Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S (2017) The growing tree of archaea: new perspectives on their diversity, evolution and ecology. ISME J 11:2407-2425 doi: 10.1038/ismej.2017.122
Allison SD, Martiny JBH (2008) Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci USA 105:11512-11519 doi: 10.1073/pnas.0801925105
Alves RJE, Minh BQ, Urich T, von Haeseler A, Schleper C (2018) Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat Commun 9:1517
Andersson B, Sundbäck K, Hellman M, Hallin S, Alsterberg C (2014) Nitrogen fxation in shallow-water sediments: spatial distribution and controlling factors. Limnol Oceanogr 59:1932-1944 doi: 10.4319/lo.2014.59.6.1932
Aßhauer KP, Wemheuer B, Daniel R, Meinicke P (2015) Tax4Fun: predicting functional profles from metagenomic 16S rRNA data. Bioinformatics 31:2882-2884 doi: 10.1093/bioinformatics/btv287
Baas-Becking LGM (1934) Geobiologie of inleiding tot de milieukunde. W.P. van Stockum & Zoon, Den Haag
Bairey E, Kelsic ED, Kishony R (2016) High-order species interactions shape ecosystem diversity. Nat Commun 7:12285
Baldrian P, Kolarik M, Stursova M, Kopecky J, Valaskova V, Vetrovsky T, Zifcakova L, Snajdr J, Ridl J, Vlcek C, Voriskova J (2012) Active and total microbial communities in forest soil are largely diferent and highly stratifed during decomposition. ISME J 6:248-258 doi: 10.1038/ismej.2011.95
Banerjee S, Schlaeppi K, van der Heijden MGA (2018) Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol 16:567-576 doi: 10.1038/s41579-018-0024-1
Barberán A, Bates ST, Casamayor EO, Fierer N (2012) Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 6:343-351 doi: 10.1038/ismej.2011.119
Becker J, Eisenhauer N, Scheu S, Jousset A (2012) Increasing antagonistic interactions cause bacterial communities to collapse at high diversity. Ecol Lett 15:468-474 doi: 10.1111/j.1461-0248.2012.01759.x
Beman JM, Steele JA, Fuhrman JA (2011) Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California. ISME J 5:1077-1085 doi: 10.1038/ismej.2010.204
Berdjeb L, Parada A, Needham DM, Fuhrman JA (2018) Short-term dynamics and interactions of marine protist communities during the spring-summer transition. ISME J 12:1907-1917 doi: 10.1038/s41396-018-0097-x
Berry D, Widder S (2014) Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol 5:219 
Bibby TS, Mary I, Nield J, Partensky F, Barber J (2003) Low-lightadapted Prochlorococcus species possess specifc antennae for each photosystem. Nature 424:1051-1054 doi: 10.1038/nature01933
Blazewicz SJ, Barnard RL, Daly RA, Firestone MK (2013) Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J 7:2061-2068 doi: 10.1038/ismej.2013.102
Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, Wilkins MJ, Wrighton KC, Williams KH, Banfeld JF (2015) Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523:208-211 doi: 10.1038/nature14486
Bryant JA, Aylward FO, Eppley JM, Karl DM, Church MJ, DeLong EF (2016) Wind and sunlight shape microbial diversity in surface waters of the North Pacifc Subtropical Gyre. ISME J 10:1308-1322 doi: 10.1038/ismej.2015.221
Bryson S, Li Z, Chavez F, Weber PK, Pett-Ridge J, Hettich RL, Pan C, Mayali X, Mueller RS (2017) Phylogenetically conserved resource partitioning in the coastal microbial loop. ISME J 11:2781-2792 doi: 10.1038/ismej.2017.128
Buttigieg PL, Ramette A (2015) Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments (HAUSGARTEN, Fram Strait). Front Microbiol 5:660 
Campbell BJ, Kirchman DL (2013) Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. ISME J 7:210-220 doi: 10.1038/ismej.2012.93
Campbell BJ, Yu LY, Heidelberg JF, Kirchman DL (2011) Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci USA 108:12776-12781 doi: 10.1073/pnas.1101405108
Cardinale BJ, Matulich KL, Hooper DU, Byrnes JE, Dufy E, Gamfeldt L, Balvanera P, O'Connor MI, Gonzalez A (2011) The functional role of producer diversity in ecosystems. Am J Bot 98:572-592 doi: 10.3732/ajb.1000364
Cardinale BJ, Dufy JE, Gonzalez A, Hooper DU, Perrings C, Venail P, Narwani A, Mace GM, Tilman D, Wardle DA, Kinzig AP, Daily GC, Loreau M, Grace JB, Larigauderie A, Srivastava DS, Naeem S (2012) Biodiversity loss and its impact on humanity. Nature 486:59-67 doi: 10.1038/nature11148
Caruso T, Chan YK, Lacap DC, Lau MCY, Mckay CP, Pointing SB (2011) Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale. ISME J 5:1406-1413 doi: 10.1038/ismej.2011.21
Chafee M, Fernandez-Guerra A, Buttigieg PL, Gerdts G, Eren AM, Teeling H, Amann RI (2018) Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME J 12:237-252 doi: 10.1038/ismej.2017.165
Chase JM, Leibold MA (2003) Ecological niches: linking classical and contemporary approaches. University of Chicago Press, Chicago
Chase JM, Myers JA (2011) Disentangling the importance of ecological niches from stochastic processes across scales. Philos Trans R Soc B 366:2351-2363 doi: 10.1098/rstb.2011.0063
Chave J (2004) Neutral theory and community ecology. Ecol Lett 7:241-253 doi: 10.1111/j.1461-0248.2003.00566.x
Chen W, Pan Y, Yu L, Yang J, Zhang W (2017) Patterns and processes in marine microeukaryotic community biogeography from Xiamen coastal waters and intertidal sediments, southeast China. Front Microbiol 8:1912 doi: 10.3389/fmicb.2017.01912
Chow CET, Sachdeva R, Cram JA, Steele JA, Needham DM, Patel A, Parada AE, Fuhrman JA (2013) Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. ISME J 7:2259-2273 doi: 10.1038/ismej.2013.122
Cram JA, Xia LC, Needham DM, Sachdeva R, Sun F, Fuhrman JA (2015) Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes. ISME J 9:2573-2586 doi: 10.1038/ismej.2015.76
Cui Y, Chun SJ, Baek SH, Lee M, Kim Y, Lee HG, Ko SR, Hwang S, Ahn CY, Oh HM (2019) The water depth-dependent co-occurrence patterns of marine bacteria in shallow and dynamic Southern Coast, Korea. Sci Rep 9:9176 doi: 10.1038/s41598-019-45512-5
Dai W, Zhang J, Tu Q, Deng Y, Qiu Q, Xiong J (2017) Bacterioplankton assembly and interspecies interaction indicating increasing coastal eutrophication. Chemosphere 177:317-325 doi: 10.1016/j.chemosphere.2017.03.034
Delgado-Baquerizo M, Giaramida L, Reich PB, Khachane AN, Hamonts K, Edwards C, Lawton LA, Singh BK (2016a) Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning. J Ecol 104:936-946 doi: 10.1111/1365-2745.12585
Delgado-Baquerizo M, Maestre FT, Reich PB, Jefries TC, Gaitan JJ, Encinar D, Berdugo M, Campbell CD, Singh BK (2016b) Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun 7:10541 doi: 10.1038/ncomms10541
DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685-5689 doi: 10.1073/pnas.89.12.5685
Dini-Andreote F, Stegen JC, van Elsas JD, Salles JF (2015) Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc Natl Acad Sci USA 112:E1326-E1332 doi: 10.1073/pnas.1414261112
Dolan KL, Pena J, Allison SD, Martiny JBH (2017) Phylogenetic conservation of substrate use specialization in leaf litter bacteria. PLoS ONE 12:e0174472 doi: 10.1371/journal.pone.0174472
Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH (2010) Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J 4:337-345 doi: 10.1038/ismej.2009.122
Enright MC, Spratt BG (1999) Multilocus sequence typing. Trends Microbiol 7:482-487 doi: 10.1016/S0966-842X(99)01609-1
Evans S, Martiny JBH, Allison SD (2017) Efects of dispersal and selection on stochastic assembly in microbial communities. ISME J 11:176-185
Galand PE, Casamayor EO, Kirchman DL, Lovejoy C (2009) Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci USA 106:22427-22432
Galand PE, Salter I, Kalenitchenko D (2015) Ecosystem productivity is associated with bacterial phylogenetic distance in surface marine waters. Mol Ecol 24:5785-5795 doi: 10.1111/mec.13347
Galand PE, Pereira O, Hochart C, Auguet JC, Debroas D (2018) A strong link between marine microbial community composition and function challenges the idea of functional redundancy. ISME J 12:2470-2478 doi: 10.1038/s41396-018-0158-1
Goberna M, Verdu M (2018) Phylogenetic-scale disparities in the soil microbial diversity-ecosystem functioning relationship. ISME J 12:2152-2162 doi: 10.1038/s41396-018-0162-5
Gong J, Shi F, Ma B, Dong J, Pachiadaki M, Zhang XL, Edgcomb VP (2015) Depth shapes alpha- and beta-diversities of microbial eukaryotes in surfcial sediments of coastal ecosystems. Environ Microbiol 17:3722-3737 doi: 10.1111/1462-2920.12763
Graham EB, Wieder WR, Lef JW, Weintraub SR, Townsend AR, Cleveland CC, Philippot L, Nemergut DR (2014) Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes. Soil Biol Biochem 68:279-282 doi: 10.1016/j.soilbio.2013.08.023
Graham EB, Knelman JE, Schindlbacher A, Siciliano S, Breulmann M, Yannarell A, Bemans JM, Abell G, Philippot L, Prosser J, Foulquier A, Yuste JC, Glanville HC, Jones DL, Angel F, Salminen J, Newton RJ, Burgmann H, Ingram LJ, Hamer U et al (2016) Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Front Microbiol 7: 214
Graham EB, Crump AR, Resch CT, Fansler S, Arntzen E, Kennedy DW, Fredrickson JK, Stegen JC (2017) Deterministic infuences exceed dispersal efects on hydrologically-connected microbiomes. Environ Microbiol 19:1552-1567 doi: 10.1111/1462-2920.13720
Gravel D, Bell T, Barbera C, Combe M, Pommier T, Mouquet N (2012) Phylogenetic constraints on ecosystem functioning. Nat Commun 3:1117 doi: 10.1038/ncomms2123
Gutknecht JLM, Field CB, Balser TC (2012) Microbial communities and their responses to simulated global change fuctuate greatly over multiple years. Glob Change Biol 18:2256-2269 doi: 10.1111/j.1365-2486.2012.02686.x
Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JB (2012) Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol 10:497-506 doi: 10.1038/nrmicro2795
Hooper DU, Chapin FS, Ewel JJ, Hector A, Inchausti P, Lavorel S, Lawton JH, Lodge DM, Loreau M, Naeem S, Schmid B, Setala H, Symstad AJ, Vandermeer J, Wardle DA (2005) Efects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecol Monogr 75:3-35 doi: 10.1890/04-0922
Horner-Devine MC, Lage M, Hughes JB, Bohannan BJ (2004) A taxaarea relationship for bacteria. Nature 432:750-753 doi: 10.1038/nature03073
Hubbell SP (2001) The unifed neutral theory of biodiversity and biogeography (MPB-32), vol 32. Princeton University Press, Princeton
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfeld CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfeld JF (2016) A new view of the tree of life. Nat Microbiol 1: 16048
Hugoni M, Taib N, Debroas D, Domaizon I, Dufournel IJ, Bronner G, Salter I, Agogué H, Mary I, Galand PE (2013) Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proc Natl Acad Sci USA 110:6004-6009 doi: 10.1073/pnas.1216863110
Hunt DE, Lin Y, Church MJ, Karl DM, Tringe SG, Izzo LK, Johnson ZI (2013) Relationship between abundance and specifc activity of bacterioplankton in open ocean surface waters. Appl Environ Microbiol 79:177-184 doi: 10.1128/AEM.02155-12
Hutchins DA, Fu F (2017) Microorganisms and ocean global change. Nat Microbiol 2:17058 doi: 10.1038/nmicrobiol.2017.58
Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K, Nealson KH, Horikoshi K (2003) Microbial communities associated with geological horizons in coastal subseafoor sediments from the Sea of Okhotsk. Appl Environ Microbiol 69:7224-7235 doi: 10.1128/AEM.69.12.7224-7235.2003
Ivars-Martinez E, D'Auria G, Rodriguez-Valera F, Sanchez-Porro C, Ventosa A, Joint I, Muhling M (2008) Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis. Mol Ecol 17:4092-4106 doi: 10.1111/j.1365-294X.2008.03883.x
Jeraldo P, Sipos M, Chia N, Brulc JM, Dhillon AS, Konkel ME, Larson CL, Nelson KE, Qu A, Schook LB, Yang F, White BA, Goldenfeld N (2012) Quantifcation of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes. Proc Natl Acad Sci USA 109:9692-9698 doi: 10.1073/pnas.1206721109
Jia X, Dini-Andreote F, Salles JF (2018) Community assembly processes of the microbial rare biosphere. Trends Microbiol 26:738-747 doi: 10.1016/j.tim.2018.02.011
Jones SE, Lennon JT (2010) Dormancy contributes to the maintenance of microbial diversity. Proc Natl Acad Sci USA 107:5881-5886 doi: 10.1073/pnas.0912765107
Ju F, Xia Y, Guo F, Wang Z, Zhang T (2014) Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants. Environ Microbiol 16:2421-2432 doi: 10.1111/1462-2920.12355
Kirchman DL (2016) Growth rates of microbes in the oceans. Ann Rev Mar Sci 8:285-309 doi: 10.1146/annurev-marine-122414-033938
Krause S, Le Roux X, Niklaus PA, Van Bodegom PM, Lennon JT, Bertilsson S, Grossart HP, Philippot L, Bodelier PLE (2014) Trait-based approaches for understanding microbial biodiversity and ecosystem functioning. Front Microbiol 5:251 
Kubo K, Lloyd KG, Biddle JF, Amann R, Teske A, Knittel K (2012) Archaea of the miscellaneous crenarchaeotal group are abundant, diverse and widespread in marine sediments. ISME J 6:1949-1965 doi: 10.1038/ismej.2012.37
Langenheder S, Berga M, Östman Ö, Székely AJ (2012) Temporal variation of β-diversity and assembly mechanisms in a bacterial metacommunity. ISME J 6:1107-1114 doi: 10.1038/ismej.2011.177
Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814-821 doi: 10.1038/nbt.2676
Lankiewicz TS, Cottrell MT, Kirchman DL (2016) Growth rates and rRNA content of four marine bacteria in pure cultures and in the Delaware estuary. ISME J 10:823-832 doi: 10.1038/ismej.2015.156
Larkin AA, Martiny AC (2017) Microdiversity shapes the traits, niche space, and biogeography of microbial taxa. Environ Microbiol Rep 9:55-70 doi: 10.1111/1758-2229.12523
Layeghifard M, Hwang DM, Guttman DS (2017) Disentangling interactions in the microbiome: a network perspective. Trends Microbiol 25:217-228 doi: 10.1016/j.tim.2016.11.008
Lazar CS, Baker BJ, Seitz K, Hyde AS, Dick GJ, Hinrichs KU, Teske AP (2016) Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Environ Microbiol 18:1200-1211 doi: 10.1111/1462-2920.13142
Leibold MA (1995) The niche concept revisited-mechanistic models and community context. Ecology 76:1371-1382 doi: 10.2307/1938141
Leibold MA, McPeek MA (2006) Coexistence of the niche and neutral perspectives in community ecology. Ecology 87:1399-1410 doi: 10.1890/0012-9658(2006)87[1399:COTNAN]2.0.CO;2
Li J, Salam N, Wang P, Chen L, Jiao J, Li X, Xian W, Han M, Fang B, Mou X, Li W (2018) Discordance between resident and active bacterioplankton in free-living and particle-associated communities in estuary ecosystem. Microb Ecol 76:637-647 doi: 10.1007/s00248-018-1174-4
Liang Y, Zhao H, Deng Y, Zhou J, Li G, Sun B (2016) Long-term oil contamination alters the molecular ecological networks of soil microbial functional genes. Front Microbiol 7:60 
Liao J, Cao X, Zhao L, Wang J, Gao Z, Wang MC, Huang Y (2016) The importance of neutral and niche processes for bacterial community assembly difers between habitat generalists and specialists. FEMS Microbiol Ecol 92: fw174
Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chafron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F et al (2015) Ocean plankton. Determinants of community structure in the global plankton interactome. Science 348: 1262073
Liu J, Yu S, Zhao M, He B, Zhang X-H (2014a) Shifts in archaeaplankton community structure along ecological gradients of Pearl Estuary. FEMS Microbiol Ecol 90:424-435
Liu J, Yang H, Zhao M, Zhang X-H (2014b) Spatial distribution patterns of benthic microbial communities along the Pearl Estuary, China. Syst Appl Microbiol 37:578-589 doi: 10.1016/j.syapm.2014.10.005
Liu J, Fu B, Yang H, Zhao M, He B, Zhang X-H (2015a) Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients. Front Microbiol 6:64
Liu L, Yang J, Yu Z, Wilkinson DM (2015b) The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China. ISME J 9:2068-2077 doi: 10.1038/ismej.2015.29
Liu J, Zheng Y, Lin H, Wang X, Li M, Liu Y, Yu M, Zhao M, Pedentchouk N, Lea-Smith DJ, Todd JD, Magill CR, Zhang WJ, Zhou S, Song D, Zhong H, Xin Y, Yu M, Tian J, Zhang X-H (2019) Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench. Microbiome 7:47 doi: 10.1186/s40168-019-0652-3
Logares R, Tesson SV, Canback B, Pontarp M, Hedlund K, Rengefors K (2018) Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes. Environ Microbiol 20:2231-2240 doi: 10.1111/1462-2920.14265
Louca S, Parfrey LW, Doebeli M (2016) Decoupling function and taxonomy in the global ocean microbiome. Science 353:1272-1277 doi: 10.1126/science.aaf4507
Louca S, Jacques SMS, Pires APF, Leal JS, Srivastava DS, Parfrey LW, Farjalla VF, Doebeli M (2017) High taxonomic variability despite stable functional structure across microbial communities. Nat Ecol Evol 1:15 doi: 10.1038/s41559-016-0015
Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104:11436-11440 doi: 10.1073/pnas.0611525104
Ma B, Wang H, Dsouza M, Lou J, He Y, Dai Z, Brookes PC, Xu J, Gilbert JA (2016) Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J 10:1891-1901 doi: 10.1038/ismej.2015.261
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 doi: 10.1038/nrmicro1341
Martiny AC, Treseder K, Pusch G (2013) Phylogenetic conservatism of functional traits in microorganisms. ISME J 7:830-838 doi: 10.1038/ismej.2012.160
Martiny JB, Jones SE, Lennon JT, Martiny AC (2015) Microbiomes in light of traits: a phylogenetic perspective. Science 350:aac9323 doi: 10.1126/science.aac9323
Mayali X, Weber PK (2018) Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community. FEMS Microbiol Ecol 94:fy047
Milici M, Deng ZL, Tomasch J, Decelle J, Wos-Oxley ML, Wang H, Jauregui R, Plumeier I, Giebel HA, Badewien TH, Wurst M, Pieper DH, Simon M, Wagner-Dobler I (2016) Co-occurrence analysis of microbial taxa in the Atlantic Ocean reveals high connectivity in the free-living bacterioplankton. Front Microbiol 7:649 
Mo Y, Zhang W, Yang J, Lin Y, Yu Z, Lin S (2018) Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes. ISME J 12:2198-2210 doi: 10.1038/s41396-018-0153-6
Morrissey EM, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, Koch BJ, Liu CM, Hayer M, McHugh TA, Marks JC, Price LB, Hungate BA (2016) Phylogenetic organization of bacterial activity. ISME J 10:2336-2340 doi: 10.1038/ismej.2016.28
Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Eur J Soil Sci 54:655-670 doi: 10.1046/j.1351-0754.2003.0556.x
Needham DM, Sachdeva R, Fuhrman JA (2017) Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters. ISME J 11:1614-1629 doi: 10.1038/ismej.2017.29
Nekola JC, White PS (1999) The distance decay of similarity in biogeography and ecology. J Biogeogr 26:867-878 doi: 10.1046/j.1365-2699.1999.00305.x
Nemergut DR, Schmidt SK, Fukami T, O'Neill SP, Bilinski TM, Stanish LF, Knelman JE, Darcy JL, Lynch RC, Wickey P, Ferrenberg S (2013) Patterns and processes of microbial community assembly. Microbiol Mol Biol Rev 77:342-356 doi: 10.1128/MMBR.00051-12
Neumann AM, Balmonte JP, Berger M, Giebel H-A, Arnosti C, Voget S, Simon M, Brinkhof T, Wietz M (2015) Diferent utilization of alginate and other algal polysaccharides by marine Alteromonas macleodii ecotypes. Environ Microbiol 17:3858-3868
Newman MEJ (2003) The structure and function of complex networks. SIAM Rev 45:167-256 doi: 10.1137/S003614450342480
Nielsen UN, Ayres E, Wall DH, Bardgett RD (2011) Soil biodiversity and carbon cycling: a review and synthesis of studies examining diversity-function relationships. Eur J Soil Sci 62:105-116 doi: 10.1111/j.1365-2389.2010.01314.x
Orland C, Emilson EJS, Basiliko N, Mykytczuk NCS, Gunn JM, Tanentzap AJ (2018) Microbiome functioning depends on individual and interactive efects of the environment and community structure. ISME J 13:1-11
Pedrós-Alió C (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14:257-263 
Pedrós-Alió C (2012) The rare bacterial biosphere. Annu Rev Mar Sci 4:449-466 doi: 10.1146/annurev-marine-120710-100948
Pérez-Valera E, Goberna M, Verdu M (2015) Phylogenetic structure of soil bacterial communities predicts ecosystem functioning. FEMS Microbiol Ecol 91:fv031
Petchey OL, Gaston KJ (2002) Extinction and the loss of functional diversity. Proc R Soc Lond B 269:1721-1727 doi: 10.1098/rspb.2002.2073
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 doi: 10.1038/nrmicro2367
Powell JR, Karunaratne S, Campbell CD, Yao H, Robinson L, Singh BK (2015a) Deterministic processes vary during community assembly for ecologically dissimilar taxa. Nat Commun 6:8444 doi: 10.1038/ncomms9444
Powell JR, Welsh A, Hallin S (2015b) Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties. Ecology 96:1985-1993 doi: 10.1890/14-1127.1
Preston FW (1948) The commonness, and rarity, of species. Ecology 29:254-283 doi: 10.2307/1930989
Qiao Y, Liu J, Zhao M, Zhang X-H (2018) Sediment depth-dependent spatial variations of bacterial communities in mud deposits of the eastern China marginal seas. Front Microbiol 9:1128 doi: 10.3389/fmicb.2018.01128
Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA (2019) Diferential co-occurrence relationships shaping ecotype diversifcation within Thaumarchaeota populations in the coastal ocean water column. ISME J 13:1144-1158 doi: 10.1038/s41396-018-0311-x
Richa K, Balestra C, Piredda R, Benes V, Borra M, Passarelli A, Margiotta F, Saggiomo M, Bifali E, Sanges R, Scanlan DJ, Casotti R (2017) Distribution, community composition, and potential metabolic activity of bacterioplankton in an urbanized mediterranean sea coastal zone. Appl Environ Microbiol 83:e00494-17 
Roguet A, Laigle GS, Therial C, Bressy A, Soulignac F, Catherine A, Lacroix G, Jardillier L, Bonhomme C, Lerch TZ (2015) Neutral community model explains the bacterial community assembly in freshwater lakes. FEMS Microbiol Ecol 91:fv125 doi: 10.1093/femsec/fiv125
Romanowicz KJ, Freedman ZB, Upchurch RA, Argirof WA, Zak DR (2016) Active microorganisms in forest soils difer from the total community yet are shaped by the same environmental factors: the infuence of pH and soil moisture. FEMS Microbiol Ecol 92:fw149
Salazar G, Cornejo-Castillo FM, Borrull E, Diez-Vives C, Lara E, Vaque D, Arrieta JM, Duarte CM, Gasol JM, Acinas SG (2015) Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol Ecol 24:5692-5706 doi: 10.1111/mec.13419
Salter I, Galand PE, Fagervold SK, Lebaron P, Obernosterer I, Oliver MJ, Suzuki MT, Tricoire C (2015) Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea. ISME J 9:347-360 doi: 10.1038/ismej.2014.129
Schmidt ML, White JD, Denef VJ (2016) Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla. Environ Microbiol 18:1212-1226 doi: 10.1111/1462-2920.13143
Schnyder E, Bodelier PLE, Hartmann M, Henneberger R, Niklaus PA (2018) Positive diversity-functioning relationships in model communities of methanotrophic bacteria. Ecology 99:714-723 doi: 10.1002/ecy.2138
Sebastián M, Auguet JC, Restrepo-Ortiz CX, Sala MM, Marrase C, Gasol JM (2018) Deep ocean prokaryotic communities are remarkably malleable when facing long-term starvation. Environ Microbiol 20:713-723 doi: 10.1111/1462-2920.14002
Severin I, Ostman O, Lindstrom ES (2013) Variable efects of dispersal on productivity of bacterial communities due to changes in functional trait composition. PLoS ONE 8:e80825 doi: 10.1371/journal.pone.0080825
Singh BK, Bardgett RD, Smith P, Reay DS (2010) Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat Rev Microbiol 8:779-790 doi: 10.1038/nrmicro2439
Spang A, Saw JH, Jorgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJG (2015) Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173-179 doi: 10.1038/nature14447
Stegen JC, Lin XJ, Fredrickson JK, Chen XY, Kennedy DW, Murray CJ, Rockhold ML, Konopka A (2013) Quantifying community assembly processes and identifying features that impose them. ISME J 7:2069-2079 doi: 10.1038/ismej.2013.93
Stegen JC, Lin XJ, Fredrickson JK, Konopka AE (2015) Estimating and mapping ecological processes infuencing microbial community assembly. Front Microbiol 6:370
Sunagawa S, Coelho LP, Chafron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F et al (2015) Ocean plankton. Structure and function of the global ocean microbiome. Science 348: 1261359
Tripp HJ, Schwalbach MS, Meyer MM, Kitner JB, Breaker RR, Giovannoni SJ (2009) Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11. Environ Microbiol 11:230-238 doi: 10.1111/j.1462-2920.2008.01758.x
Volkov I, Banavar JR, Hubbell SP, Maritan A (2003) Neutral theory and relative species abundance in ecology. Nature 424:1035-1037 doi: 10.1038/nature01883
Wang J, Shen J, Wu Y, Tu C, Soininen J, Stegen JC, He J, Liu X, Zhang L, Zhang E (2013) Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes. ISME J 7:1310-1321 doi: 10.1038/ismej.2013.30
Wang K, Hu H, Yan H, Hou D, Wang Y, Dong P, Zhang D (2019) Archaeal biogeography and interactions with microbial community across complex subtropical coastal waters. Mol Ecol. https://doi.org/10.1111/mec.15105
Wei G, Li M, Li F, Li H, Gao Z (2016) Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary. Appl Microbiol Biotechnol 100:9683-9697 doi: 10.1007/s00253-016-7802-3
Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun FZ, Zhou JZ, Knight R (2016) Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J 10:1669-1681 doi: 10.1038/ismej.2015.235
Wieder WR, Bonan GB, Allison SD (2013) Global soil carbon projections are improved by modelling microbial processes. Nat Clim Change 3:909-912 doi: 10.1038/nclimate1951
Wu W, Logares R, Huang B, Hsieh CH (2017) Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacifc Ocean. Environ Microbiol 19:287-300 doi: 10.1111/1462-2920.13606
Wu W, Lu H, Sastri A, Yeh YC, Gong G, Chou W, Hsieh CH (2018) Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities. ISME J 12:485-494 doi: 10.1038/ismej.2017.183
Zhang Y, Zhao Z, Dai M, Jiao N, Herndl GJ (2014) Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea. Mol Ecol 23:2260-2274 doi: 10.1111/mec.12739
Zhang X, Zhang Q, Yang A, Hou L, Zheng Y, Zhai W, Gong J (2018) Incorporation of microbial functional traits in biogeochemistry models provides better estimations of benthic denitrifcation and anammox rates in coastal oceans. J Geophys Res Biogeosci 123:3331-3352 doi: 10.1029/2018JG004682
Zhou J, Ning D (2017) Stochastic community assembly: Does it matter in microbial ecology? Microbiol Mol Biol Rev 81:e00002-e00017
Zhou J, Liu W, Deng Y, Jiang Y, Xue K, He Z, Van Nostrand JD, Wu L, Yang Y, Wang A (2013) Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community. Mbio 4:e00584-12
Zhou J, Song X, Zhang CY, Chen GF, Lao YM, Jin H, Cai ZH (2018) Distribution patterns of microbial community structure along a 7000-mile latitudinal transect from the mediterranean sea across the Atlantic Ocean to the Brazilian coastal sea. Microb Ecol 76:592-609 doi: 10.1007/s00248-018-1150-z
Zimmerman AE, Martiny AC, Allison SD (2013) Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. ISME J 7:1187-1199 doi: 10.1038/ismej.2012.176