Kallmeyer J, Pockalny R, Adhikari RR, Smith DC, D’Hondt S. Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci USA. 2012;109:16213–6.
Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sørensen KB, Anderson R, et al. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA. 2006;103:3846–51.
Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol. 2015;25:690–701.
Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature. 2015;521:173–9.
Liu Y, Zhou Z, Pan J, Baker BJ, Gu JD, Li M. Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota. ISME J. 2018;12:1021–31.
Orphan VJ, House CH, Hinrichs KU, McKeegan KD, DeLong EF. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci USA. 2002;99:7663–8.
Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature. 2005;437:543–6.
Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD, et al. Predominant archaea in marine sediments degrade detrital proteins. Nature. 2013;496:215–8.
Wang Y, Wegener G, Hou J, Wang F, Xiao X. Expanding anaerobic alkane metabolism in the domain of Archaea. Nat Microbiol. 2019;4:595–602.
Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J, Sieber JR, et al. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat Commun. 2019;10:1822.
Petro C, Starnawski P, Schramm A, Kjeldsen KU. Microbial community assembly in marine sediments. Aquat Micro Ecol. 2017;79:177–95.
Liu J, Meng Z, Liu X, Zhang X-H. Microbial assembly, interaction, functioning, activity and diversification: a review derived from community compositional data. Mar Life Sci Technol. 2019;1:112–28.
Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006;4:102–12.
Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol. 2012;10:497–506.
Nekola JC, White PS. The distance decay of similarity in biogeography and ecology. J Biogeogr. 1999;26:867–78.
Hubbell SP. The unified neutral theory of biodiversity and biogeography. Princeton: Princeton University Press; 2001.
Leibold MA, McPeek MA. Coexistence of the niche and neutral perspectives in community ecology. Ecology. 2006;87:1399–410.
Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH. Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J. 2010;4:337–45.
Caruso T, Chan YK, Lacap DC, Lau MCY, Mckay CP, Pointing SB. Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale. ISME J. 2011;5:1406–13.
Wang J, Shen J, Wu Y, Tu C, Soininen J, Stegen JC, et al. Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes. ISME J. 2013;7:1310–21.
Zhou J, Deng Y, Zhang P, Xue K, Liang Y, Van Nostrand JD, et al. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proc Natl Acad Sci USA. 2014;111:E836–45.
Stegen JC, Lin X, Konopka AE, Fredrickson JK. Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. 2012;6:1653–64.
Liao J, Cao X, Wang J, Zhao L, Sun J, Jiang D, et al. Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China. Limnol Oceanogr. 2017;62:723–35.
Mo Y, Zhang W, Yang J, Lin Y, Yu Z, Lin S. Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes. ISME J. 2018;12:2198–210.
Liu L, Yang J, Yu Z, Wilkinson DM. The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China. ISME J. 2015;9:2068–77.
Logares R, Tesson SVM, Canbäck B, Pontarp M, Hedlund K, Rengefors K. Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes. Environ Microbiol. 2018;20:2231–40.
Wu W, Lu HP, Sastri A, Yeh YC, Gong GC, Chou WC, et al. Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities. ISME J. 2018;12:485–94.
Zhou J, Ning D. Stochastic community assembly: does it matter in microbial ecology? Microbiol Mol Biol R. 2017;81:e00002–17.
Stegen JC, Lin X, Fredrickson JK, Chen X, Kennedy DW, Murray CJ, et al. Quantifying community assembly processes and identifying features that impose them. ISME J. 2013;7:2069–79.
Stegen JC, Lin X, Fredrickson JK, Konopka AE. Estimating and mapping ecological processes influencing microbial community assembly. Front Microbiol. 2015;6:370.
Wang K, Hu H, Yan H, Hou D, Wang Y, Dong P, et al. Archaeal biogeography and interactions with microbial community across complex subtropical coastal waters. Mol Ecol. 2019;28:3101–18.
Faust K, Raes J. Microbial interactions: from networks to models. Nat Rev Microbiol. 2012;10:538–50.
Ma B, Wang H, Dsouza M, Lou J, He Y, Dai Z, et al. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. 2016;10:1891–901.
McKee BA, Aller RC, Allison MA, Bianchi TS, Kineke GC. Transport and transformation of dissolved and particulate materials on continental margins influenced by major rivers: benthic boundary layer and seabed processes. Cont Shelf Res. 2004;24:899–926.
Shi W, Wang M. Satellite views of the Bohai Sea, Yellow Sea, and East China Sea. Prog Oceanogr. 2012;104:30–45.
Zhai W, Zhao H, Su J, Liu P, Li Y, Zheng N. Emergence of summertime hypoxia and concurrent carbonate mineral suppression in the central Bohai Sea, China. J Geophys Res-Biogeosci. 2019;124:2768–85.
Wei H, He Y, Li Q, Liu Z, Wang H. Summer hypoxia adjacent to the Changjiang Estuary. J Mar Syst. 2007;67:292–303.
Qiao S, Shi X, Wang G, Zhou L, Hu B, Hu L, et al. Sediment accumulation and budget in the Bohai Sea, Yellow Sea and East China Sea. Mar Geol. 2017;390:270–81.
Liu J, Liu X, Wang M, Qiao Y, Zheng Y, Zhang X-H. Bacterial and archaeal communities in sediments of the north Chinese marginal seas. Micro Ecol. 2015;70:105–17.
Yao P, Zhao B, Bianchi TS, Guo Z, Zhao M, Li D, et al. Remineralization of sedimentary organic carbon in mud deposits of the Changjiang Estuary and adjacent shelf: Implications for carbon preservation and authigenic mineral formation. Cont Shelf Res. 2014;91:1–11.
Cadillo-Quiroz H, Bräuer S, Yashiro E, Sun C, Yavitt J, Zinder S. Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA. Environ Microbiol. 2006;8:1428–40.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 2014;30:614–20.
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2015. https://www.R-project.org/.
Dini-Andreote F, Stegen JC, van Elsas JD, Salles JF. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc Natl Acad Sci USA. 2015;112:E1326–32.
Petro C, Zäncker B, Starnawski P, Jochum LM, Ferdelman TG, Jørgensen BB, et al. Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay. Front Microbiol. 2019;10:758.
Zhou Z, Zhang GX, Xu YB, Gu JD. Successive transitory distribution of Thaumarchaeota and partitioned distribution of Bathyarchaeota from the Pearl River estuary to the northern South China Sea. Appl Microbiol Biotechnol. 2018;102:8035–48.
Herlemann DPR, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, Andersson AF. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 2011;5:1571–9.
Liu J, Yang H, Zhao M, Zhang X-H. Spatial distribution patterns of benthic microbial communities along the Pearl Estuary, China. Syst Appl Microbiol. 2014;37:578–89.
Lazar CS, Baker BJ, Seitz K, Hyde AS, Dick GJ, Hinrichs KU, et al. Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Environ Microbiol. 2016;18:1200–11.
Zhou Z, Pan J, Wang F, Gu JD, Li M. Bathyarchaeota: globally distributed metabolic generalists in anoxic environments. FEMS Microbiol Rev. 2018;42:639–55.
Yu T, Wu W, Liang W, Lever MA, Hinrichs KU, Wang F. Growth of sedimentary Bathyarchaeota on lignin as an energy source. Proc Natl Acad Sci USA. 2018;115:6022–7.
Yao P, Yu Z, Bianchi TS, Guo Z, Zhao M, Knappy CS, et al. A multiproxy analysis of sedimentary organic carbon in the Changjiang Estuary and adjacent shelf. J Geophys Res Biogeosci. 2015;120:1407–29.
Wei G, Li M, Li F, Li H, Gao Z. Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary. Appl Microbiol Biotechnol. 2016;100:9683–97.
Lavergne C, Hugoni M, Dupuy C, Agogué H. First evidence of the presence and activity of archaeal C3 group members in an Atlantic intertidal mudflat. Sci Rep. 2018;8:11790.
He Y, Li M, Perumal V, Feng X, Fang J, Xie J, et al. Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments. Nat Microbiol. 2016;1:16035.
Böer SI, Hedtkamp SIC, van Beusekom JEE, Fuhrman JA, Boetius A, Ramette A. Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. ISME J. 2009;3:780–91.
Gong J, Shi F, Ma B, Dong J, Pachiadaki M, Zhang X, et al. Depth shapes alpha- and beta-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems. Environ Microbiol. 2015;17:3722–37.
Pearman JK, Ellis J, Irigoien X, Sarma YVB, Jones BH, Carvalho S. Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence. Sci Rep. 2017;7:6611.
Wu W, Logares R, Huang B, Hsieh CH. Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean. Environ Microbiol. 2017;19:287–300.
Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, Welch DB, et al. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE. 2011;6:e24570.
Liu Y, Liu J, Yao P, Ge T, Qiao Y, Zhao M, et al. Distribution patterns of ammonia-oxidizing archaea and bacteria in sediments of the eastern China marginal seas. Syst Appl Microbiol. 2018;41:658–68.
Zinger L, Boetius A, Ramette A. Bacterial taxa-area and distance-decay relationships in marine environments. Mol Ecol. 2014;23:954–64.
Östman O, Drakare S, Kritzberg ES, Langenheder S, Logue JB, Lindström ES. Regional invariance among microbial communities. Ecol Lett. 2010;13:118–27.
Gilbert B, Bennett JR. Partitioning variation in ecological communities: do the numbers add up? J Appl Ecol. 2010;47:1071–82.
Smith TW, Lundholm JT. Variation partitioning as a tool to distinguish between niche and neutral processes. Ecography. 2010;33:648–55.
Chen W, Ren K, Isabwe A, Chen H, Liu M, Yang J. Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons. Microbiome. 2019;7:138.
Zhang W, Pan Y, Yang J, Chen H, Holohan B, Vaudrey J, et al. The diversity and biogeography of abundant and rare intertidal marine microeukaryotes explained by environment and dispersal limitation. Environ Microbiol. 2018;20:462–76.
Chen W, Pan Y, Yu L, Yang J, Zhang W. Patterns and processes in marine microeukaryotic community biogeography from Xiamen coastal waters and intertidal sediments, southeast China. Front Microbiol. 2017;8:1912.
Shi Y, Li Y, Xiang X, Sun R, Yang T, He D, et al. Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain. Microbiome. 2018;6:27.
Jacob M, Soltwedel T, Boetius A, Ramette A. Biogeography of deep-sea benthic bacteria at regional scale (LTER HAUSGARTEN, Fram Strait, Arctic). PLoS ONE. 2013;8:e72779.
Starnawski P, Bataillon T, Ettema TJG, Jochum LM, Schreiber L, Chen X, et al. Microbial community assembly and evolution in subseafloor sediment. Proc Natl Acad Sci USA. 2017;114:2940–5.
Berga M, Östman O, Lindström ES, Langenheder S. Combined effects of zooplankton grazing and dispersal on the diversity and assembly mechanisms of bacterial metacommunities. Environ Microbiol. 2015;17:2275–87.
Yan Q, Stegen JC, Yu Y, Deng Y, Li X, Wu S, et al. Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China). Mol Ecol. 2017;26:3839–50.
Logares R, Deutschmann IM, Junger PC, Giner CR, Krabberød AK, Schmidt TSB, et al. Disentangling the mechanisms shaping the surface ocean microbiota. Microbiome. 2020; https://doi.org/10.21203/rs.2.17228/v1.
Wu W, Huang B. Protist diversity and community assembly in surface sediments of the South China Sea. MicrobiologyOpen. 2019;8:e891.
Slatkin M. Isolation by distance in equilibrium and nonequilibrium populations. Evolution. 1993;47:264–79.
Zhang S, Wang Q, Lü Y, Cui H, Yuan Y. Observation of the seasonal evolution of the Yellow Sea Cold Water Mass in 1996-1998. Cont Shelf Res. 2008;28:442–57.
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