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.
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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
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
Alldredge AL, Cohen Y (1987) Can microscale chemical patches persist in the sea? Microelectrode study of marine snow, fecal pellets. Science 235:689–691
Alldredge AL, Silver MW (1988) Characteristics, dynamics and significance of marine snow. Prog Oceanogr 20:41–82
Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in-situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
Amann R, Ludwig W (2000) Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol Rev 24:555–565
Andersson AF, Banfield JF (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320:1047–1050
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
Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D (2011) Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 474:604–608
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
Bahr M, Hobbie JE, Sogin ML (1996) Bacterial diversity in an Arctic lake: a freshwater SAR11 cluster. Aquat Microb Ecol 11:271–277
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
Barton AD, Dutkiewicz S, Flierl G, Bragg J, Follows MJ (2010) Patterns of diversity in marine phytoplankton. Science 327:1509–1511
Bates JM, Mittge E et al (2006) Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation. Dev Biol 297:374–386
Baumann P (2005) Biology of bacteriocyte-associated endosymbionts of plant sap-sucking insects. Annu Rev Microbiol 59:155–189
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
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
Beijerinck MW (1913) De infusies en de ontdekking der backteriën. In Jaarboek van de Koninklijke Akademie v. Wetenschappen. Amsterdam, Müller
Bergh O, Borsheim KY, Bratbak G, Heldal M (1989) High abundance of viruses found in aquatic environments. Nature 340:467–468
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
Blackburn N, Fenchel T, Mitchell J (1998) Microscale nutrient patches in planktonic habitats shown by chemotactic bacteria. Science 282:2254–2256
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
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
Bouvier T, del Giorgio PA (2007) Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol 9:287–297
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
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
Breznak JA (1982) Intestinal microbiota of termites and other xylophagous insects. Annu Rev Microbiol 36:323–343
Bright M, Bulgheresi S (2010) A complex journey: transmission of microbial symbionts. Nat Rev Microbiol 8:218–230
Bright M, Sorgo A (2003) Ultrastructural reinvestigation of the trophosome in adults of Riftia pachyptila (Annelida, Siboglinidae). Invertebr Biol 122:347–368
Brochier-Armanet C, Gribaldo S, Forterre P (2012) Spotlight on the thaumarchaeota. ISME J 6:227–230
Brownlie JC, Johnson KN (2009) Symbiont-mediated protection in insect hosts. Trends Microbiol 17:348–354
Brune A, Friedrich M (2000) Microecology of the termite gut: structure and function on a microscale. Curr Opin Microbiol 3:263–269
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
Bryant MP, Wolin EA, Wolin MJ, Wolfe RS (1967) Methanobacillus omelianskii: a symbiotic association of two species of bacteria. Arch Microbiol 59:20–31
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
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
Button DK (1994) The physical base of marine bacterial ecology. Microb Ecol 28:273–285
Calbet A (2008) The trophic roles of microzooplankton in marine systems. Ices J Marine Sci 65:325–331
Canfield DE, DeMarais DJ (1991) Aerobic sulfate reduction in microbial mats. Science 251:1471–1473
Canfield DE, Marais DJD (1993) Biogeochemical cycles of carbon, sulfur, and free oxygen in a microbial mat. Geochim Cosmochim Acta 57:3971–3984
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
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
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
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
Casjens S (1998) The diverse and dynamic structure of bacterial genomes. Annu Rev Genet 32:339–445
Characklis WG, Marshall KC (1990) Biofilms. Wiley, New York
Chavez FP, Messie M, Pennington JT (2011) Marine primary production in relation to climate variability and change. Ann Rev Marine Sci 3:227–260
Cheesman SE, Guillemin K (2007) We know you are in there: conversing with the indigenous gut microbiota. Res Microbiol 158:2–9
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
Childress JJ, Felbeck H, Somero GN (1987) Symbiosis in the deep-sea. Sci Am 256:114–130
Cho BC, Azam F (1988) Major role of bacteria in biogeochemical fluxes in the oceans interior. Nature 332:441–443
Ciche TA, Darby C et al (2006) Dangerous liaisons: the symbiosis of entomopathogenic nematodes and bacteria. Biol Control 38:22–46
Cohen Y, Rosenberg E (1989) Microbial mats: physiological ecology of benthic microbial communities. American Society of Microbiology, Washington, DC
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
Conrad TM, Lewis NE, Palsson BO (2011) Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol 7
Cossart P, Boquet P, Normark S, Rappuoli R (1996) Cellular microbiology emerging. Science 271:315–316
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
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
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
Currie CR, Scott JA, Summerbell RC, Malloch D (1999) Fungus growing ants use antibiotic producing bacteria to control garden parasites. Nature 398:701–704
Currie CR, Poulsen M et al (2006) Coevolved crypts and exocrine glands support mutualistic bacteria in fungus-growing ants. Science 311:81–83
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
Darby AC, Chandler SM et al (2005) Aphid-symbiotic bacteria cultured in insect cell lines. Appl Environ Microbiol 71:4833–4839
Darwin C (1969) On the origin of species: facsimile edition. Harvard University Press, Cambridge, MA
Daubin V, Moran NA, Ochman H (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301:829–832
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
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
Davidson SK, Stahl DA (2008) Selective recruitment of bacteria during embryogenesis of an earthworm. ISME J 2:510–518
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
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
Decho AW, Herndl GJ (1995) Microbial activities and the transformation of organic matter within mucilaginous material. Sci Total Environ 165:33–42
Dekas AE, Poretsky RS, Orphan VJ (2009) Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. Science 326:422–426
Delong EF, Pace NR (2001) Environmental diversity of Bacteria and Archaea. Syst Biol 50:470–481
Delong EF, Frankel RB, Bazylinski DA (1993) Multiple evolutionary origins of magnetotaxis in bacteria. Science 259:803–806
Delong EF, Wu KY, Prézelin BB, Jovine RVM (1994) High abundance of archaea in Antarctic marine picoplankton. Nature 371:695–697
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
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
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
Devereux R, Delaney M, Widdel F, Stahl DA (1989) Natural relationships among sulfate reducing eubacteria. J Bacteriol 171:6689–6695
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
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
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
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
Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124–2128
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
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
Douglas AE (2009) The microbial dimension in insect nutritional ecology. Funct Ecol 23:38–47
Dubilier N, Mulders C et al (2001) Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm. Nature 411:298–302
Dubilier N, Bergin C et al (2008) Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol 6:725–740
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
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
Dvornyk V, Knudsen B (2005) Functional divergence of the circadian clock proteins in prokaryotes. Genetica 124:247–254
Elena SF, Lenski RE (2003) Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4:457–469
Faulkner J, Unson MD, Bewley CA (1994) The chemistry of some sponges and their symbionts. Pure Appl Chem 66:1983–1990
Fenchel T, Finlay BJ (1995) Ecology and evolution in anoxic worlds. Oxford University Press, Oxford
Fenchel T, Glud RN (1998) Veil architecture in a sulphide-oxidizing bacterium enhances countercurrent flux. Nature 394:367–369
Fenchel T (2002) Microbial behavior in a heterogeneous world. Science 296:1068–1071
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
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
Fiedler PC (2002) Environmental change in the eastern tropical Pacific Ocean: review of ENSO and decadal variability. Mar Ecol Prog Ser 244:265–283
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
Findlay RH, Yeates C, Hullar MA, Stahl DA, Kaplan LA (2008) Biome-level biogeography of streambed microbiota. Appl Environ Microbiol 74:3014–3021
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
Fisher CR (1990) Chemoautotrophic and methanotrophic symbioses in marine-invertebrates. Rev Aquat Sci 2:399–436
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
Follows MJ, Dutkiewicz S (2011) Modeling diverse communities of marine microbes. Ann Rev Mar Sci 3(3):427–451
Follows MJ, Dutkiewicz S, Grant S, Chisholm SW (2007) Emergent biogeography of microbial communities in a model ocean. Science 315:1843–1846
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
Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148–149
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
Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399:541–548
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
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
Fuhrman JA (2009) Microbial community structure and its functional implications. Nature 459:193–199
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
Fukui M, Teske A, Assmus B (1999) Physiology, phylogenetic relationships, and ecology of filamentous sulfate-reducing bacteria (genus Desulfonema). Arch Microbiol 172:193–203
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
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
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
Fuqua C, Greenberg EP (2002) Listening in on bacteria: acyl-homoserine lactone signaling. Nature Rev Mole Cell Biol 3:685–695
Gallardo CS (1977) Two modes of development in morph-species Crepidula dilatata (Gastropoda: Calyptraeidae) from Southern Chile. Mar Biol 39:241–251
Garcia-Pichel F, Mechling M, Castenholz RW (1994) Diel migrations of microorganisms within a benthic, hypersaline mat community. Appl Environ Microbiol 60:1500–1511
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
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
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
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
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
Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63
Giovannoni SJ, Cary SC (1993) Probing marine systems with ribosomal RNAs. Oceanography 6:95–104
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
Giovannoni SJ, Vergin KL (2012) Seasonality in ocean microbial communities. Science 335:671–676
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
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
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
Goodrich-Blair H, Clarke DJ (2007) Mutualism and pathogenesis in Xenorhabdus and Photorhabdus: two roads to the same destination. Mol Microbiol 64:260–268
Graf J, Kikuchi Y et al (2006) Leeches and their microbiota: naturally simple symbiosis models. Trends Microbiol 14:365–371
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
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
Grobbelaar N, Huang T-C, Lin H-Y, Chow T-J (1986) FEMS Microbiol Lett 37:173–177
Grotzinger JP, Knoll AH (1999) Stromatolites in precambrian carbonates: evolutionary mileposts or environmental dipsticks? Ann Rev Earth Planet Sci 27:313–358
Hahn MW, Hofle MG (2001) Grazing of protozoa and its effect on populations of aquatic bacteria. FEMS Microbiol Ecol 35:113–121
Harmer TL, Rotjan RD et al (2008) Free-living tube worm endosymbionts found at deep-sea vents. Appl Environ Microbiol 74:3895–3898
Hastings JW (1971) Light to hide by – ventral luminescence to camouflage silhouette. Science 173:1016
Hastings JW, Mitchell G (1971) Endosymbiotic bioluminescent bacteria from light organ of pony fish. Biol Bull 141:261–268
Hastings JW, Makemson J, Dunlap PV (1987) Are growth and luminescence regulated independently in light organ symbionts? Symbiosis 4:3–24
Hastings JW, Greenberg EP (1999) Quorum sensing: the explanation of a curious phenomenon reveals a common characteristic of bacteria. J Bacteriol 181:2667–2668
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
Haygood MG (1993) Light organ symbioses in fishes. Crit Rev Microbiol 19:191–216
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
Heidelberg KB, Gilbert JA, Joint I (2010) Marine genomics: at the interface of marine microbial ecology and biodiscovery. Microb Biotechnol 3:531–543
Herbert EE, Goodrich-Blair H (2007) Friend and foe: the two faces of Xenorhabdus nematophila. Nat Rev Microbiol 5:634–646
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
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
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
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
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
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
Hooper LV (2009) OPINION Do symbiotic bacteria subvert host immunity? Nat Rev Microbiol 7:367–374
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
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
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
Hullar MAJ, Kaplan LA, Stahl DA (2006) Recurring seasonal dynamics of microbial communities in stream habitats. Appl Environ Microbiol 72:713–722
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
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
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
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
Johnson CH, Stewart PL, Egli M (2011) The cyanobacterial circadian system: from biophysics to bioevolution. Annu Rev Biophys 40:143–167
Jorgensen BB, Cohen Y (1977) Solar Lake (Sinai) sulfur cycle of benthic cyanobacterial mats. Limnol Oceanogr 22:657–666
Jorgensen BB, Revsbech NP (1983) Colorless sulfur bacteria, Beggiatoa Spp and Thiovulum Spp in O2 and H2S microgradients. Appl Environ Microbiol 45:1261–1270
Jorgensen BB (1994) Sulfate reduction and thiosulfate transformations in a cyanobacterial mat during a diel oxygen cycle. FEMS Microbiol Ecol 13:303–312
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic, New York, pp 21–132
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
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
Karl DM (1994) Accurate estimation of microbial loop processes and rates. Microb Ecol 28:147–150
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
Karl DM (2010) Oceanic ecosystem time-series programs: ten lessons learned. Oceanography 23:104–125
Karner MB, Delong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507–510
Kau AL, Ahern PP et al (2011) Human nutrition, the gut microbiome and the immune system. Nature 474:327–336
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
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
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
Klitgord N, Segre D (2010) Environments that induce synthetic microbial ecosystems. PLOS Comput Biol 6
Knittel K, Boetius A (2009) Anaerobic oxidation of methane: progress with an unknown process. Ann Rev Microbiol 63:311–334
Kobayashi J, Ishibashi M (1993) Bioactive metabolites of symbiotic marine microorganisms. Chem Rev 93:1753–1769
Kolenbrander PE (2000) Oral microbial communities: biofilms, interactions, and genetic systems. Annu Rev Microbiol 54:413–437
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
Koonin EV (2009) Darwinian evolution in the light of genomics. Nucleic Acids Res 37:1011–1034
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
Kukor JJ, Martin MM (1986) The effect of acquired microbial enzymes on assimilation efficiency in the common woodlouse, Tracheoniscus-Rathkei. Oecologia 69:360–366
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
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
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
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
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
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
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
Lipson DA, Schmidt SK (2004) Seasonal changes in an alpine soil bacterial community in the Colorado Rocky Mountains. Appl Environ Microbiol 70:2867–2879
Llabres M, Agusti S (2006) Picophytoplankton cell death induced by UV radiation: evidence for oceanic Atlantic communities. Limnol Oceanogr 51:21–29
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
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
Maier S, Volker H, Beese M, Gallardo VA (1990) The fine structure of Thioploca aruacae and Thioploca chileae. Can J Microbiol 36:438–448
Margulis L, Fester R (eds) (1991) Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. The MIT Press, Cambridge, MA
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
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
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
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
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
Massana R (2011) Eukaryotic picoplankton in surface oceans. Annu Rev Microbiol 65:91–110
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
Mayr E (1982) The growth of biological thought: diversity, evolution, and inheritance. Belknap Press of Harvard University Press, Cambridge, MA
McCutcheon JP, Moran NA (2012) Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10:13–26
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
McFall-Ngai MJ (2001) Identifying “prime suspects”: symbioses and the evolution of multicellularity. Comp Biochem Phys B 129:711–723
McFall-Ngai MJ (2002) Unseen forces: The influence of bacteria on animal development. Dev Biol 242:1–14
McFall-Ngai MJ, Henderson B, Ruby E (eds) (2005) The influence of cooperative bacteria on animal host biology. Cambridge University Press, New York
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
McInerney MJ, Sieber JR, Gunsalus RP (2009) Syntrophy in anaerobic global carbon cycles. Curr Opin Biotechnol 20:623–632
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
Medina M, Sachs JL (2010) Symbiont genomics, our new tangled bank. Genomics 96:377–378
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
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
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
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
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
Moore LR, Rocap G, Chisholm SW (1998) Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393:464–467
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
Moran NA, McCutcheon JP et al (2008) Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet 42:165–190
Moran NA, McLaughlin HJ et al (2009) The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323:379–382
Morin JG, Harrington A et al (1975) Light for all reasons – versatility in behavioral repertoire of flashlight fish. Science 190:74–76
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
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
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
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
Nakabachi A, Yamashita A et al (2006) The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314:267
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
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
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
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
Ng WL, Bassler BL (2009) Bacterial quorum-sensing network architectures. Annu Rev Genet 43:197–222
Nussbaumer AD, Fisher CR et al (2006) Horizontal endosymbiont transmission in hydrothermal vent tubeworms. Nature 441:345–348
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
Nyholm SV, Mcfall-Ngai MJ (2004) The winnowing: establishing the squid-vibrio symbiosis. Nat Rev Microbiol 2:632–642
Nyholm SV, Stewart JJ et al (2009) Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes. Environ Microbiol 11:483–493
Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304
Ochman H, Moran NA (2001) Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:1096–1098
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
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
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
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
Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740
Pace NR (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol R 73:565–576
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
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
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
Papke RT, Ramsing NB, Bateson MM, Ward DM (2003) Geographical isolation in hot spring cyanobacteria. Environ Microbiol 5:650–659
Passow U (2002) Transparent exopolymer particles (TEP) in aquatic environments. Prog Oceanogr 55:287–333
Pennisi E (2001) Microbial genomes: sequences reveal borrowed genes. Science 294:1634–1635
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
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
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
Pernthaler J (2005) Predation on prokaryotes in the water column and its ecological implications. Nat Rev Microbiol 3:537–546
Philander SG, Fedorov A (2003) Is El Nino sporadic or cyclic? Ann Rev Earth Planet Sci 31:579–594
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
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
Pomeroy LR (1974) The ocean’s foodweb: a changing paradigm. Bioscience 24:499–504
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
Proctor LM (2011) The human microbiome project in 2011 and beyond. Cell Host Microbe 10:287–291
Purcell EM (1977) Life at low Reynolds-number. Am J Phys 45:3–11
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
Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633
Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394
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
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
Relman DA, Falkow S (2001) The meaning and impact of the human genome sequence for microbiology. Trends Microbiol 9:206–208
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
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
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
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
Risatti JB, Capman WC, Stahl DA (1994) Community structure of a microbial mat – the phylogenetic dimension. Proc Natl Acad Sci USA 91:10173–10177
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
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
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
Rohwer F, Thurber RV (2009) Viruses manipulate the marine environment. Nature 459:207–212
Ruby EG, Lee KH (1998) The Vibrio fischeri Euprymna scolopes light organ association: current ecological paradigms. Appl Environ Microbiol 64:805–812
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
Ruby EG (2008) Symbiotic conversations are revealed under genetic interrogation. Nat Rev Microbiol 6:752–762
Sachs JL, Skophammer RG et al (2011) Evolutionary transitions in bacterial symbiosis. Proc Natl Acad Sci USA 108:10800–10807
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
Schaecter M (2003) Integrative microbiology: the third golden age. J Biosci 28:149–154
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
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
Schulz HN, Jorgensen BB (2001) Big bacteria. Ann Rev Microbiol 55:105–137
Scott JJ, Oh DC et al (2008) Bacterial protection of beetle-fungus mutualism. Science 322:63
Seckbach J (2002) Symbiosis: mechanisms and model systems. In: Seckbach J (ed) Cellular origin and life in extreme habitats. Kluwer, Norwell
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
Shimoyama T, Kato S, Ishii S, Watanabe K (2009) Flagellum mediates symbiosis. Science 323:1574
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
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
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
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
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
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
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
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
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
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
Southward EC (1999) Development of Perviata and Vestimentifera (Pogonophora). Hydrobiologia 402:185–202
Spaulding AW, von Dohlen CD (1998) Phylogenetic characterization and molecular evolution of bacterial endosymbionts in psyllids (Hemiptera: Sternorrhyncha). Mol Biol Evol 15:1506–1513
Stahl DA, Lane DJ, Olsen GJ, Pace NR (1984) Analysis of hydrothermal vent-associated symbionts by ribosomal-RNA sequences. Science 224:409–411
Stahl D (1993) The natural history of microorganisms. ASM News 59:609–613
Staley JT, Gosink JJ (1999) Poles apart: biodiversity and biogeography of sea ice bacteria. Annu Rev Microbiol 53:189–215
Stams AJM, Plugge CM (2009) Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 7:568–577
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
Stern A, Sorek R (2011) The phage-host arms race: shaping the evolution of microbes. Bioessays 33:43–51
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
Stougaerd J (2000) Regulators and regulation of legume root nodule development. Plant Physiol 124:531–539
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
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
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
Suttle CA (2005) Viruses in the sea. Nature 437:356–361
Suttle CA (2007) Marine viruses – major players in the global ecosystem. Nat Rev Microbiol 5:801–812
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
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
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
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
Thamdrup B, Canfield DE (1996) Fate of elemental sulfur in an intertidal sediment. FEMS Microbiol Ecol 19:95–103
Thar R, Fenchel T (2001) True chemotaxis in oxygen gradients of the sulfur-oxidizing bacterium Thiovulum majus. Appl Environ Microbiol 67:3299–3303
Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245
Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity – magnitude, dynamics, and controlling factors. Science 296:1064–1066
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
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
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
Turner JT (2002) Zooplankton fecal pellets, marine snow and sinking phytoplankton blooms. Aquat Microbial Ecol 27:57–102
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
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
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
van Loosdrecht MCM, Lyklema J, Norde W, Zehnder AJB (1990) Influence of interfaces on microbial activity. Microbiol Rev 54:75–87
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
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
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
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
Wang CZ, Fiedler PC (2006) ENSO variability and the eastern tropical Pacific: a review. Prog Oceanogr 69:239–266
Ward DM, Weller R, Bateson MM (1990) 16S ribosomal-RNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63–65
Warnecke F, Luginbuhl P et al (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–U517
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
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
Werren JH (1997) Biology of Wolbachia. Annu Rev Entomol 42:587–609
Werren JH, Baldo L et al (2008) Wolbachia: master manipulators of invertebrate biology. Nat Rev Microbiol 6:741–751
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
Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976–978
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
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
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
Wilkinson TL, Douglas AE (1996) The impact of aposymbiosis on amino acid metabolism of pea aphids. Entomol Exp Appl 80:279–282
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
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
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
Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97:8392–8396
Woese CR (2004) A new biology for a new century. Microbiol Mol Biol R 68:173–186
Wolin MJ, Miller TL (1982) Interspecies hydrogen transfer: 15 years later. ASM News 48:561–565
Woyke T, Teeling H et al (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443:950–955
Wren BW (2000) Microbial genome analysis: Insights into virulence, host adaptation and evolution. Nat Rev Genet 1:30–39
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
Xavier KB, Bassler BL (2003) LuxS quorum sensing: more than just a numbers game. Curr Opin Microbiol 6:191–197
Young RE, Roper CFE (1976) Bioluminescent counter-shading in midwater animals – evidence from living squid. Science 191:1046–1048
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
Zaura E, Keijser BJF, Huse SM, Crielaard W (2009) Defining the healthy “core microbiome” of oral microbial communities. BMC Microbiol 9:259
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
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
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
Zimmer M, Topp W (1998) Microorganisms and cellulose digestion in the gut of the woodlouse Porcellio scaber. J Chem Ecol 24:1397–1408
Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. J Theoret Biol 8:357–366
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
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.
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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
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