiology of bacteria as relates to pathogenicity, food spoilage, and commercial and medical product development. Such reductionist studies were also used to infer the role of microorganisms in important global and local processes. However, devoid of natural biotic associations, it is increasingly clear that laboratory cultivation conditions do not reflect in situ lifestyles. As Darwin suggested, the primary driver for change is biotic interaction and not changes in the physical/chemical environment. Thus, to provide a more complete understanding of bacteria, it is essential to fully resolve the natural drivers shaping the structure and function of microbial communities. The main thrust of this chapter is to examine the evolutionary, biotic, abiotic, and temporal dimensions that shape microbial communities through time and space. To this end, this chapter strives to integrate the classical with more recently developed methods of inquiry that together are bringing predictive understanding of natural communities of microorganisms.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   599.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   549.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Abboudi M, Jeffrey WH, Ghiglione JF, Pujo-Pay M, Oriol L, Sempere R, Charriere B, Joux F (2008) Effects of photochemical transformations of dissolved organic matter on bacterial metabolism and diversity in three contrasting coastal sites in the Northwestern Mediterranean sea during summer. Microb Ecol 55:344–357

    Article  PubMed  CAS  Google Scholar 

  • Aeckersberg F, Lupp C, Feliciano B, Ruby EG (2001) Vibrio fischeri outer membrane protein OmpU plays a role in normal symbiotic colonization. J Bacteriol 183:6590–6597

    Article  PubMed  CAS  Google Scholar 

  • Alldredge AL, Cohen Y (1987) Can microscale chemical patches persist in the sea? Microelectrode study of marine snow, fecal pellets. Science 235:689–691

    Article  PubMed  CAS  Google Scholar 

  • Alldredge AL, Silver MW (1988) Characteristics, dynamics and significance of marine snow. Prog Oceanogr 20:41–82

    Article  Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in-situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    PubMed  CAS  Google Scholar 

  • Amann R, Ludwig W (2000) Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol Rev 24:555–565

    Article  PubMed  CAS  Google Scholar 

  • Andersson AF, Banfield JF (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320:1047–1050

    Article  PubMed  CAS  Google Scholar 

  • Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM et al (2011) Enterotypes of the human gut microbiome. Nature 473:174–180

    Article  PubMed  CAS  Google Scholar 

  • Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D (2011) Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 474:604–608

    Article  PubMed  CAS  Google Scholar 

  • Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA, Thingstad F (1983) The ecological role of water column microbes in the sea. Mar Ecol Prog Ser 10:257–263

    Article  Google Scholar 

  • Bahr M, Hobbie JE, Sogin ML (1996) Bacterial diversity in an Arctic lake: a freshwater SAR11 cluster. Aquat Microb Ecol 11:271–277

    Article  Google Scholar 

  • Bamford CV, D’Mello A, Nobbs AH, Dutton LC, Vickerman MM, Jenkinson HF (2009) Streptococcus gordonii modulates Candida albicans biofilm formation through intergeneric communication. Infect Immun 77:3696–3704

    Article  PubMed  CAS  Google Scholar 

  • Barton AD, Dutkiewicz S, Flierl G, Bragg J, Follows MJ (2010) Patterns of diversity in marine phytoplankton. Science 327:1509–1511

    Article  PubMed  CAS  Google Scholar 

  • Bates JM, Mittge E et al (2006) Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation. Dev Biol 297:374–386

    Article  PubMed  CAS  Google Scholar 

  • Baumann P (2005) Biology of bacteriocyte-associated endosymbionts of plant sap-sucking insects. Annu Rev Microbiol 59:155–189

    Article  PubMed  CAS  Google Scholar 

  • Baumann P, Baumann L, Lai CY, Roubakhsh D, Moran NA, Clark MA (1995) Genetics, physiology, and evolutionary relationships of the genus Buchnera intracellular symbionts of aphids. Annu Rev Microbiol 49:55–94

    Article  PubMed  CAS  Google Scholar 

  • Behrenfeld MJ, O'Malley RT, Siegel DA, McClain CR, Sarmiento JL, Feldman GC, Milligan AJ, Falkowski PG, Letelier RM, Boss ES (2006) Climate-driven trends in contemporary ocean productivity. Nature 444:752–755

    Article  PubMed  CAS  Google Scholar 

  • Beijerinck MW (1913) De infusies en de ontdekking der backteriën. In Jaarboek van de Koninklijke Akademie v. Wetenschappen. Amsterdam, Müller

    Google Scholar 

  • Bergh O, Borsheim KY, Bratbak G, Heldal M (1989) High abundance of viruses found in aquatic environments. Nature 340:467–468

    Article  PubMed  CAS  Google Scholar 

  • Blackburn N, Fenchel T (1999) Influence of bacteria, diffusion and sheer on microscale nutrient patches, and implications for bacterial chemotaxis. Mar Ecol Prog Ser 189:1–7

    Article  CAS  Google Scholar 

  • Blackburn N, Fenchel T, Mitchell J (1998) Microscale nutrient patches in planktonic habitats shown by chemotactic bacteria. Science 282:2254–2256

    Article  PubMed  CAS  Google Scholar 

  • Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, Gieseke A, Amann R, Jorgensen BB, Witte U, Pfannkuche O (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623–626

    Article  PubMed  CAS  Google Scholar 

  • Booth MG, Jeffrey WH, Miller RV (2001) RecA expression in response to solar UVR in the marine bacterium Vibrio natriegens. Microb Ecol 42:531–539

    Article  PubMed  CAS  Google Scholar 

  • Bouvier T, del Giorgio PA (2007) Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol 9:287–297

    Article  PubMed  CAS  Google Scholar 

  • Braschler TR, Merino S, Tomas JM, Graf J (2003) Complement resistance is essential for colonization of the digestive tract of Hirudo medicinalis by Aeromonas strains. Appl Environ Microbiol 69:4268–4271

    Article  PubMed  CAS  Google Scholar 

  • Brauman A (2000) Effect of gut transit and mound deposit on soil organic matter transformations in the soil feeding termite: a review. Eur J Soil Biol 36:117–125

    Article  Google Scholar 

  • Breznak JA (1982) Intestinal microbiota of termites and other xylophagous insects. Annu Rev Microbiol 36:323–343

    Article  PubMed  CAS  Google Scholar 

  • Bright M, Bulgheresi S (2010) A complex journey: transmission of microbial symbionts. Nat Rev Microbiol 8:218–230

    Article  PubMed  CAS  Google Scholar 

  • Bright M, Sorgo A (2003) Ultrastructural reinvestigation of the trophosome in adults of Riftia pachyptila (Annelida, Siboglinidae). Invertebr Biol 122:347–368

    Article  Google Scholar 

  • Brochier-Armanet C, Gribaldo S, Forterre P (2012) Spotlight on the thaumarchaeota. ISME J 6:227–230

    Article  PubMed  CAS  Google Scholar 

  • Brownlie JC, Johnson KN (2009) Symbiont-mediated protection in insect hosts. Trends Microbiol 17:348–354

    Article  PubMed  CAS  Google Scholar 

  • Brune A, Friedrich M (2000) Microecology of the termite gut: structure and function on a microscale. Curr Opin Microbiol 3:263–269

    Article  PubMed  CAS  Google Scholar 

  • Brusseau GA, Rittmann BE, Stahl DA (1998) Addressing the microbial ecology of marine biofilms. In: Cooksey KE (ed) Molecular approaches to the study of the ocean. Chapman and Hall, New York

    Google Scholar 

  • Bryant MP, Wolin EA, Wolin MJ, Wolfe RS (1967) Methanobacillus omelianskii: a symbiotic association of two species of bacteria. Arch Microbiol 59:20–31

    CAS  Google Scholar 

  • Bryant MP, Campbell LL, Reddy CA, Crabill MR (1977) Growth of Desulfovibrio in lactate or ethanol media low in sulfate in association with H2-utilizing methanogenic bacteria. Appl Environ Microbiol 33:1162–1169

    PubMed  CAS  Google Scholar 

  • Buttner M, Xie DL, Nelson H, Pinther W, Hauska G, Nelson N (1992) Photosynthetic reaction center genes in green sulfur bacteria and in photosystem-1 are related. Proc Natl Acad Sci 89:8135–8139

    Article  PubMed  CAS  Google Scholar 

  • Button DK (1994) The physical base of marine bacterial ecology. Microb Ecol 28:273–285

    Article  CAS  Google Scholar 

  • Calbet A (2008) The trophic roles of microzooplankton in marine systems. Ices J Marine Sci 65:325–331

    Article  Google Scholar 

  • Canfield DE, DeMarais DJ (1991) Aerobic sulfate reduction in microbial mats. Science 251:1471–1473

    Article  PubMed  CAS  Google Scholar 

  • Canfield DE, Marais DJD (1993) Biogeochemical cycles of carbon, sulfur, and free oxygen in a microbial mat. Geochim Cosmochim Acta 57:3971–3984

    Article  PubMed  CAS  Google Scholar 

  • Cantalupo PG, Calgua B, Zhao GY, Hundesa A, Wier AD, Katz JP, Grabe M, Hendrix RW, Girones R, Wang D, Pipas JM (2011) Raw sewage harbors diverse viral populations. Mbio 2

    Google Scholar 

  • Carlson CA, Morris R, Parsons R, Treusch AH, Giovannoni SJ, Vergin K (2009) Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea. ISME J 3:283–295

    Article  PubMed  CAS  Google Scholar 

  • Cary SC, Cottrell MT, Stein JL, Camacho F, Desbruyeres D (1997) Molecular identification and localization of filamentous symbiotic bacteria associated with the hydrothermal vent annelid Alvinella pompejana. Appl Environ Microbiol 63:1124–1130

    PubMed  CAS  Google Scholar 

  • Casamayor EO, Pedros-Alio C, Muyzer G, Amann R (2002) Microheterogeneity in 16 S ribosomal DNA defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations. Appl Environ Microbiol 68:1706–1714

    Article  PubMed  CAS  Google Scholar 

  • Casjens S (1998) The diverse and dynamic structure of bacterial genomes. Annu Rev Genet 32:339–445

    Article  PubMed  CAS  Google Scholar 

  • Characklis WG, Marshall KC (1990) Biofilms. Wiley, New York

    Google Scholar 

  • Chavez FP, Messie M, Pennington JT (2011) Marine primary production in relation to climate variability and change. Ann Rev Marine Sci 3:227–260

    Article  Google Scholar 

  • Cheesman SE, Guillemin K (2007) We know you are in there: conversing with the indigenous gut microbiota. Res Microbiol 158:2–9

    Article  PubMed  Google Scholar 

  • Chen L, Liu MY, Legall J, Fareleira P, Santos H, Xavier AV (1993) Rubredoxin oxidase, a new flavo-hemo-protein, is the site of oxygen reduction to water by the strict anaerobe desulfovibrio-gigas. Biochem Bioph Res Commun 193:100–105

    Article  CAS  Google Scholar 

  • Childress JJ, Felbeck H, Somero GN (1987) Symbiosis in the deep-sea. Sci Am 256:114–130

    Article  Google Scholar 

  • Cho BC, Azam F (1988) Major role of bacteria in biogeochemical fluxes in the oceans interior. Nature 332:441–443

    Article  CAS  Google Scholar 

  • Ciche TA, Darby C et al (2006) Dangerous liaisons: the symbiosis of entomopathogenic nematodes and bacteria. Biol Control 38:22–46

    Article  Google Scholar 

  • Cohen Y, Rosenberg E (1989) Microbial mats: physiological ecology of benthic microbial communities. American Society of Microbiology, Washington, DC

    Google Scholar 

  • Coleman ML, Sullivan MB, Martiny AC, Steglich C, Barry K, DeLong EF, Chisholm SW (2006) Genomic islands and the ecology and evolution of Prochlorococcus. Science 311:1768–1770

    Article  PubMed  CAS  Google Scholar 

  • Conrad TM, Lewis NE, Palsson BO (2011) Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol 7

    Google Scholar 

  • Cossart P, Boquet P, Normark S, Rappuoli R (1996) Cellular microbiology emerging. Science 271:315–316

    Article  PubMed  CAS  Google Scholar 

  • Crump BC, Kling GW, Bahr M, Hobbie JE (2003) Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl Environ Microbiol 69:2253–2268

    Article  PubMed  Google Scholar 

  • Crump BC, Peterson BJ, Raymond PA, Amon RMW, Rinehart A, McClelland JW, Holmes RM (2009) Circumpolar synchrony in big river bacterioplankton. Proc Natl Acad Sci USA 106:21208–21212

    Article  PubMed  CAS  Google Scholar 

  • Cruz-Martinez K, Suttle KB, Brodie EL, Power ME, Andersen GL, Banfield JF (2009) Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J 3:738–744

    Article  PubMed  CAS  Google Scholar 

  • Currie CR, Scott JA, Summerbell RC, Malloch D (1999) Fungus growing ants use antibiotic producing bacteria to control garden parasites. Nature 398:701–704

    Article  CAS  Google Scholar 

  • Currie CR, Poulsen M et al (2006) Coevolved crypts and exocrine glands support mutualistic bacteria in fungus-growing ants. Science 311:81–83

    Article  PubMed  CAS  Google Scholar 

  • Danovaro R, Corinaldesi C, Dell'Anno A, Fuhrman JA, Middelburg JJ, Noble RT, Suttle CA (2011) Marine viruses and global climate change. FEMS Microbiol Rev 35:993–1034

    Article  PubMed  CAS  Google Scholar 

  • Darby AC, Chandler SM et al (2005) Aphid-symbiotic bacteria cultured in insect cell lines. Appl Environ Microbiol 71:4833–4839

    Article  PubMed  CAS  Google Scholar 

  • Darwin C (1969) On the origin of species: facsimile edition. Harvard University Press, Cambridge, MA

    Google Scholar 

  • Daubin V, Moran NA, Ochman H (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301:829–832

    Article  PubMed  CAS  Google Scholar 

  • Davidson SK, Allen SW, Lim GE, Anderson CM, Haygood MG (2001) Evidence for the biosynthesis of bryostatins by the bacterial symbiont Candidatus endobugula sertula of the bryozoan Bugula neritina. Appl Environ Microbiol 67:4531–4537

    Article  PubMed  CAS  Google Scholar 

  • Davidson SK, Koropatnick TA, Kossmehl R, Sycuro L, McFall-Ngai MJ (2004) No means ‘yes’ in the squid-vibrio symbiosis: nitric oxide during the initial stages of a beneficial association. Cell Microbiol 6:1139–1151

    Article  PubMed  CAS  Google Scholar 

  • Davidson SK, Stahl DA (2008) Selective recruitment of bacteria during embryogenesis of an earthworm. ISME J 2:510–518

    Article  PubMed  Google Scholar 

  • Davies DG, Parsek MR, Pearson JP, Iglewski BH, Costerton JW, Greenberg EP (1998) The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 280:295–298

    Article  PubMed  CAS  Google Scholar 

  • De Bary A (1879) Die erscheinumg der symbiose: Vortrag gehalten auf der Versammlung Deutscher Naturforscher und Aerzte zu Cassel. Verlag von Karl J, Trübner, Strasburg

    Google Scholar 

  • Decho AW, Herndl GJ (1995) Microbial activities and the transformation of organic matter within mucilaginous material. Sci Total Environ 165:33–42

    Article  CAS  Google Scholar 

  • Dekas AE, Poretsky RS, Orphan VJ (2009) Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. Science 326:422–426

    Article  PubMed  CAS  Google Scholar 

  • Delong EF, Pace NR (2001) Environmental diversity of Bacteria and Archaea. Syst Biol 50:470–481

    Article  PubMed  CAS  Google Scholar 

  • Delong EF, Frankel RB, Bazylinski DA (1993) Multiple evolutionary origins of magnetotaxis in bacteria. Science 259:803–806

    Article  PubMed  CAS  Google Scholar 

  • Delong EF, Wu KY, Prézelin BB, Jovine RVM (1994) High abundance of archaea in Antarctic marine picoplankton. Nature 371:695–697

    Article  PubMed  CAS  Google Scholar 

  • DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM (2006) Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311:496–503

    Article  PubMed  CAS  Google Scholar 

  • Deming JW, Reysenbach AL, Macko SA, Smith CR (1997) Evidence for the microbial basis of a chemoautotrophic invertebrate community at a whale fall on the deep seafloor: bone colonizing bacteria and invertebrate endosymbionts. Microsc Res Techniq 37:162–170

    Article  CAS  Google Scholar 

  • Dermott R, Legner M (2002) Dense mat-forming bacterium Thioploca ingrica (Beggiatoaceae) in eastern Lake Ontario. Implications to the benthic food web. J Great Lakes Res 28:688–697

    Article  CAS  Google Scholar 

  • Devereux R, Delaney M, Widdel F, Stahl DA (1989) Natural relationships among sulfate reducing eubacteria. J Bacteriol 171:6689–6695

    PubMed  CAS  Google Scholar 

  • Devereux R, He SH, Doyle CL, Orkland S, Stahl DA, Legall J, Whitman WB (1990) Diversity and origin of desulfovibrio specie: phylogenetic definition of a family. J Bacteriol 172:3609–3619

    PubMed  CAS  Google Scholar 

  • Dillon JG, Miller S, Bebout B, Hullar M, Pinel N, Stahl DA (2009) Spatial and temporal variability in a stratified hypersaline microbial mat community. FEMS Microbiol Ecol 68:46–58

    Article  PubMed  CAS  Google Scholar 

  • Distel DL, Beaudoin DJ, Morrill W (2002) Coexistence of multiple proteobacterial endosymbionts in the gills of the wood-boring bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae). Appl Environ Microbiol 68:6292–6299

    Article  PubMed  CAS  Google Scholar 

  • Dobrindt U, Agerer F, Michaelis K, Janka A, Buchrieser C, Samuelson M, Svanborg C, Gottschalk G, Karch H, Hacker J (2003) Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J Bacteriol 185:1831–1840

    Article  PubMed  CAS  Google Scholar 

  • Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124–2128

    Article  PubMed  CAS  Google Scholar 

  • Douglas AE (1996) Reproductive failure and the free amino acid pools in pea aphids (Acyrthosiphon pisum) lacking symbiotic bacteria. J Insevt Physiol 42:247–255

    Article  CAS  Google Scholar 

  • Douglas AE (1997) Parallels and contrasts between symbiotic bacteria and bacterial-derived organelles: evidence from Buchnera, the bacterial symbiont of aphids. FEMS Microbiol Ecol 24:1–9

    Article  CAS  Google Scholar 

  • Douglas AE (2009) The microbial dimension in insect nutritional ecology. Funct Ecol 23:38–47

    Article  Google Scholar 

  • Dubilier N, Mulders C et al (2001) Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm. Nature 411:298–302

    Article  PubMed  CAS  Google Scholar 

  • Dubilier N, Bergin C et al (2008) Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol 6:725–740

    Article  PubMed  CAS  Google Scholar 

  • Dulla G, Go R et al (2012) Verminephrobacter eiseniae type IV pili and flagella are required to colonize earthworm nephridia. ISME J 6:1166–1175

    Google Scholar 

  • Dumbrell AJ, Ashton PD, Aziz N, Feng G, Nelson M, Dytham C, Fitter AH, Helgason T (2011) Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytol 190:794–804

    Article  PubMed  CAS  Google Scholar 

  • Dvornyk V, Knudsen B (2005) Functional divergence of the circadian clock proteins in prokaryotes. Genetica 124:247–254

    Article  PubMed  Google Scholar 

  • Elena SF, Lenski RE (2003) Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4:457–469

    Article  PubMed  CAS  Google Scholar 

  • Faulkner J, Unson MD, Bewley CA (1994) The chemistry of some sponges and their symbionts. Pure Appl Chem 66:1983–1990

    Article  CAS  Google Scholar 

  • Fenchel T, Finlay BJ (1995) Ecology and evolution in anoxic worlds. Oxford University Press, Oxford

    Google Scholar 

  • Fenchel T, Glud RN (1998) Veil architecture in a sulphide-oxidizing bacterium enhances countercurrent flux. Nature 394:367–369

    Article  CAS  Google Scholar 

  • Fenchel T (2002) Microbial behavior in a heterogeneous world. Science 296:1068–1071

    Article  PubMed  CAS  Google Scholar 

  • Ferdelman TG, Lee C, Pantoja S, Harder J, Bebout BM, Fossing H (1997) Sulfate reduction and methanogenesis in a thioploca dominated sediment off the coast of Chile. Geochim Cosmochim Acta 61:3065–3079

    Article  CAS  Google Scholar 

  • Ffrench-Constant R, Waterfield N, Daborn P, Joyce S, Bennett H, Au C, Dowling A, Boundy S, Reynolds S, Clarke D (2003) Photorhabdus: towards a functional genomic analysis of a symbiont and pathogen. FEMS Microbiol Rev 26:433–456

    Article  PubMed  CAS  Google Scholar 

  • Fiedler PC (2002) Environmental change in the eastern tropical Pacific Ocean: review of ENSO and decadal variability. Mar Ecol Prog Ser 244:265–283

    Article  Google Scholar 

  • Field KG, Gordon D, Wright T, Rappe M, Urbach E, Vergin K, Giovannoni SJ (1997) Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl Environ Microbiol 63:63–70

    PubMed  CAS  Google Scholar 

  • Findlay RH, Yeates C, Hullar MA, Stahl DA, Kaplan LA (2008) Biome-level biogeography of streambed microbiota. Appl Environ Microbiol 74:3014–3021

    Article  PubMed  CAS  Google Scholar 

  • Fisher CR, Childress JJ, Sanders NK (1988) The role of Vestimentiferan hemoglobin in providing an environment suitable for chemoautotrophic sulfide-oxidizing endosymbionts. Symbiosis 5:229–246

    CAS  Google Scholar 

  • Fisher CR (1990) Chemoautotrophic and methanotrophic symbioses in marine-invertebrates. Rev Aquat Sci 2:399–436

    CAS  Google Scholar 

  • Fisher CR (1995) Towards and appreciation of hydrothermal-vent animals: their environment, physiological ecology, and tissue stable isotope values. In: Humphris SE, Zierenberg RA, Multineaux LS, Thompson RE (ed) Seafloor hydrothermal systems: physical, chemical, biological, and geological interactions. AGU, Washington DC, pp 297–316

    Google Scholar 

  • Follows MJ, Dutkiewicz S (2011) Modeling diverse communities of marine microbes. Ann Rev Mar Sci 3(3):427–451

    Article  PubMed  Google Scholar 

  • Follows MJ, Dutkiewicz S, Grant S, Chisholm SW (2007) Emergent biogeography of microbial communities in a model ocean. Science 315:1843–1846

    Article  PubMed  CAS  Google Scholar 

  • Fossing H, Gallardo VA, Jorgensen BB, Huttel M, Nielsen LP, Schulz H, Canfield DE, Forster S, Glud RN, Gundersen JK, Kuver J, Ramsing NB, Teske A, Thamdrup B, Ulloa O (1995) Concentration and transport of nitrate by the mat-forming sulfur bacterium Thioploca. Nature 374:713–715

    Article  CAS  Google Scholar 

  • Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148–149

    Article  PubMed  CAS  Google Scholar 

  • Fuhrman JA, Mccallum K, Davis AA (1993) Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol 59:1294–1302

    PubMed  CAS  Google Scholar 

  • Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399:541–548

    Article  PubMed  CAS  Google Scholar 

  • Fuhrman JA (2000) Impact of viruses on bacterial processes. In: Kirchman DL (ed) Microbial ecology of the sea. Wiley-Liss, New York, pp 327–350

    Google Scholar 

  • Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL, Brown JH (2008) A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci USA 105:7774–7778

    Article  PubMed  CAS  Google Scholar 

  • Fuhrman JA (2009) Microbial community structure and its functional implications. Nature 459:193–199

    Article  PubMed  CAS  Google Scholar 

  • Fujiwara Y, Kato C, Masui N, Fujikura K, Kojima S (2001) Dual symbiosis in the cold seep thyasirid clam Maorithyas hadalis from the hadal zone in the Japan Trench, western Pacific. Mar Ecol-Prog Ser 214:151–159

    Article  Google Scholar 

  • Fukui M, Teske A, Assmus B (1999) Physiology, phylogenetic relationships, and ecology of filamentous sulfate-reducing bacteria (genus Desulfonema). Arch Microbiol 172:193–203

    Article  PubMed  CAS  Google Scholar 

  • Fuqua WC, Winans SC, Greenberg EP (1994) Quorum sensing in bacteria: the LuxR-LuxI family of cell density responsive transcriptional regulators. J Bacteriol 176:269–275

    PubMed  CAS  Google Scholar 

  • Fuqua C, Winans SC, Greenberg EP (1996) Census and consensus in bacterial ecosystems: the LuxR-LuxI family of quorum-sensing transcriptional regulators. Annu Rev Microbiol 50:727–751

    Article  PubMed  CAS  Google Scholar 

  • Fuqua C, Parsek MR, Greenberg EP (2001) Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu Rev Genet 35:439–468

    Article  PubMed  CAS  Google Scholar 

  • Fuqua C, Greenberg EP (2002) Listening in on bacteria: acyl-homoserine lactone signaling. Nature Rev Mole Cell Biol 3:685–695

    Article  CAS  Google Scholar 

  • Gallardo CS (1977) Two modes of development in morph-species Crepidula dilatata (Gastropoda: Calyptraeidae) from Southern Chile. Mar Biol 39:241–251

    Article  Google Scholar 

  • Garcia-Pichel F, Mechling M, Castenholz RW (1994) Diel migrations of microorganisms within a benthic, hypersaline mat community. Appl Environ Microbiol 60:1500–1511

    PubMed  CAS  Google Scholar 

  • Garnier T, Eiglmeier K, Camus JC, Medina N, Mansoor H, Pryor M, Duthoy S, Grondin S, Lacroix C, Monsempe C, Simon S, Harris B, Atkin R, Doggett J, Mayes R, Keating L, Wheeler PR, Parkhill J, Barrell BG, Cole ST, Gordon SV, Hewinson RG (2003) The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci USA 100:7877–7882

    Article  PubMed  CAS  Google Scholar 

  • Gibson CM, Hunter MS (2010) Extraordinarily widespread and fantastically complex: comparative biology of endosymbiotic bacterial and fungal mutualists of insects. Ecol Lett 13:223–234

    Article  PubMed  Google Scholar 

  • Giere O, Erseus C et al (1998) A new species of olavius (Tubificidae) from the Algarve coast in Portugal, the first East Atlantic gutless oligochaete with symbiotic bacteria. Zool Anz 237:209–214

    Google Scholar 

  • Gilbert JA, Field D, Swift P, Thomas S, Cummings D, Temperton B, Weynberg K, Huse S, Hughes M, Joint I, Somerfield PJ, Muhling M (2010) The taxonomic and functional diversity of microbes at a temperate coastal site: a ‘multi-omic’ study of seasonal and diel temporal variation. Plos one 5(11): e15545. doi:10.1371/journal.pone.0015545

    Google Scholar 

  • Gilbert JA, Steele JA, Caporaso JG, Steinbrueck L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I, Somerfield P, Fuhrman JA, Field D (2012) Defining seasonal marine microbial community dynamics. ISMEJ 6:298–308

    Article  CAS  Google Scholar 

  • Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63

    Article  PubMed  CAS  Google Scholar 

  • Giovannoni SJ, Cary SC (1993) Probing marine systems with ribosomal RNAs. Oceanography 6:95–104

    Article  Google Scholar 

  • Giovannoni SJ, Rappe MS, Vergin KL, Adair NL (1996) 16 S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria. Proc Natl Acad Sci USA 93:7979–7984

    Article  PubMed  CAS  Google Scholar 

  • Giovannoni SJ, Vergin KL (2012) Seasonality in ocean microbial communities. Science 335:671–676

    Article  PubMed  CAS  Google Scholar 

  • Glockner FO, Fuchs BM, Amann R (1999) Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65:3721–3726

    PubMed  CAS  Google Scholar 

  • Goffredi SK, Childress JJ, Desaulniers NT, Lallier FH (1997) Sulfide acquisition by the vent worm Riftia pachyptila appears to be via uptake of HS-, rather than H2S. J Exp Biol 200:2609–2616

    PubMed  CAS  Google Scholar 

  • Goffredi SK, Paull CK et al (2004) Unusual benthic fauna associated with a whale fall in Monterey Canyon. Deep-Sea Res Pt I 51:1295–1306, California

    Article  Google Scholar 

  • Goodrich-Blair H, Clarke DJ (2007) Mutualism and pathogenesis in Xenorhabdus and Photorhabdus: two roads to the same destination. Mol Microbiol 64:260–268

    Article  PubMed  CAS  Google Scholar 

  • Graf J, Kikuchi Y et al (2006) Leeches and their microbiota: naturally simple symbiosis models. Trends Microbiol 14:365–371

    Article  PubMed  CAS  Google Scholar 

  • Gram L, Grossart HP, Schlingloff A, Kiorboe T (2002) Possible quorum sensing in marine snow bacteria: production of acylated homoserine lactones by Roseobacter strains isolated from marine snow. Appl Environ Microbiol 68:4111–4116

    Article  PubMed  CAS  Google Scholar 

  • Greenblum S, Turnbaugh PJ et al (2012) Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci USA 109:594–599

    Article  PubMed  CAS  Google Scholar 

  • Grobbelaar N, Huang T-C, Lin H-Y, Chow T-J (1986) FEMS Microbiol Lett 37:173–177

    Article  CAS  Google Scholar 

  • Grotzinger JP, Knoll AH (1999) Stromatolites in precambrian carbonates: evolutionary mileposts or environmental dipsticks? Ann Rev Earth Planet Sci 27:313–358

    Article  CAS  Google Scholar 

  • Hahn MW, Hofle MG (2001) Grazing of protozoa and its effect on populations of aquatic bacteria. FEMS Microbiol Ecol 35:113–121

    Article  PubMed  CAS  Google Scholar 

  • Harmer TL, Rotjan RD et al (2008) Free-living tube worm endosymbionts found at deep-sea vents. Appl Environ Microbiol 74:3895–3898

    Article  PubMed  CAS  Google Scholar 

  • Hastings JW (1971) Light to hide by – ventral luminescence to camouflage silhouette. Science 173:1016

    Article  PubMed  CAS  Google Scholar 

  • Hastings JW, Mitchell G (1971) Endosymbiotic bioluminescent bacteria from light organ of pony fish. Biol Bull 141:261–268

    Article  Google Scholar 

  • Hastings JW, Makemson J, Dunlap PV (1987) Are growth and luminescence regulated independently in light organ symbionts? Symbiosis 4:3–24

    Google Scholar 

  • Hastings JW, Greenberg EP (1999) Quorum sensing: the explanation of a curious phenomenon reveals a common characteristic of bacteria. J Bacteriol 181:2667–2668

    PubMed  CAS  Google Scholar 

  • Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, Tanaka M, Tobe T, Iida T, Takami H, Honda T, Sasakawa C, Ogasawara N, Yasunaga T, Kuhara S, Shiba T, Hattori M, Shinagawa H (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157: H7 and genomic comparison with a laboratory strain K-12. DNA Res 8:11–22

    Article  PubMed  CAS  Google Scholar 

  • Haygood MG (1993) Light organ symbioses in fishes. Crit Rev Microbiol 19:191–216

    Article  PubMed  CAS  Google Scholar 

  • Head IM, Hiorns WD, Embley TM, McCarthy AJ, Saunders JR (1993) The phylogeny of autotrophic ammonia oxidizing bacteria as determined by analysis of 16 s ribosomal-RNA gene-sequences. J Gen Microbiol 139:1147–1153

    PubMed  CAS  Google Scholar 

  • Heidelberg KB, Gilbert JA, Joint I (2010) Marine genomics: at the interface of marine microbial ecology and biodiscovery. Microb Biotechnol 3:531–543

    Article  PubMed  CAS  Google Scholar 

  • Herbert EE, Goodrich-Blair H (2007) Friend and foe: the two faces of Xenorhabdus nematophila. Nat Rev Microbiol 5:634–646

    Article  PubMed  CAS  Google Scholar 

  • Herndl GJ, Mullerniklas G, Frick J (1993) Major role of ultraviolet in controlling bacterioplankton growth in the surface layer of the ocean. Nature 361:717–719

    Article  Google Scholar 

  • Heungens K, Cowles CE, Goodrich-Blair H (2002) Identification of Xenorhabdus nematophila genes required for mutualistic colonization of Steinernema carpocapsae nematodes. Mol Microbiol 45:1337–1353

    Article  PubMed  CAS  Google Scholar 

  • Hillesland KL, Stahl DA (2010) Rapid evolution of stability and productivity at the origin of a microbial mutualism. Proc Natl Acad Sci USA 107:2124–2129

    Article  PubMed  CAS  Google Scholar 

  • Hirsch AM, McFall-Ngai MJ (2000) Fundamental concepts in symbiotic interactions: light and dark, day and night, squid and legume. J Plant Growth Reg 19:113–130

    CAS  Google Scholar 

  • Hmelo LR, Mincer TJ, Van Mooy BAS (2011) Possible influence of bacterial quorum sensing on the hydrolysis of sinking particulate organic carbon in marine environments. Environ Microb Rep 3:682–688

    Article  CAS  Google Scholar 

  • Holm-Hansen O, Lubin D, Hebling EW (1993) Ultraviolet radiation and its effect on organisms in aquatic environments. In: Young AR, Bjorn L, Moan J, Nultsch W (eds) Environmental UV photobiology. Plenum, New York, pp 379–425

    Google Scholar 

  • Hooper LV (2009) OPINION Do symbiotic bacteria subvert host immunity? Nat Rev Microbiol 7:367–374

    Article  PubMed  CAS  Google Scholar 

  • Huber B, Riedel K, Hentzer M, Heydorn A, Gotschlich A, Givskov M, Molin S, Eberl L (2001) The cep quorum sensing system of Burkholderia cepacia H111 controls biofilm formation and swarming motility. Microbiology 47:2517–2528

    Google Scholar 

  • Huettel M, Forster S, Kloser S, Fossing H (1996) Vertical migration in the sediment-dwelling sulfur bacteria Thioploca spp in overcoming diffusion limitations. Appl Environ Microbiol 62:1863–1872

    PubMed  CAS  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    PubMed  CAS  Google Scholar 

  • Hullar MAJ, Kaplan LA, Stahl DA (2006) Recurring seasonal dynamics of microbial communities in stream habitats. Appl Environ Microbiol 72:713–722

    Article  PubMed  CAS  Google Scholar 

  • Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, Sogin ML (2008) Exploring microbial diversity and taxonomy using SSU rRNA Hypervariable Tag Sequencing. Plos Genet 4

    Google Scholar 

  • Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV (2012) Untangling genomes from metagenomes: revealing an uncultured class of marine euryarchaeota. Science 335:587–590

    Article  PubMed  CAS  Google Scholar 

  • Jannasch HW, Nelson DC, Wirsen CO (1989) Massive natural occurrence of unusually large bacteria (Beggiatoa sp) at a hydrothermal deep-sea vent site. Nature 342:834–836

    Article  CAS  Google Scholar 

  • Jeffrey W, Kase JP, Wilhelm SW (2000) UV radiation effects on heterotrophic bacterioplankton and viruses in marine ecosystems. In: Mora SD (ed) The effects of UV radiation in the marine environment. Cambridge University Press, New York, pp 206–236

    Chapter  Google Scholar 

  • Johnson CH, Stewart PL, Egli M (2011) The cyanobacterial circadian system: from biophysics to bioevolution. Annu Rev Biophys 40:143–167

    Article  PubMed  CAS  Google Scholar 

  • Jorgensen BB, Cohen Y (1977) Solar Lake (Sinai) sulfur cycle of benthic cyanobacterial mats. Limnol Oceanogr 22:657–666

    Article  Google Scholar 

  • Jorgensen BB, Revsbech NP (1983) Colorless sulfur bacteria, Beggiatoa Spp and Thiovulum Spp in O2 and H2S microgradients. Appl Environ Microbiol 45:1261–1270

    PubMed  CAS  Google Scholar 

  • Jorgensen BB (1994) Sulfate reduction and thiosulfate transformations in a cyanobacterial mat during a diel oxygen cycle. FEMS Microbiol Ecol 13:303–312

    Article  CAS  Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic, New York, pp 21–132

    Google Scholar 

  • Jurgens K, Matz C (2002) Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria. Anton Leeuw Int J G 81:413–434

    Article  CAS  Google Scholar 

  • Kaltenpoth M, Yildirim E et al (2012) Refining the roots of the beewolf-Streptomyces symbiosis: antennal symbionts in the rare genus Philanthinus (Hymenoptera, Crabronidae). Appl Environ Microb 78:822–827

    Article  CAS  Google Scholar 

  • Karl DM (1994) Accurate estimation of microbial loop processes and rates. Microb Ecol 28:147–150

    Article  Google Scholar 

  • Karl DM, Lukas R (1996) The Hawaii Ocean time-series (HOT) program: background, rationale and field implementation. Deep-Sea Res Pt II 43:129–156

    Article  CAS  Google Scholar 

  • Karl DM (2010) Oceanic ecosystem time-series programs: ten lessons learned. Oceanography 23:104–125

    Article  Google Scholar 

  • Karner MB, Delong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507–510

    Article  PubMed  CAS  Google Scholar 

  • Kau AL, Ahern PP et al (2011) Human nutrition, the gut microbiome and the immune system. Nature 474:327–336

    Article  PubMed  CAS  Google Scholar 

  • Kaufman MR, Ikeda Y, Patton C, Van Dykhuizen G, Epel D (1998) Bacterial symbionts colonize the accessory nidamental gland of the squid Loligo opalescens via horizontal transmission. Biol Bull-Us 194:36–43

    Article  Google Scholar 

  • Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, Steglich C, Church GM, Richardson P, Chisholm SW (2007) Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet 3:2515–2528

    Article  CAS  Google Scholar 

  • Kiorboe T, Tang K, Grossart HP, Ploug H (2003) Dynamics of microbial communities on marine snow aggregates: colonization, growth, detachment, and grazing mortality of attached bacteria. Appl Environ Microbiol 69:3036–3047

    Article  PubMed  CAS  Google Scholar 

  • Klitgord N, Segre D (2010) Environments that induce synthetic microbial ecosystems. PLOS Comput Biol 6

    Google Scholar 

  • Knittel K, Boetius A (2009) Anaerobic oxidation of methane: progress with an unknown process. Ann Rev Microbiol 63:311–334

    Article  CAS  Google Scholar 

  • Kobayashi J, Ishibashi M (1993) Bioactive metabolites of symbiotic marine microorganisms. Chem Rev 93:1753–1769

    Article  CAS  Google Scholar 

  • Kolenbrander PE (2000) Oral microbial communities: biofilms, interactions, and genetic systems. Annu Rev Microbiol 54:413–437

    Article  PubMed  CAS  Google Scholar 

  • Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546

    Article  PubMed  CAS  Google Scholar 

  • Koonin EV (2009) Darwinian evolution in the light of genomics. Nucleic Acids Res 37:1011–1034

    Article  PubMed  CAS  Google Scholar 

  • Kruger M, Meyerdierks A, Glockner FO, Amann R, Widdel F, Kube M, Reinhardt R, Kahnt J, Bocher R, Thauer RK, Shima S (2003) A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426:878–881

    Article  PubMed  CAS  Google Scholar 

  • Kukor JJ, Martin MM (1986) The effect of acquired microbial enzymes on assimilation efficiency in the common woodlouse, Tracheoniscus-Rathkei. Oecologia 69:360–366

    Article  Google Scholar 

  • Lane DJ, Harrison AP, Stahl D, Pace B, Giovannoni SJ, Olsen GJ, Pace NR (1992) Evolutionary relationships among sulfur-oxidizing and iron-oxidizing eubacteria. J Bacteriol 174:269–278

    PubMed  CAS  Google Scholar 

  • Le Bourgne R, Barber RT, Delacroix T, Inoue HY, Mackey DJ, Rodier M (2002) Pacific warm pool and divergence: temporal and zonal variations on the equator and their effects on the biological pump. Deep-Sea Res Pt II 49:2471–2512

    Article  Google Scholar 

  • Lebaron P, Servais P, Troussellier M, Courties C, Muyzer G, Bernard L, Schafer H, Pukall R, Stackebrandt E, Guindulain T, Vives-Rego J (2001) Microbial community dynamics in Mediterranean nutrient enriched seawater mesocosms: changes in abundances, activity and composition. FEMS Microbiol Ecol 34:255–266

    Article  PubMed  CAS  Google Scholar 

  • Lee KH, Ruby EG (1994) Effect of the squid host on the abundance and distribution of symbiotic Vibrio fischeri in nature. Appl Environ Microbiol 60:1565–1571

    PubMed  CAS  Google Scholar 

  • Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA, Sogin ML, Pace NR (2006) Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol 72:3685–3695

    Article  PubMed  CAS  Google Scholar 

  • Li F, Hullar MAJ, Schwarz Y, Lampe JW (2009) Human gut bacterial communities are altered by addition of cruciferous vegetables to a controlled fruit- and vegetable-free diet. J Nutr 139:1685–1691

    Article  PubMed  CAS  Google Scholar 

  • Lilburn TC, Kim KS, Ostrom NE, Byzek KR, Leadbetter JR, Breznak JA (2001) Nitrogen fixation by symbiotic and free-living spirochetes. Science 292:2495–2498

    Article  PubMed  CAS  Google Scholar 

  • Lipson DA, Schmidt SK (2004) Seasonal changes in an alpine soil bacterial community in the Colorado Rocky Mountains. Appl Environ Microbiol 70:2867–2879

    Article  PubMed  CAS  Google Scholar 

  • Llabres M, Agusti S (2006) Picophytoplankton cell death induced by UV radiation: evidence for oceanic Atlantic communities. Limnol Oceanogr 51:21–29

    Article  Google Scholar 

  • Lum MR, Hirsch AM (2003) Roots and their symbiotic microbes: strategies to obtain nitrogen and phosphorus in a nutrient limiting environment. Am J Plant Growth Reg 21:368–382

    Article  CAS  Google Scholar 

  • MacGregor BJ, Moser DP, Baker BJ, Alm EW, Maurer M, Nealson KH, Stahl DA (2001) Seasonal and spatial variability in Lake Michigan sediment small-subunit rRNA concentrations. Appl Environ Microbiol 67:3908–3922

    Article  PubMed  CAS  Google Scholar 

  • Maier S, Volker H, Beese M, Gallardo VA (1990) The fine structure of Thioploca aruacae and Thioploca chileae. Can J Microbiol 36:438–448

    Article  Google Scholar 

  • Margulis L, Fester R (eds) (1991) Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. The MIT Press, Cambridge, MA

    Google Scholar 

  • Martens EC, Heungens K, Goodrich-Blair H (2003) Early colonization events in the mutualistic association between Steinernema carpocapsae nematodes and Xenorhabdus nematophila bacteria. J Bacteriol 185:3147–3154

    Article  PubMed  CAS  Google Scholar 

  • Martin HG, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He SM, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol 24:1263–1269

    Article  CAS  Google Scholar 

  • Massana R, Murray AE, Preston CM, Delong EF (1997) Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl Environ Microbiol 63:50–56

    PubMed  CAS  Google Scholar 

  • Massana R, Taylor LJ, Murray AE, Wu KY, Jeffrey WH, Delong EF (1998) Vertical distribution and temporal variation of marine planktonic archaea in the Gerlache Strait, Antarctica, during early spring. Limnol Oceanogr 43:607–617

    Article  CAS  Google Scholar 

  • Massana R, Delong EF, Pedros-Alio C (2000) A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl Environ Microbiol 66:1777–1787

    Article  PubMed  CAS  Google Scholar 

  • Massana R (2011) Eukaryotic picoplankton in surface oceans. Annu Rev Microbiol 65:91–110

    Article  PubMed  CAS  Google Scholar 

  • Matsumoto K, Furuya K (2011) Variations in phytoplankton dynamics and primary production associated with ENSO cycle in the western and central equatorial Pacific during 1994–2003. J Geophys Res Oceans 116

    Google Scholar 

  • Mayr E (1982) The growth of biological thought: diversity, evolution, and inheritance. Belknap Press of Harvard University Press, Cambridge, MA

    Google Scholar 

  • McCutcheon JP, Moran NA (2012) Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10:13–26

    CAS  Google Scholar 

  • McCutcheon JP, McDonald BR et al (2009) Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proc Natl Acad Sci USA 106:15394–15399

    Article  PubMed  CAS  Google Scholar 

  • McFall-Ngai MJ (2001) Identifying “prime suspects”: symbioses and the evolution of multicellularity. Comp Biochem Phys B 129:711–723

    Article  CAS  Google Scholar 

  • McFall-Ngai MJ (2002) Unseen forces: The influence of bacteria on animal development. Dev Biol 242:1–14

    Article  PubMed  CAS  Google Scholar 

  • McFall-Ngai MJ, Henderson B, Ruby E (eds) (2005) The influence of cooperative bacteria on animal host biology. Cambridge University Press, New York

    Google Scholar 

  • McFall-Ngai M, Heath-Heckman EA, Gilette AA, Peyer SM, Harvie EA (2012) The Secret Language of coevolved symbioses: insights from the Euprymna scolopes-Vibrio fischeri symbiosis. Semin Immunol 24:3–8

    Article  PubMed  Google Scholar 

  • McInerney MJ, Sieber JR, Gunsalus RP (2009) Syntrophy in anaerobic global carbon cycles. Curr Opin Biotechnol 20:623–632

    Article  PubMed  CAS  Google Scholar 

  • McNab R, Ford SK, El-Sabaeny A, Barbieri B, Cook GS, Lamont RJ (2003) LuxS-based signaling in Streptococcus gordonii: autoinducer 2 controls carbohydrate metabolism and biofilm formation with Porphyromonas gingivalis. J Bacteriol 185:274–284

    Article  PubMed  CAS  Google Scholar 

  • Medina M, Sachs JL (2010) Symbiont genomics, our new tangled bank. Genomics 96:377–378

    Article  CAS  Google Scholar 

  • Michaelis W, Seifert R, Nauhaus K, Treude T, Thiel V, Blumenberg M, Knittel K, Gieseke A, Peterknecht K, Pape T, Boetius A, Amann R, Jorgensen BB, Widdel F, Peckmann JR, Pimenov NV, Gulin MB (2002) Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297:1013–1015

    Article  PubMed  CAS  Google Scholar 

  • Minz D, Flax JL, Green SJ, Muyzer G, Cohen Y, Wagner M, Rittmann BE, Stahl DA (1999a) Diversity of sulfate-reducing bacteria in oxic and anoxic regions of a microbial mat characterized by comparative analysis of dissimilatory sulfite reductase genes. Appl Environ Microbiol 65:4666–4671

    PubMed  CAS  Google Scholar 

  • Minz D, Fishbain S, Green SJ, Muyzer G, Cohen Y, Rittmann BE, Stahl DA (1999b) Unexpected population distribution in a microbial mat community: sulfate reducing bacteria localized to the highly oxic chemocline in contrast to an eukaryotic preference for anoxia. Appl Environ Microbiol 65:4659–4665

    PubMed  CAS  Google Scholar 

  • Mitchell DL, Kerntz D (1993) The induction and repair of DNA photodamage in the environment. In: Young AR, Bjorn L, Moan J, Nultsch W (eds) Environmental UV photobiology. Plenum, New York, pp 379–425

    Google Scholar 

  • Monds RD, O'Toole GA (2009) The developmental model of microbial biofilms: ten years of a paradigm up for review. Trends Microbiol 17:73–87

    Article  PubMed  CAS  Google Scholar 

  • Moore LR, Rocap G, Chisholm SW (1998) Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393:464–467

    Article  PubMed  CAS  Google Scholar 

  • Moran MA, Zepp RG (2000) UV radiation effects on microbes and microbial processes. In: Kirchman DL (ed) Microbial ecology of the oceans. Wiley-Liss, New York, pp 201–228

    Google Scholar 

  • Moran NA, McCutcheon JP et al (2008) Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet 42:165–190

    Article  PubMed  CAS  Google Scholar 

  • Moran NA, McLaughlin HJ et al (2009) The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323:379–382

    Article  PubMed  CAS  Google Scholar 

  • Morin JG, Harrington A et al (1975) Light for all reasons – versatility in behavioral repertoire of flashlight fish. Science 190:74–76

    Google Scholar 

  • Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806–810

    Article  PubMed  CAS  Google Scholar 

  • Morris RM, Vergin KL, Cho JC, Rappe MS, Carlson CA, Giovannoni SJ (2005) Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic time-series Study site. Limnol Oceanogr 50:1687–1696

    Article  CAS  Google Scholar 

  • Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, Haselkorn R, Galperin MY (2006) The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci USA 103:13126–13131

    Article  PubMed  CAS  Google Scholar 

  • Murray AE, Preston CM, Massana R, Taylor LT, Blakis WK, Delong EF (1998) Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island Antarctica. Appl Environ Microbiol 64:2585–2595

    PubMed  CAS  Google Scholar 

  • Nakabachi A, Yamashita A et al (2006) The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314:267

    Google Scholar 

  • Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyarna T, Kondo T (2005) Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 308:414–415

    Article  PubMed  CAS  Google Scholar 

  • Nauhaus K, Boetius A, Kruger M, Widdel F (2002) In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area. Environ Microbiol 4:296–305

    Article  PubMed  CAS  Google Scholar 

  • Nealson KH, Stahl D (1997) Biogeochemical cycling and bacterial metabolism: what can we learn from layered microbial communities? In: Banfield J (ed) Geomicrobiology: interactions between microbes and minerals. Mineralogical Society of America, New York

    Google Scholar 

  • Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S (2011) A guide to the natural history of freshwater lake bacteria. Microbiol Molec Biol Rev 75:14–49

    Article  CAS  Google Scholar 

  • Ng WL, Bassler BL (2009) Bacterial quorum-sensing network architectures. Annu Rev Genet 43:197–222

    Article  PubMed  CAS  Google Scholar 

  • Nussbaumer AD, Fisher CR et al (2006) Horizontal endosymbiont transmission in hydrothermal vent tubeworms. Nature 441:345–348

    Article  PubMed  CAS  Google Scholar 

  • Nyholm SV, McFall-Ngai MJ (2003) Dominance of Vibrio fischeri in secreted mucus outside the light organ of Euprymna scolopes: the first site of symbiont specificity. Appl Environ Microbiol 69:3932–3937

    Article  PubMed  CAS  Google Scholar 

  • Nyholm SV, Mcfall-Ngai MJ (2004) The winnowing: establishing the squid-vibrio symbiosis. Nat Rev Microbiol 2:632–642

    Article  PubMed  CAS  Google Scholar 

  • Nyholm SV, Stewart JJ et al (2009) Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes. Environ Microbiol 11:483–493

    Article  PubMed  Google Scholar 

  • Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304

    Article  PubMed  CAS  Google Scholar 

  • Ochman H, Moran NA (2001) Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:1096–1098

    Article  PubMed  CAS  Google Scholar 

  • Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365

    Article  PubMed  CAS  Google Scholar 

  • Orphan VJ, House CH, Hinrichs KU, McKeegan KD, Delong EF (2001) Methane consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293:484–487

    Article  PubMed  CAS  Google Scholar 

  • Ouyang Y, Andersson CR, Kondo T, Golden SS, Johnson CH (1998) Resonating circadian clocks enhance fitness in cyanobacteria. Proc Natl Acad Sci USA 95:8660–8664

    Article  PubMed  CAS  Google Scholar 

  • Ovreas L, Bourne D, Sandaa RA, Casamayor EO, Benlloch S, Goddard V, Smerdon G, Heldal M, Thingstad TF (2003) Response of bacterial and viral communities to nutrient manipulations in seawater mesocosms. Aquat Microb Ecol 31:109–121

    Article  Google Scholar 

  • Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740

    Article  PubMed  CAS  Google Scholar 

  • Pace NR (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol R 73:565–576

    Article  CAS  Google Scholar 

  • Pace NR, Sapp J, Goldenfeld N (2012) Phylogeny and beyond: scientific, historical, and conceptual significance of the first tree of life. Proc Natl Acad Sci USA 109:1011–1018

    Article  PubMed  CAS  Google Scholar 

  • Paerl HW, Prufert LE (1987) Oxygen-poor microzones as potential sites of microbial N2 fixation in nitrogen depleted aerobic marine waters. Appl Environ Microbiol 53:1078–1087

    PubMed  CAS  Google Scholar 

  • Pakulski JD, Aas P, Jeffrey W, Lyons M, van Waasbergen LG, Mitchell D, Coffin R (1998) Influence of light on bacterioplankton production and respiration in a subtropical coral reef. Aquat Microb Ecol 15:137–148

    Article  Google Scholar 

  • Papke RT, Ramsing NB, Bateson MM, Ward DM (2003) Geographical isolation in hot spring cyanobacteria. Environ Microbiol 5:650–659

    Article  PubMed  CAS  Google Scholar 

  • Passow U (2002) Transparent exopolymer particles (TEP) in aquatic environments. Prog Oceanogr 55:287–333

    Article  Google Scholar 

  • Pennisi E (2001) Microbial genomes: sequences reveal borrowed genes. Science 294:1634–1635

    Article  PubMed  CAS  Google Scholar 

  • Perna NT, Plunkett G, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Postal G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin JY, Yen G, Schwartz DC, Welch RA, Blattner FR (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157: H. Nature 410:240–245

    Article  CAS  Google Scholar 

  • Pernthaler J, Glockner FO, Unterholzner S, Alfreider A, Psenner R, Amann R (1998) Seasonal community and population dynamics of pelagic bacteria and archaea in a high mountain lake. Appl Environ Microbiol 64:4299–4306

    PubMed  CAS  Google Scholar 

  • Pernthaler J, Posch T, Simek K, Vrba J, Pernthaler A, Glockner FO, Nubel U, Psenner R, Amann R (2001) Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture. Appl Environ Microbiol 67:2145–2155

    Article  PubMed  CAS  Google Scholar 

  • Pernthaler J (2005) Predation on prokaryotes in the water column and its ecological implications. Nat Rev Microbiol 3:537–546

    Article  PubMed  CAS  Google Scholar 

  • Philander SG, Fedorov A (2003) Is El Nino sporadic or cyclic? Ann Rev Earth Planet Sci 31:579–594

    Article  CAS  Google Scholar 

  • Pinel N, Davidson SK et al (2008) Verminephrobacter eiseniae gen. nov., sp nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny). Int J Syst Evol Micr 58:2147–2157

    Article  CAS  Google Scholar 

  • Polz MF, Robinson JJ, Cavanaugh CM, Van Dover CL (1998) Trophic ecology of massive shrimp aggregations at a mid-Atlantic ridge hydrothermal vent site. Limnol Oceanogr 43:1631–1638

    Article  CAS  Google Scholar 

  • Pomeroy LR (1974) The ocean’s foodweb: a changing paradigm. Bioscience 24:499–504

    Article  Google Scholar 

  • Posch T, Simek K, Vrba J, Pernthaler S, Nedoma J, Sattler B, Sonntag B, Psenner R (1999) Predator-induced changes of bacterial size-structure and productivity studied on an experimental microbial community. Aquat Microb Ecol 18:235–246

    Article  Google Scholar 

  • Proctor LM (2011) The human microbiome project in 2011 and beyond. Cell Host Microbe 10:287–291

    Article  PubMed  CAS  Google Scholar 

  • Purcell EM (1977) Life at low Reynolds-number. Am J Phys 45:3–11

    Article  Google Scholar 

  • Ramsing NB, Ferris MJ, Ward DM (1997) Light-induced motility of thermophilic Synechococcus isolates from octopus spring, Yellowstone National Park. Appl Environ Microbiol 63:2347–2354

    PubMed  CAS  Google Scholar 

  • Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633

    Article  PubMed  CAS  Google Scholar 

  • Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    Article  PubMed  CAS  Google Scholar 

  • Raskin L, Stromley JM, Rittman BE, Stahl DA (1994) Group specific 16 S ribosomal RNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol 60:1232–1240

    PubMed  CAS  Google Scholar 

  • Rawls JF, Samuel BS et al (2004) Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci USA 101:4596–4601

    Article  PubMed  CAS  Google Scholar 

  • Relman DA, Falkow S (2001) The meaning and impact of the human genome sequence for microbiology. Trends Microbiol 9:206–208

    Article  PubMed  CAS  Google Scholar 

  • Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ (2009) Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci USA 106:8605–8610

    Article  PubMed  CAS  Google Scholar 

  • Revsbech NP, Jorgensen BB (1983) Photosynthesis of benthic microflora measured with high spatial-resolution by the oxygen microprofile method – capabilities and limitations of the method. Limnol Oceanogr 28:749–756

    Article  Google Scholar 

  • Riemann L, Farnelid H, Steward GF (2010) Nitrogenase genes in non-cyanobacterial plankton: prevalence, diversity and regulation in marine waters. Aquat Microb Ecol 61:225–237

    Article  Google Scholar 

  • Rio RVM, Anderegg M et al (2007) Characterization of a catalase gene from Aeromonas veronii, the digestive-tract symbiont of the medicinal leech. Microbiol-SGM 153:1897–1906

    Article  CAS  Google Scholar 

  • Risatti JB, Capman WC, Stahl DA (1994) Community structure of a microbial mat – the phylogenetic dimension. Proc Natl Acad Sci USA 91:10173–10177

    Article  PubMed  CAS  Google Scholar 

  • Rocap G, Distel DL, Waterbury JB, Chisholm SW (2002) Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl Environ Microbiol 68:1180–1191

    Article  PubMed  CAS  Google Scholar 

  • Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042–1047

    Article  PubMed  CAS  Google Scholar 

  • Rodrigues JLM, Serres MH, Tiedje JM (2011) Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of Shewanella species and identify metabolic pathways conserved at the genus level. Appl Environ Microbiol 77:5352–5360

    Article  PubMed  CAS  Google Scholar 

  • Rohwer F, Thurber RV (2009) Viruses manipulate the marine environment. Nature 459:207–212

    Article  PubMed  CAS  Google Scholar 

  • Ruby EG, Lee KH (1998) The Vibrio fischeri Euprymna scolopes light organ association: current ecological paradigms. Appl Environ Microbiol 64:805–812

    PubMed  CAS  Google Scholar 

  • Ruby EG (1999) The Euprymna scolopes-Vibrio fischeri symbiosis: a biomedical model for the study of bacterial colonization of animal tissue. J Molec Microbiol Biotech 1:13–21

    CAS  Google Scholar 

  • Ruby EG (2008) Symbiotic conversations are revealed under genetic interrogation. Nat Rev Microbiol 6:752–762

    Article  PubMed  CAS  Google Scholar 

  • Sachs JL, Skophammer RG et al (2011) Evolutionary transitions in bacterial symbiosis. Proc Natl Acad Sci USA 108:10800–10807

    Article  PubMed  CAS  Google Scholar 

  • Sassen R, Roberts HH, Aharon P, Larkin J, Chinn EW, Carney R (1993) Chemosynthetic bacterial mats at cold hydrocarbon seeps, Gulf of Mexico continental slope. Org Geochem 20:77–85

    Article  CAS  Google Scholar 

  • Schaecter M (2003) Integrative microbiology: the third golden age. J Biosci 28:149–154

    Article  Google Scholar 

  • Schink B (1988) Principles and limits of anaerobic degradation, environmental and technological aspects. In: Zehnder AJB (ed) Biology of anaerobic microorganisms. Wiley, New York, pp 771–846

    Google Scholar 

  • Schoenian I, Spiteller M et al (2011) Chemical basis of the synergism and antagonism in microbial communities in the nests of leaf-cutting ants. Proc Natl Acad Sci USA 108:1955–1960

    Article  PubMed  CAS  Google Scholar 

  • Schulz HN, Jorgensen BB (2001) Big bacteria. Ann Rev Microbiol 55:105–137

    Article  CAS  Google Scholar 

  • Scott JJ, Oh DC et al (2008) Bacterial protection of beetle-fungus mutualism. Science 322:63

    Google Scholar 

  • Seckbach J (2002) Symbiosis: mechanisms and model systems. In: Seckbach J (ed) Cellular origin and life in extreme habitats. Kluwer, Norwell

    Google Scholar 

  • Sekiguchi Y, Kamagata Y, Nakamura K, Ohashi A, Harada H (1999) Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules. Appl Environ Microbiol 65:1280–1288

    PubMed  CAS  Google Scholar 

  • Shimoyama T, Kato S, Ishii S, Watanabe K (2009) Flagellum mediates symbiosis. Science 323:1574

    Google Scholar 

  • Sigalevich P, Meshorer E, Helman Y, Cohen Y (2000) Transition from anaerobic to aerobic growth conditions for the sulfate-reducing bacterium desulfovibrio oxyclinae results in flocculation. Appl Environ Microbiol 66:5005

    Article  PubMed  CAS  Google Scholar 

  • Silver AC, Kikuchi Y et al (2007) Interaction between innate immune cells and a bacterial type III secretion system in mutualistic and pathogenic associations. Proc Natl Acad Sci USA 104:9481–9486

    Article  PubMed  CAS  Google Scholar 

  • Simek K, Armengol J, Comerma M, Garcia JC, Kojecka P, Nedoma J, Hejzlar J (2001a) Changes in the epilimnetic bacterial community composition, production, and protist induced mortality along the longitudinal axis of a highly eutrophic reservoir. Microbial Ecol 42:359–371

    Article  CAS  Google Scholar 

  • Simek K, Pernthaler J, Weinbauer MG, Hornak K, Dolan JR, Nedoma J, Masin M, Amann R (2001b) Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. Appl Environ Microbiol 67:2723–2733

    Article  PubMed  CAS  Google Scholar 

  • Simek K, Hornak K, Masin M, Christaki U, Nedoma J, Weinbauer MG, Dolan JR (2003) Comparing the effects of resource enrichment and grazing on a bacterioplankton community of a mesoeutrophic reservoir. Aquat Microb Ecol 31:123–135

    Article  Google Scholar 

  • Singh PK, Schaefer AL, Parsek MR, Moninger TO, Welsh MJ, Greenberg EP (2000) Quorum-sensing signals indicate that cystic fibrosis lungs are infected with bacterial biofilms. Nature 407:762–764

    Article  PubMed  CAS  Google Scholar 

  • Small AL, McFall-Ngai MJ (1999) Halide peroxidase in tissues that interact with bacteria in the host squid Euprymna scolopes. J Cell Biochem 72:445–457

    Article  PubMed  CAS  Google Scholar 

  • 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 480:241–244

    Article  PubMed  CAS  Google Scholar 

  • 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 USA 103:12115–12120

    Article  PubMed  CAS  Google Scholar 

  • Sommaruga R, Obernosterer I, Herndl GJ, Psenner R (1997) Inhibitory effect of solar radiation on thymidine and leucine incorporation by freshwater and marine bacterioplankton. Appl Environ Microbiol 63:4178–4184

    PubMed  CAS  Google Scholar 

  • Southward EC (1999) Development of Perviata and Vestimentifera (Pogonophora). Hydrobiologia 402:185–202

    Article  Google Scholar 

  • Spaulding AW, von Dohlen CD (1998) Phylogenetic characterization and molecular evolution of bacterial endosymbionts in psyllids (Hemiptera: Sternorrhyncha). Mol Biol Evol 15:1506–1513

    Article  PubMed  CAS  Google Scholar 

  • Stahl DA, Lane DJ, Olsen GJ, Pace NR (1984) Analysis of hydrothermal vent-associated symbionts by ribosomal-RNA sequences. Science 224:409–411

    Article  PubMed  CAS  Google Scholar 

  • Stahl D (1993) The natural history of microorganisms. ASM News 59:609–613

    Google Scholar 

  • Staley JT, Gosink JJ (1999) Poles apart: biodiversity and biogeography of sea ice bacteria. Annu Rev Microbiol 53:189–215

    Article  PubMed  CAS  Google Scholar 

  • Stams AJM, Plugge CM (2009) Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 7:568–577

    Article  PubMed  CAS  Google Scholar 

  • Steele JA, Countway PD, Xia L, Vigil PD, Beman JM, Kim DY, Chow CET, Sachdeva R, Jones AC, Schwalbach MS, Rose JM, Hewson I, Patel A, Sun FZ, Caron DA, Fuhrman JA (2011) Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J 5:1414–1425

    Article  PubMed  Google Scholar 

  • Stern A, Sorek R (2011) The phage-host arms race: shaping the evolution of microbes. Bioessays 33:43–51

    Article  PubMed  CAS  Google Scholar 

  • Stolyar S, Van Dien S, Hillesland KL, Pinel N, Lie TJ, Leigh JA, Stahl DA (2007) Metabolic modeling of a mutualistic microbial community. Mol Syst Biol 3:92

    Article  PubMed  CAS  Google Scholar 

  • Stougaerd J (2000) Regulators and regulation of legume root nodule development. Plant Physiol 124:531–539

    Article  Google Scholar 

  • Streams ME, Fisher CR, Fiala-Medioni A (1997) Methanotrophic symbiont location and fate of carbon incorporated from methane in a hydrocarbon seep mussel. Mar Biol 129:465–476

    Article  CAS  Google Scholar 

  • Sullivan JT, Ronson CW (1998) Evolution of Rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc Natl Acad Sci USA 95:5145–5149

    Article  PubMed  CAS  Google Scholar 

  • Suttle CA (2002) Community structure: viruses. In: Hurst CJ, Crawford RL, Knudsen GR, McInerney MJ, Stetzenbach LD (eds) Manual of environmental microbiology. ASM press, Washington, DC, pp 364–370

    Google Scholar 

  • Suttle CA (2005) Viruses in the sea. Nature 437:356–361

    Article  PubMed  CAS  Google Scholar 

  • Suttle CA (2007) Marine viruses – major players in the global ecosystem. Nat Rev Microbiol 5:801–812

    Article  PubMed  CAS  Google Scholar 

  • Taillefert M, MacGregor BJ, Gaillard JF, Lienemann CP, Perret D, Stahl DA (2002) Evidence for a dynamic cycle between Mn and Co in the water column of a stratified lake. Environ Sci Technol 36:468–476

    Article  PubMed  CAS  Google Scholar 

  • Tamas I, Klasson L, Canback B, Naslund AK, Eriksson AS, Wernegreen JJ, Sandstrom JP, Moran NA, Andersson SGE (2002) 50 million years of genomic stasis in endosymbiotic bacteria. Science 296:2376–2379

    Article  PubMed  CAS  Google Scholar 

  • Teske A, Alm E, Regan JM, Toze S, Rittmann BE, Stahl DA (1994) Evolutionary relationships among ammonia-oxidizing and nitrite-oxidizing bacteria. J Bacteriol 176:6623–6630

    PubMed  CAS  Google Scholar 

  • Teske A, Ramsing NB, Habicht K et al (1998) Sulfate-reducing bacteria and their activities in cyanobacterial mats of Solar Lake (Sinai, Egypt). Appl Environ Microbiol 64:2943–2951

    PubMed  CAS  Google Scholar 

  • Thamdrup B, Canfield DE (1996) Fate of elemental sulfur in an intertidal sediment. FEMS Microbiol Ecol 19:95–103

    Article  Google Scholar 

  • Thar R, Fenchel T (2001) True chemotaxis in oxygen gradients of the sulfur-oxidizing bacterium Thiovulum majus. Appl Environ Microbiol 67:3299–3303

    Article  PubMed  CAS  Google Scholar 

  • Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245

    Article  PubMed  CAS  Google Scholar 

  • Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity – magnitude, dynamics, and controlling factors. Science 296:1064–1066

    Article  PubMed  CAS  Google Scholar 

  • Treusch AH, Vergin KL, Finlay LA, Donatz MG, Burton RM, Carlson CA, Giovannoni SJ (2009) Seasonality and vertical structure of microbial communities in an ocean gyre. ISME J 3:1148–1163

    Article  PubMed  Google Scholar 

  • Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308:554–557

    Article  PubMed  CAS  Google Scholar 

  • Turley CM, Mackie PJ (1995) Bacterial and cyanobacterial flux to the deep NE Atlantic on sediment particles. Deep-Sea Res Pt I 42:1453–1474

    Article  Google Scholar 

  • Turner JT (2002) Zooplankton fecal pellets, marine snow and sinking phytoplankton blooms. Aquat Microbial Ecol 27:57–102

    Article  Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43

    Article  PubMed  CAS  Google Scholar 

  • van Hannen EJ, Mooij W, van Agterveld MP, Gons HJ, Laanbroek HJ (1999a) Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:2478–2484

    PubMed  Google Scholar 

  • van Hannen EJ, Zwart G, van Agterveld MP, Gons HJ, Ebert J, Laanbroek HJ (1999b) Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Appl Environ Microbiol 65:795–801

    PubMed  Google Scholar 

  • van Loosdrecht MCM, Lyklema J, Norde W, Zehnder AJB (1990) Influence of interfaces on microbial activity. Microbiol Rev 54:75–87

    PubMed  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

    Article  PubMed  CAS  Google Scholar 

  • Vivas EI, Goodrich-Blair H (2001) Xenorhabdus nematophilus as a model for host-bacterium interactions: rpoS is necessary for mutualism with nematodes. J Bacteriol 183:4687–4693

    Article  PubMed  CAS  Google Scholar 

  • Walker CB, He ZL, Yang ZK, Ringbauer JA, He Q, Zhou JH, Voordouw G, Wall JD, Arkin AP, Hazen TC, Stolyar S, Stahl DA (2009) The electron transfer system of syntrophically grown Desulfovibrio vulgaris. J Bacteriol 191:5793–5801

    Article  PubMed  CAS  Google Scholar 

  • Walls JT, Blackman AJ, Ritz DA (1995) Localization of the amathamide alkaloids in surface bacteria of Amathia-Wilsoni Kirkpatrick, 1888 (Bryozoa, Ctenostomata). Hydrobiologia 297:163–172

    Article  CAS  Google Scholar 

  • Wang CZ, Fiedler PC (2006) ENSO variability and the eastern tropical Pacific: a review. Prog Oceanogr 69:239–266

    Article  Google Scholar 

  • Ward DM, Weller R, Bateson MM (1990) 16S ribosomal-RNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63–65

    Article  PubMed  CAS  Google Scholar 

  • Warnecke F, Luginbuhl P et al (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–U517

    Article  PubMed  CAS  Google Scholar 

  • Waterbury JB, Calloway CB, Turner RD (1983) A cellulolytic nitrogen-fixing bacterium cultured from the gland of Deshayes in shipworms (Bivalvia, Teredinidae). Science 221:1401–1403

    Article  PubMed  CAS  Google Scholar 

  • Weis VM, Small AL, McFallNgai MJ (1996) A peroxidase related to the mammalian antimicrobial protein myeloperoxidase in the Euprymna-Vibrio mutualism. Proc Natl Acad Sci USA 93:13683–13688

    Article  PubMed  CAS  Google Scholar 

  • Werren JH (1997) Biology of Wolbachia. Annu Rev Entomol 42:587–609

    Article  PubMed  CAS  Google Scholar 

  • Werren JH, Baldo L et al (2008) Wolbachia: master manipulators of invertebrate biology. Nat Rev Microbiol 6:741–751

    Article  PubMed  CAS  Google Scholar 

  • West NJ, Scanlan DJ (1999) Niche-partitioning of Prochlorococcus populations in a stratified water column in the eastern North Atlantic Ocean. Appl Environ Microbiol 65:2585–2591

    PubMed  CAS  Google Scholar 

  • Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976–978

    Article  PubMed  CAS  Google Scholar 

  • Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM, Lory S, Greenberg EP (2001) Gene expression in Pseudomonas aeruginosa biofilms. Nature 413:860–864

    Article  PubMed  CAS  Google Scholar 

  • Wilcox JL, Dunbar HE, Wolfinger RD, Moran NA (2003) Consequences of reductive evolution for gene expression in an obligate endosymbiont. Mol Microbiol 48:1491–1500

    Article  PubMed  CAS  Google Scholar 

  • Wilhelm LJ, Tripp HJ, Givan SA, Smith DP, Giovannoni SJ (2007) Natural variation in SARII marine bacterioplankton genomes inferred from metagenomic data. Biol Direct 2

    Google Scholar 

  • Wilkinson TL, Douglas AE (1996) The impact of aposymbiosis on amino acid metabolism of pea aphids. Entomol Exp Appl 80:279–282

    Article  CAS  Google Scholar 

  • Williams LB (2000) Heterotrophic bacteria and the dynamics of dissolved organic material. In: Kirchman DL (ed) Microbial ecology of the oceans. Wiley-Liss, New York, pp 153–200

    Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

    PubMed  CAS  Google Scholar 

  • Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms – proposal for the domains archaea, bacteria, and eucarya. Proc Natl Acad Sci USA 87:4576–4579

    Article  PubMed  CAS  Google Scholar 

  • Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97:8392–8396

    Article  PubMed  CAS  Google Scholar 

  • Woese CR (2004) A new biology for a new century. Microbiol Mol Biol R 68:173–186

    Article  CAS  Google Scholar 

  • Wolin MJ, Miller TL (1982) Interspecies hydrogen transfer: 15 years later. ASM News 48:561–565

    Google Scholar 

  • Woyke T, Teeling H et al (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443:950–955

    Article  PubMed  CAS  Google Scholar 

  • Wren BW (2000) Microbial genome analysis: Insights into virulence, host adaptation and evolution. Nat Rev Genet 1:30–39

    Article  PubMed  CAS  Google Scholar 

  • Wright TD, Vergin KL, Boyd PW, Giovannoni SJ (1997) A novel delta-subdivision proteobacterial lineage from the lower ocean surface layer. Appl Environ Microbiol 63:1441–1448

    PubMed  CAS  Google Scholar 

  • Xavier KB, Bassler BL (2003) LuxS quorum sensing: more than just a numbers game. Curr Opin Microbiol 6:191–197

    Article  PubMed  CAS  Google Scholar 

  • Young RE, Roper CFE (1976) Bioluminescent counter-shading in midwater animals – evidence from living squid. Science 191:1046–1048

    Article  PubMed  CAS  Google Scholar 

  • Zal F, Leize E, Lallier FH, Toulmond A, Van Dorsselaer A, Childress JJ (1998) S-sulfohemoglobin and disulfide exchange: the mechanisms of sulfide binding by Riftia pachyptila hemoglobins. Proc Natl Acad Sci USA 95:8997–9002

    Article  PubMed  CAS  Google Scholar 

  • Zaura E, Keijser BJF, Huse SM, Crielaard W (2009) Defining the healthy “core microbiome” of oral microbial communities. BMC Microbiol 9:259

    Article  PubMed  CAS  Google Scholar 

  • Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M (2002) Cultivating the uncultured. Proc Natl Acad Sci USA 99:15681–15686

    Article  PubMed  CAS  Google Scholar 

  • Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell MD, Wing R, Rittmann BE, Krajmalnik-Brown R (2009) Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci USA 106:2365–2370

    Article  PubMed  CAS  Google Scholar 

  • Zimmer M, Brune A (2005) Physiological properties of the gut lumen of terrestrial isopods (Isopoda: Oniscidea): adaptive to digesting lignocellulose? J Comp Physiol B 175:275–283

    Article  PubMed  CAS  Google Scholar 

  • Zimmer M, Topp W (1998) Microorganisms and cellulose digestion in the gut of the woodlouse Porcellio scaber. J Chem Ecol 24:1397–1408

    Article  CAS  Google Scholar 

  • Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. J Theoret Biol 8:357–366

    Article  CAS  Google Scholar 

  • Zwart G, Hiorns WD, Methe BA, Van Agterveld MP, Huismans R, Nold SC, Zehr JP, Laanbroek HJ (1998) Nearly identical 16 S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst Appl Microbiol 21:546–556

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We are grateful to grants from NSF Oceanography (OCE-0623174) and Molecular and Cellular Biosciences (MCB-0604448 & MCB-0920741); the dimensions of biodiversity program in Biological Oceanography (OCE-1046017); ENIGMA, a scientific focus area program supported by the US Department of Energy, Office of Science, and Office of Biological and Environmental Research; and Genomics: GTL Foundational Science through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US Department of Energy for partial support of the studies reported in this chapter.

Author information

Authors and Affiliations

  1. Department of Microbiology and Civil and Environmental Engineering, University of Washington, Box 357242, Seattle, WA, 98195-7242, USA

    Dr. David A. Stahl

  2. Department of Civil and Environmental Engineering, University of Washington, Box 357242, Seattle, WA, 98195-7242, USA

    Jason J. Flowers & Seana Davidson

  3. Public Health Sciences, Fred Hutchinson Cancer Research Center, Box 19024, Seattle, WA, 98109, USA

    Meredith Hullar

Authors
  1. Dr. David A. Stahl
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jason J. Flowers
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Meredith Hullar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Seana Davidson
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to David A. Stahl .

Editor information

Editors and Affiliations

  1. Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel

    Eugene Rosenberg

  2. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Edward F. DeLong

  3. Department of Microbiology and Immunology, Harvard Medical School, Boston, MA, USA

    Stephen Lory

  4. Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany

    Erko Stackebrandt

  5. Laboratory of Microbiology, Institute of Biology, Center for Health Sciences, Federal University of Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil

    Fabiano Thompson

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this entry

Cite this entry

Stahl, D.A., Flowers, J.J., Hullar, M., Davidson, S. (2013). Structure and Function of Microbial Communities. In: Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E., Thompson, F. (eds) The Prokaryotes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30123-0_34

Download citation

Publish with us

Policies and ethics

Search

Navigation