Patterns and processes of microbial community assembly

Microbiology and Molecular Biology Reviews

Volumn 77, Issue 3, 2013, Pages 342-356

  Nemergut, Diana R ^a   Schmidt, Steven K ^a   Fukami, Tadashi ^b   O'Neill, Sean P ^a   Bilinski, Teresa M ^a   Stanish, Lee F ^a   Knelman, Joseph E ^a   Darcy, John L ^a   Lynch, Ryan C ^a   Wickey, Phillip ^a   Ferrenberg, Scott ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; BIOGEOGRAPHY; COMMUNITY ECOLOGY; GENETIC SELECTION; MICROBIAL COMMUNITY; MICROORGANISM; MOLECULAR PHYLOGENY; NONHUMAN; PHYLOGENY; REVIEW;

BIODIVERSITY; ECOSYSTEM; MICROBIOLOGY;

EID: 84884520264     PISSN: 10922172     EISSN: 10985557     Source Type: Journal    
DOI: 10.1128/MMBR.00051-12     Document Type: Review

References (159)

1. Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, Lauro FM, Fuhrman JA, Donachie SP. 2009. Microbial community structure in the North Pacific Ocean. ISME J. 3:1374-1386.
2. 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:e15545. doi:10.1371/journal.pone.0015545.
3. Lee CK, Barbier BA, Bottos EM, McDonald IR, Cary SC. 2012. The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities. ISME J. 6:1046-1057.
4. Pommier T, Neal PR, Gasol JM, Coll M, Acinas SG, Pedros-Alio C. 2010. Spatial patterns of bacterial richness and evenness in theNWMediterranean Sea explored by pyrosequencing of the 16S rRNA. Aquat. Microb. Ecol. 61:212-224.
5. Vellend M. 2010. Conceptual synthesis in community ecology. Q. Rev. Biol. 85:183-206.
6. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Tumbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7:335-336.
7. Giongo A, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LFW, Walts B, Riva A, King G, Triplett EW. 2010. PANGEA: pipeline for analysis of next generation amplicons. ISME J. 4:852-861.
8. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PSG, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, Gil IS, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, et al. 2011. Minimum information about a marker gene sequence (MIMARKS) and minimuminformation about any (x) sequence (MIxS) specifications. Nat. Biotechnol. 29:415-420.
9. Jansson JK, Prosser JI. 2013. Microbiology: the life beneath our feet. Nature 494:40-41.
10. Wennekes PL, Rosindell J, Etienne RS. 2012. The neutral-niche debate: a philosophical perspective. Acta Biotheor. 60:257-271.
11. Weiher E, Keddy PA. 1995. Assembly rules, null models and trait dispersion- new questions from old patterns. Oikos 74:159-164. (Pubitemid 3005216)
12. Roughgarden J. 2009. Is there a general theory of community ecology? Biol. Philos. 24:521-529.
13. Hugenholtz P, Goebel BM, Pace NR. 1998. Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774. (Pubitemid 28429361)
14. Kirk JL, Beaudette LA, Hart M, Moutoglis P, Khironomos JN, Lee H, Trevors JT. 2004. Methods of studying soil microbial diversity. J. Microbiol. Methods 58:169-188. (Pubitemid 38960722)
15. Schloss PD, Handelsman J. 2004. Status of the microbial census. Microbiol. Mol. Biol. Rev. 68:686-691. (Pubitemid 39628533)
16. Darcy JL, Lynch RC, King AJ, Robeson MS, Schmidt SK. 2011. Global distribution of Polaromonas phylotypes-evidence for a highly successful dispersal capacity. PLoS One 6:e23742. doi:10.1371/journal.pone .0023742.
17. Finlay BJ. 2002. Global dispersal of free-living microbial eukaryote species. Science 296:1061-1063. (Pubitemid 34517112)
18. Finlay BJ, Clarke KJ. 1999. Ubiquitous dispersal of microbial species. Nature 400:828.
19. Wilkinson DM, Koumoutsaris S, Mitchell EAD, Bey I. 2012. Modelling the effect of size on the aerial dispersal of microorganisms. J. Biogeogr. 39:89-97.
20. Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin PJ, Naeem S, Ovreas L, Reysenbach AL, Smith VH, Staley JT. 2006. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4:102-112. (Pubitemid 43158153)
21. Jones SE, Lennon JT. 2010. Dormancy contributes to the maintenance of microbial diversity. Proc. Natl. Acad. Sci. U. S. A. 107:5881-5886.
22. Lennon JT, Jones SE. 2011. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat. Rev. Microbiol. 9:119-130.
23. Locey KJ. 2010. Synthesizing traditional biogeography with microbial ecology: the importance of dormancy. J. Biogeogr. 37:1835-1841.
24. Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JLM, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM. 2008. Towards environmental systems biology of Shewanella. Nat. Rev. Microbiol. 6:592-603.
25. Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, Seshadri R, Ward N, Methe B, Clayton RA, Meyer T, Tsapin A, Scott J, Beanan M, Brinkac L, Daugherty S, DeBoy RT, Dodson RJ, Durkin AS, Haft DH, Kolonay JF, Madupu R, Peterson JD, Umayam LA, White O, Wolf AM, Vamathevan J, Weidman J, Impraim M, Lee K, Berry K, Lee C, Mueller J, Khouri H, Gill J, Utterback TR, McDonald LA, Feldblyum TV, Smith HO, Venter JC, Nealson KH, Fraser CM. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20:1118-1123. (Pubitemid 35285440)
26. Polz MF, Hunt DE, Preheim SP, Weinreich DM. 2006. Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361:2009-2021. (Pubitemid 44787035)
27. Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabo G, Polz MF, Alm EJ. 2012. Population genomics of early events in the ecological differentiation of bacteria. Science 336:48-51.
28. Thompson JR, Pacocha S, Pharino C, Klepac-Ceraj V, Hunt DE, Benoit J, Sarma-Rupavtarm R, Distel DL, Polz MF. 2005. Genotypic diversity within a natural coastal bacterioplankton population. Science 307:1311-1313. (Pubitemid 40299980)
29. Schmidt SK, Costello EK, Nemergut DR, Cleveland CC, Reed SC, Weintraub MN, Meyer AF, Martin AM. 2007. Biogeochemical consequences of rapid microbial turnover and seasonal succession in soil. Ecology 88:1379-1385. (Pubitemid 351345213)
30. Yoshida T, Ellner SP, Jones LE, Bohannan BJM, Lenski RE, Hairston NG. 2007. Cryptic population dynamics: rapid evolution masks trophic interactions. PLoS Biol. 5:e235. doi:10.1371/journal.pbio.0050235. (Pubitemid 47416585)
31. Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304. (Pubitemid 30337055)
32. Sexstone AJ, Revsbech NP, Parkin TB, Tiedje JM. 1985. Direct measurement of oxygen profiles and denitrification rates in soil aggregates. Soil Sci. Soc. Am. J. 49:645-651.
33. Pernthaler A, Pernthaler J, Amann R. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68:3094-3101. (Pubitemid 34602035)
34. Behrens S, Losekann T, Pett-Ridge J, Weber PK, Ng WO, Stevenson BS, Hutcheon ID, Relman DA, Spormann AM. 2008. Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS. Appl. Environ. Microbiol. 74:3143-3150. (Pubitemid 351747021)
35. Magurran AE. 2003. Measuring biological diversity. Blackwell Publishing, Victoria, Australia.
36. Leibold MA, Holyoak M, Mouquet N, Amarasekare P, Chase JM, Hoopes MF, Holt RD, Shurin JB, Law R, Tilman D, Loreau M, Gonzalez A. 2004. The metacommunity concept: a framework for multiscale community ecology. Ecol. Lett. 7:601-613. (Pubitemid 38847749)
37. Lawton JH, Bignell DE, Bolton B, Bloemers GF, Eggleton P, Hammond PM, Hodda M, Holt RD, Larsen TB, Mawdsley NA, Stork NE, Srivastava DS, Watt AD. 1998. Biodiversity inventories, indicator taxa and effects of habitat modification in tropical forest. Nature 391:72-76. (Pubitemid 28079216)
38. Odum EP. 1968. Energy flow in ecosystems-a historical review. Am. Zool. 8:11-18.
39. Fauth JE, Bernardo J, Camara M, Resetarits WJ, VanBuskirk J, Mc-Collum SA. 1996. Simplifying the jargon of community ecology: a conceptual approach. Am. Nat. 147:282-286. (Pubitemid 2625422)
40. Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G. 2001. DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl. Environ. Microbiol. 67:2354-2359. (Pubitemid 33641427)
41. Gotelli NJ, Graves GR. 1996. Null models in ecology. Smithsonian Institution Press, Washington, DC.
42. Klappenbach JA, Saxman PR, Cole JR, Schmidt TM. 2001. rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res. 29:181-184. (Pubitemid 32054441)
43. Whittaker RH. 1956. Vegetation of the great smoky mountains. Ecol. Monogr. 26:1-69.
44. Anderson MJ, Crist TO, Chase JM, Vellend M, Inouye BD, Freestone AL, Sanders NJ, Cornell HV, Comita LS, Davies KF, Harrison SP, Kraft NJB, Stegen JC, Swenson NG. 2011. Navigating the multiple meanings of beta diversity: a roadmap for the practicing ecologist. Ecol. Lett. 14:19-28.
45. Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61:1-10.
46. Kembel SW, Eisen JA, Pollard KS, Green JL. 2011. The phylogenetic diversity of metagenomes. PLoS One 6:e23214. doi:10.1371/journal .pone.0023214.
47. Bent SJ, Forney LJ. 2008. The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J. 2:689-695. (Pubitemid 351951570)
48. Lozupone CA, Hamady M, Kelley ST, Knight R. 2007. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73:1576-1585. (Pubitemid 46417883)
49. Lozupone CA, Knight R. 2008. Species divergence and the measurement of microbial diversity. FEMS Microbiol. Rev. 32:557-578. (Pubitemid 351799685)
50. Sloan WT, Lunn M, Woodcock S, Head IM, Nee S, Curtis TP. 2006. Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environ. Microbiol. 8:732-740. (Pubitemid 43363329)
51. Lozupone C, Hamady M, Knight R. 2006. UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371. doi:10.1186/1471-2105-7-371. (Pubitemid 44390007)
52. Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235. (Pubitemid 41803949)
53. Tuomisto H. 2010. A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity. Ecography 33:2-22.
54. Chase JM, Myers JA. 2011. Disentangling the importance of ecological niches from stochastic processes across scales. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366:2351-2363.
55. Crist TO, Veech JA, Gering JC, Summerville KS. 2003. Partitioning species diversity across landscapes and regions: a hierarchical analysis of alpha, beta, and gamma diversity. Am. Nat. 162:734-743. (Pubitemid 38157780)
56. Kraft NJB, Comita LS, Chase JM, Sanders NJ, Swenson NG, Crist TO, Stegen JC, Vellend M, Boyle B, Anderson MJ, Cornell HV, Davies KF, Freestone AL, Inouye BD, Harrison SP, Myers JA. 2011. Disentangling the drivers of beta diversity along latitudinal and elevational gradients. Science 333:1755-1758.
57. Astorga A, Oksanen J, Luoto M, Soininen J, Virtanen R, Muotka T. 2012. Distance decay of similarity in freshwater communities: do macroand microorganisms follow the same rules? Glob. Ecol. Biogeogr. 21:365-375.
58. Fenchel T, Finlay BJ. 2004. The ubiquity of small species: patterns of local and global diversity. Bioscience 54:777-784. (Pubitemid 39073976)
59. Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. U. S. A. 103:626-631. (Pubitemid 43153076)
60. Fuhrman JA. 2009. Microbial community structure and its functional implications. Nature 459:193-199.
61. Curtis TP, Sloan WT, Scannell JW. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. U. S. A. 99:10494-10499.
62. McGill BJ, Etienne RS, Gray JS, Alonso D, Anderson MJ, Benecha HK, Dornelas M, Enquist BJ, Green JL, He FL, Hurlbert AH, Magurran AE, Marquet PA, Maurer BA, Ostling A, Soykan CU, Ugland KI, White EP. 2007. Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecol. Lett. 10:995-1015. (Pubitemid 47383385)
63. Hubert C, Loy A, Nickel M, Arnosti C, Baranyi C, Bruchert V, Ferdelman T, Finster K, Christensen FM, de Rezende JR, Vandieken V, Jorgensen BB. 2009. A constant flux of diverse thermophilic bacteria into the cold Arctic seabed. Science 325:1541-1544.
64. Gobet A, Quince C, Ramette A. 2010. Multivariate cutoff level analysis (MultiCoLA) of large community data sets. Nucleic Acids Res. 38:e155. doi:10.1093/nar/gkq545.
65. Cleveland CC, Nemergut DR, Schmidt SK, Townsend AR. 2007. Increases in soil respiration following labile carbon additions linked to rapid shifts in soil microbial community composition. Biogeochemistry 82:229-240. (Pubitemid 46432672)
66. Szabo KE, Itor POB, Bertilsson S, Tranvik L, Eiler A. 2007. Importance of rare and abundant populations for the structure and functional potential of freshwater bacterial communities. Aquat. Microb. Ecol. 47:1-10. (Pubitemid 47343603)
67. Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK. 2005. The contribution of species richness and composition to bacterial services. Nature 436:1157-1160. (Pubitemid 41232293)
68. Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, Green JL. 2008. Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc. Natl. Acad. Sci. U. S. A. 105:11505-11511.
69. Green JL, Holmes AJ, Westoby M, Oliver I, Briscoe D, Dangerfield M, Gillings M, Beattie AJ. 2004. Spatial scaling of microbial eukaryote diversity. Nature 432:747-750. (Pubitemid 39656292)
70. Horner-Devine MC, Lage M, Hughes JB, Bohannan BJM. 2004. A taxa-area relationship for bacteria. Nature 432:750-753. (Pubitemid 39656293)
71. Bissett A, Richardson AE, Baker G, Wakelin S, Thrall PH. 2010. Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales. Mol. Ecol. 19:4315-4327.
72. Storch D, Sizling AL. 2008. The concept of taxon invariance in ecology: do diversity patterns vary with changes in taxonomic resolution? Folia Geobot. 43:329-344.
73. King AJ, Freeman KR, McCormick KF, Lynch RC, Lozupone C, Knight R, Schmidt SK. 2010. Biogeography and habitat modelling of high-alpine bacteria. Nat. Commun. 1:53. doi:10.1038/ncomms1055.
74. Preston FW. 1948. The commonness, and rarity, of species. Ecology 29:254-283.
75. Adler PB, Lauenroth WK. 2003. The power of time: spatiotemporal scaling of species diversity. Ecol. Lett. 6:749-756. (Pubitemid 36941110)
76. Ayarza JM, Erijman L. 2011. Balance of neutral and deterministic components in the dynamics of activated sludge floc assembly. Microb. Ecol. 61:486-495.
77. Redford AJ, Fierer N. 2009. Bacterial succession on the leaf surface: a novel system for studying successional dynamics. Microb. Ecol. 58:189-198.
78. van der Gast CJ, Ager D, Lilley AK. 2008. Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors. Environ. Microbiol. 10:1411-1418. (Pubitemid 351670240)
79. Horner-Devine MC, Bohannan BJM. 2006. Phylogenetic clustering and overdispersion in bacterial communities. Ecology 87:S100-S108. doi:10 .1890/0012-9658(2006)87[100:PCAOIB]2.0.CO;2. (Pubitemid 44564729)
80. Chaffron S, Rehrauer H, Pernthaler J, von Mering C. 2010. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res. 20:947-959.
81. Cardillo M, Gittleman JL, Purvis A. 2008. Global patterns in the phylogenetic structure of island mammal assemblages. Proc. Biol. Sci. 275:1549-1556. (Pubitemid 351693546)
82. Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF. 2005. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol. 71:8966-8969. (Pubitemid 41804041)
83. Rainey PB, Travisano M. 1998. Adaptive radiation in a heterogeneous environment. Nature 394:69-72. (Pubitemid 28321802)
84. Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH. 2012. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat. Rev. Microbiol. 10:497-506.
85. Baas-Becking LGM. 1934. Geobiologie of inleiding tot de milieukunde. WP Van Stockum & Zoon, The Hague, The Netherlands.
86. Hubbell SP. 2001. The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, NJ.
87. Rosindell J, Hubbell SP, Etienne RS. 2011. The unified neutral theory of biodiversity and biogeography at age ten. Trends Ecol. Evol. 26(7):340-348.
88. Lozupone CA, Knight R. 2007. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci. U. S. A. 104:11436-11440. (Pubitemid 47175158)
89. Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, Fierer N, Townsend AR, Cleveland CC, Stanish L, Knight R. 2011. Global patterns in the biogeography of bacterial taxa. Environ. Microbiol. 13:135-144.
90. Logue JB, Lindstrom ES. 2010. Species sorting affects bacterioplankton community composition as determined by 16S rDNA and 16S rRNA fingerprints. ISME J. 4:729-738.
91. Nemergut DR, Cleveland CC, Wieder WR, Washenberger CL, Townsend AR. 2010. Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest. Soil Biol. Biochem. 42:2153-2160.
92. Violle C, Nemergut DR, Pu ZC, Jiang L. 2011. Phylogenetic limiting similarity and competitive exclusion. Ecol. Lett. 14:782-787.
93. Philippot L, Andersson SGE, Battin TJ, Prosser JI, Schimel JP, Whitman WB, Hallin S. 2010. The ecological coherence of high bacterial taxonomic ranks. Nat. Rev. Microbiol. 8:523-529.
94. Lewis K. 2010. Persister cells. Annu. Rev. Microbiol. 64:357-372.
95. Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T. 2011. Bacterial community assembly based on functional genes rather than species. Proc. Natl. Acad. Sci. U. S. A. 108:14288-14293.
96. Green JL, Bohannan BJM, Whitaker RJ. 2008. Microbial biogeography: from taxonomy to traits. Science 320:1039-1043. (Pubitemid 351929519)
97. Marchant R, Banat IM, Rahman TJ, Berzano M. 2002. The frequency and characteristics of highly thermophilic bacteria in cool soil environments. Environ. Microbiol. 4:595-602. (Pubitemid 35211943)
98. Bowers RM, Sullivan AP, Costello EK, Collett JL, Knight R, Fierer N. 2011. Sources of bacteria in outdoor air across cities in the Midwestern United States. Appl. Environ. Microbiol. 77:6350-6356.
99. Lindstrom ES, Ostman O. 2011. The importance of dispersal for bacterial community composition and functioning. PLoS One 6:e25883. doi: 10.1371/journal.pone.0025883.
100. Papke RT, Ward DM. 2004. The importance of physical isolation to microbial diversification. FEMS Microbiol. Ecol. 48:293-303. (Pubitemid 38648917)
101. Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW. 2009. The merging of community ecology and phylogenetic biology. Ecol. Lett. 12:693-715.
102. Buerger S, Spoering A, Gavrish E, Leslin C, Ling L, Epstein SS. 2012. Microbial scout hypothesis and microbial discovery. Appl. Environ. Microbiol. 78:3229-3233.
103. Papke RT, Gogarten JP. 2012. How bacterial lineages emerge. Science 336:45-46.
104. Boles BR, Thoendel M, Singh PK. 2004. Self-generated diversity produces "insurance effects" in biofilm communities. Proc. Natl. Acad. Sci. U. S. A. 101:16630-16635. (Pubitemid 39557764)
105. Hansen SK, Rainey PB, Haagensen JAJ, Molin S. 2007. Evolution of species interactions in a biofilm community. Nature 445:533-536. (Pubitemid 46197632)
106. Rensing C, Newby DT, Pepper IL. 2002. The role of selective pressure and selfish DNA in horizontal gene transfer and soil microbial community adaptation. Soil Biol. Biochem. 34:285-296. (Pubitemid 34179523)
107. Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP, Green JL, Green LE, Killham K, Lennon JJ, Osborn AM, Solan M, van der Gast CJ, Young JPW. 2007. The role of ecological theory in microbial ecology. Nat. Rev. Microbiol. 5:384-392. (Pubitemid 46605492)
108. Ofiteru ID, Lunn M, Curtis TP, Wells GF, Criddle CS, Francis CA, Sloan WT. 2010. Combined niche and neutral effects in a microbial wastewater treatment community. Proc. Natl. Acad. Sci. U. S. A. 107:15345-15350.
109. Yang C, Zhang W, Liu RH, Li Q, Li BB, Wang SF, Song CJ, Qiao CL, Mulchandani A. 2011. Phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale wastewater treatment plants. Environ. Sci. Technol. 45:7408-7415.
110. Lankau EW, Hong PY, Mackie RI. 2012. Ecological drift and local exposures drive enteric bacterial community differences within species of Galapagos iguanas. Mol. Ecol. 21:1779-1788.
111. Pedros-Alio C. 2006. Marine microbial diversity: can it be determined? Trends Microbiol. 14:257-263. (Pubitemid 43825732)
112. Allison SD, Martiny JBH. 2008. Resistance, resilience, and redundancy in microbial communities. Proc. Natl. Acad. Sci. U. S. A. 105:11512-11519.
113. Griffiths BS, Philippot L. 2013. Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol. Rev. 37:112-129.
114. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489:220-230.
115. Leibold MA, McPeek MA. 2006. Coexistence of the niche and neutral perspectives in community ecology. Ecology 87:1399-1410. (Pubitemid 44066088)
116. DeAngelis KM, Firestone MK. 2012. Phylogenetic clustering of soil microbial communities by 16S rRNA but not 16S rRNA genes. Appl. Environ. Microbiol. 78:2459-2461.
117. Litchman E. 2010. Invisible invaders: non-pathogenic invasive microbes in aquatic and terrestrial ecosystems. Ecol. Lett. 13:1560-1572.
118. Chase JM. 2007. Drought mediates the importance of stochastic community assembly. Proc. Natl. Acad. Sci. U. S. A. 104:17430-17434. (Pubitemid 350219855)
119. Jiang L, Brady L, Tan JQ. 2011. Species diversity, invasion, and alternative community states in sequentially assembled communities. Am. Nat. 178:411-418.
120. Ferrenberg S, O'Neill SP, Knelman JE, Todd B, Bradley D, Robinson T, Schmidt SK, Townsend AR, Williams MW, Cleveland CC, Melbourne BA, Jiang L, Nemergut D. 2013. Changes in assembly processes in soil bacterial communities following a wildfire disturbance. ISME J. 7:1102-1111.
121. Chase JM. 2003. Community assembly: when should history matter? Oecologia 136:489-498. (Pubitemid 37110754)
122. Drake JA. 1990. Communities as assembled structures: do rules govern pattern? Trends Ecol. Evol. 5(5):159-164. (Pubitemid 120036280)
123. Fukami T. 2010. Community assembly dynamics in space, p 45-53. In Verhoef HA, Morin PJ (ed), Community ecology: processes, models and applications. Oxford University Press, Oxford, United Kingdom.
124. Fukami T, Nakajima M. 2011. Community assembly: alternative stable states or alternative transient states? Ecol. Lett. 14:973-984.
125. Gleason HA. 1927. Further views on the succession concept. Ecology 8:299-326.
126. Peterson CH. 1984. Does a rigorous criterion for environmental identity preclude the existence of multiple stable points? Am. Nat. 124:127-133.
127. Luh HK, Pimm SL. 1993. The assembly of ecological communities: a minimalist approach. J. Anim. Ecol. 62:749-765. (Pubitemid 24409192)
128. Pimm SL. 1991. The balance of nature? Ecological issues in the conservation of species and communities. The University of Chicago Press, Chicago, IL.
129. Warren PH, Law R, Weatherby AJ. 2003. Mapping the assembly of protist communities in microcosms. Ecology 84:1001-1011. (Pubitemid 36893029)
130. Drake JA. 1991. Community assembly mechanics and the structure of an experimental species ensemble. Am. Nat. 137:1-26.
131. Jiang L, Patel SN. 2008. Community assembly in the presence of disturbance: a microcosm experiment. Ecology 89:1931-1940.
132. Peay KG, Belisle M, Fukami T. 2012. Phylogenetic relatedness predicts priority effects in nectar yeast communities. Proc. Biol. Sci. 279:749-758.
133. Robinson JV, Dickerson JE. 1987. Does invasion sequence affect community structure. Ecology 68:587-595.
134. Tan JQ, Pu ZC, Ryberg WA, Jiang L. 2012. Species phylogenetic relatedness, priority effects, and ecosystem functioning. Ecology 93:1164-1172.
135. Cadotte MW, Drake JA, Fukami T. 2005. Constructing nature: laboratory models as necessary tools for investigating complex ecological communities. Adv. Ecol. Res. 37:333-353.
136. Drake JA, Huxel GR, Hewitt CL. 1996. Microcosms as models for generating and testing community theory. Ecology 77:670-677. (Pubitemid 126494895)
137. Jessup CM, Kassen R, Forde SE, Kerr B, Buckling A, Rainey PB, Bohannan BJM. 2004. Big questions, small worlds: microbial model systems in ecology. Trends Ecol. Evol. 19(4):189-197. (Pubitemid 38355798)
138. Fukami T, Dickie IA, Wilkie JP, Paulus BC, Park D, Roberts A, Buchanan PK, Allen RB. 2010. Assembly history dictates ecosystem functioning: evidence from wood decomposer communities. Ecol. Lett. 13:675-684.
139. Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC. 2011. Drivers of bacterial beta-diversity depend on spatial scale. Proc. Natl. Acad. Sci. U. S. A. 108:7850-7854.
140. Fukami T. 2004. Assembly history interacts with ecosystem size to influence species diversity. Ecology 85:3234-3242. (Pubitemid 40084773)
141. Lomolino MV. 1990. The target area hypothesis: the influence of island area on immigration rates of non-volant mammals. Oikos 57:297-300. (Pubitemid 20428390)
142. Petraitis PS, Latham RE. 1999. The importance of scale in testing the origins of alternative community states. Ecology 80:429-442. (Pubitemid 29126118)
143. Robeson MS, King AJ, Freeman KR, Birky CW, Martin AP, Schmidt SK. 2011. Soil rotifer communities are extremely diverse globally but spatially autocorrelated locally. Proc. Natl. Acad. Sci. U. S. A. 108:4406-4410.
144. Robinson JV, Edgemon MA. 1988. An experimental evaluation of the effect of invasion history on community structure. Ecology 69:1410-1417. (Pubitemid 19323702)
145. Whitaker RJ, Grogan DW, Taylor JW. 2003. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976-978. (Pubitemid 36994812)
146. Cottenie K. 2005. Integrating environmental and spatial processes in ecological community dynamics. Ecol. Lett. 8:1175-1182. (Pubitemid 41532401)
147. Meyer O. 1994. Functional groups of microorganisms. In Schulze ED, MooneyHA(ed), Biodiversity and ecosystem function. Springer-Verlag, Berlin, Germany.
148. Jones CM, Hallin S. 2010. Ecological and evolutionary factors underlying global and local assembly of denitrifier communities. ISME J. 4:633-641.
149. Paul EA, Clark FE. 1996. Soil microbiology and biochemistry, 2nd ed. Academic Press, London, United Kingdom.
150. Langenheder S, Lindstrom ES, Tranvik LJ. 2005. Weak coupling between community composition and functioning of aquatic bacteria. Limnol. Oceanogr. 50:957-967. (Pubitemid 40764381)
151. Allison SD. 2012. A trait-based approach for modelling microbial litter decomposition. Ecol. Lett. 15:1058-1070.
152. Follows MJ, Dutkiewicz S, Grant S, Chisholm SW. 2007. Emergent biogeography of microbial communities in a model ocean. Science 315:1843-1846. (Pubitemid 46580143)
153. Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. 2011. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol. Syst. Biol. 7:473. doi:10.1038/msb .2011.6.
154. Hutchinson G. 1961. Paradox of plankton. Am. Nat. 95:137-145.
155. Chase JM, Leibold MA. 2002. Spatial scale dictates the productivitybiodiversity relationship. Nature 416:427-430. (Pubitemid 34272876)
156. Chesson P. 2000. Mechanisms of maintenance of species diversity. Annu. Rev. Ecol. Syst. 31:343-366. (Pubitemid 32122406)
157. Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. 2009. The bacterial species challenge: making sense of genetic and ecological diversity. Science 323:741-746.
158. Fukami T. 2008. Stochasticity in community assembly, and spatial scale, p 51-71. In Ohgushi T, Kondoh M, Noda T (ed), Community ecology, vol. 5. Kyoto University Press, Kyoto, Japan. (In Japanese.)
159. Woodcock S, Curtis TP, Head IM, Lunn M, Sloan WT. 2006. Taxaarea relationships for microbes: the unsampled and the unseen. Ecol. Lett. 9:805-812. (Pubitemid 43883030)