Hubbell SP. The unified neutral theory of biodiversity and biogeography. Princeton: Princeton University Press; 2001.
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.
Vellend M. The theory of ecological communities. 1st ed. Woodstock, UK: Princeton University Press; 2016.
McGill BJ. Towards a unification of unified theories of biodiversity. Ecol Lett. 2010;13:627–42.
Gilbert B. Joint consequences of dispersal and niche overlap on local diversity and resource use. J Ecol. 2012;100:287–96.
Chase JM, Leibold MA. Ecological niches: linking classical and contemporary approaches. Biodivers Conserv. 2004;13:1791–3.
Rosindell J, Hubbell SP, Etienne RS. The unified neutral theory of biodiversity and biogeography at age ten. Trends Ecol Evol. 2011;26:340–8.
Bell G. Neutral macroecology. Science 2001;293:2413–8.
Leibold MA, Holyoak M, Mouquet N, Amarasekare P, Chase JM, Hoopes MF, et al. The metacommunity concept: a framework for multi-scale community ecology. Ecol Lett. 2004;7:601–13.
Wilson DS. Complex interactions in metacommunities, with implications for biodiversity and higher levels of selection. Ecology. 1992;73:1984–2000.
Vellend M. Conceptual synthesis in community ecology. Q Rev Biol. 2010;85:183–206.
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.
MacArthur RH, Wilson EO. The theory of island biogeography. Woodstock, UK: Princeton University Press; 2001.
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–E1332.
Lowe WH, McPeek MA. Is dispersal neutral? Trends Ecol Evol. 2014;29:444–50.
Vellend M, Srivastava DS, Anderson KM, Brown CD, Jankowski JE, Kleynhans EJ, et al. Assessing the relative importance of neutral stochasticity in ecological communities. Oikos. 2014;123:1420–30.
Rundle HD, Nosil P. Ecological speciation. Ecol Lett. 2005;8:336–52.
Graham EB, Knelman JE, Schindlbacher A, Siciliano S, Breulmann M, Yannarell A, et al. Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Front Microbiol. 2016;7:214. https://doi.org/10.3389/fmicb.2016.00214.
Lindström ES, Langenheder S. Local and regional factors influencing bacterial community assembly. Environ Microbiol Rep. 2012;4:1–9.
Isabwe A, Ren K, Wang Y, Peng F, Chen H. Community assembly mechanisms underlying the core and random bacterioplankton and microeukaryotes in a river–reservoir system. Water. 2019;11:1–17.
Fodelianakis S, Lorz A, Valenzuela-Cuevas A, Barozzi A, Booth JM, Daffonchio D. Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity. Nat Commun. 2019;10:1. https://doi.org/10.1038/s41467-019-09306-7.
Jiao S, Yang Y, Xu Y, Zhang J, Lu Y. Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China. ISME J. 2020;14:202–16.
Grosberg RK, Vermeij GJ, Wainwright PC. Biodiversity in water and on land. Curr Biol. 2012;22:R900–R903.
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.
Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, Welch DBM, et al. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE. 2011;6:e24570.
Barberán A, Casamayor EO. Global phylogenetic community structure and β-diversity patterns in surface bacterioplankton metacommunities. Aquat Micro Ecol. 2010;59:1–10.
Nemergut DR, Schmidt SK, Fukami T, O’Neill SP, Bilinski TM, Stanish LF, et al. Patterns and processes of microbial community assembly. Microbiol Mol Biol Rev. 2013;77:342–56.
Ruiz-González C, Niño-García JP, del Giorgio PA. Terrestrial origin of bacterial communities in complex boreal freshwater networks. Ecol Lett. 2015;18:1198–206.
Widder S, Besemer K, Singer GA, Ceola S, Bertuzzo E, Quince C, et al. Fluvial network organization imprints on microbial co-occurrence networks. Proc Natl Acad Sci USA. 2014;111:12799–804.
Comte J, Lovejoy C, Crevecoeur S, Vincent WF. Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes. Biogeosciences. 2016;13:175–90.
Heino J, Melo AS, Siqueira T, Soininen J, Valanko S, Bini LM. Metacommunity organisation, spatial extent and dispersal in aquatic systems: Patterns, processes and prospects. Freshw Biol 2015;60:845–69.
Logares R, Deutschmann IM, Giner CR, Krabberød AK. Different processes shape prokaryotic and picoeukaryotic assemblages in the sunlit ocean microbiome. Environ Microbiol. 2018;20:37–49.
Östman Ö, Drakare S, Kritzberg ES, Langenheder S, Logue JB, Lindström ES. Importance of space and the local environment for linking local and regional abundances of microbes. Aquat Micro Ecol. 2012;67:35–45.
Niño-García JP, Ruiz-González C, del Giorgio PA. Interactions between hydrology and water chemistry shape bacterioplankton biogeography across boreal freshwater networks. ISME J. 2016;1:1–12.
Ofiţeru ID, Lunn M, Curtis TP, Wells GF, Criddle CS, Francis CA, et al. Combined niche and neutral effects in a microbial wastewater treatment community. Proc Natl Acad Sci USA. 2010;107:15345–50.
Evans S, Martiny JBH, Allison SD. Effects of dispersal and selection on stochastic assembly in microbial communities. ISME J. 2017;11:176–85.
Declerck SAJ, Winter C, Shurin JB, Suttle CA, Matthews B. Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses. ISME J. 2013;7:533–42.
Fernandes IM, Henriques-Silva R, Penha J, Zuanon J, Peres-Neto PR. Spatiotemporal dynamics in a seasonal metacommunity structure is predictable: the case of floodplain-fish communities. Ecography. 2014;37:464–75.
José de Paggi SB, Paggi JC. Hydrological connectivity as a shaping force in the zooplankton community of two lakes in the Paraná River floodplain. Int Rev Hydrobiol. 2008;93:659–78.
Devercelli M, Scarabotti P, Mayora G, Schneider B, Giri F. Unravelling the role of determinism and stochasticity in structuring the phytoplanktonic metacommunity of the Paraná River floodplain. Hydrobiologia. 2016;764:139–56.
Devercelli M. Changes in phytoplankton morpho-functional groups induced by extreme hydroclimatic events in the Middle Paraná river (Argentina). Hydrobiologia. 2010;639:5–19.
Scarabotti PA, López JA, Pouilly M. Flood pulse and the dynamics of fish assemblage structure from neotropical floodplain lakes. Ecol Freshw Fish. 2011;20:605–18.
Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 2016;10:1669–81.
Fuhrman JA, Cram JA, Needham DM. Marine microbial community dynamics and their ecological interpretation. Nat Rev Microbiol. 2015;13:133–46.
Faust K, Raes J. Microbial interactions: from networks to models. Nat Rev Microbiol. 2012;10:538–50.
Röttjers L, Faust K. From hairballs to hypotheses–biological insights from microbial networks. FEMS Microbiol Rev. 2018;42:761–80.
Duran-Pinedo AE, Paster B, Teles R, Frias-Lopez J. Correlation network analysis applied to complex biofilm communities. PLoS ONE. 2011;6:e28438.
Freilich MA, Wieters E, Broitman BR, Marquet PA, Navarrete SA. Species co-occurrence networks: can they reveal trophic and non-trophic interactions in ecological communities? Ecology. 2018;99:690–9.
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Structure and function of the global ocean microbiome. Science. 2015;348:1261359–1261359.
Liu J, Zhu S, Liu X, Yao P, Ge T, Zhang XH. Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship. ISME J. 2020;14:1463–78.
Layeghifard M, Hwang DM, Guttman DS. Disentangling interactions in the microbiome: a network perspective. Trends Microbiol. 2017;25:217–28.
Agler MT, Ruhe J, Kroll S, Morhenn C, Kim ST, Weigel D, et al. Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol. 2016;14:1–31.
Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol. 2018;16:567–76.
Berry D, Widder S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol. 2014;5:1–14.
Herren CM, McMahon KD. Keystone taxa predict compositional change in microbial communities. Environ Microbiol. 2018;20:2207–17.
Neiff JJ. Large rivers of South America: toward the new approach. Verh Intern Ver Limnol. 1996;26:167–80.
Drago EC. The physical dynamics of the river-lake floodplain system. In: The middle Paraná River: limnology of a subtropical wetland. Berlin, Heidelberg: Springer-Verlag; 2007. p. 83–122.
Mayora G, Devercelli M, Giri F. Spatial variability of chlorophyll-a and abiotic variables in a river-floodplain system during different hydrological phases. Hydrobiologia. 2013;717:51–63.
Mayora G, Scarabotti P, Schneider B, Alvarenga P, Marchese M. Multiscale environmental heterogeneity in a large river-floodplain system. J South Am Earth Sci. 2020;100:102546.
Thomaz SM, Bini LM, Bozelli RL. Floods increase similarity among aquatic habitats in river-floodplain systems. Hydrobiologia. 2007;579:1–13.
Camilloni IA, Barros VR. Extreme discharge events in the Paraná River and their climate forcing. J Hydrol. 2003;278:94–106.
Depetris PJ, Probst JL, Pasquini AI, Gaiero DM. The geochemical characteristics of the Paraná River suspended sediment load: an initial assessment. Hydrol Process. 2003;17:1267–77.
Marchese M, de Drago IE. Benthos of the lotic environments in the middle Paraná River system: transverse zonation. Hydrobiologia. 1992;237:1–13.
Zilli FL, Paggi AC. Ecological responses to different degrees of hydrologic connectivity: assessing patterns in the bionomy of benthic chironomids in a large river-floodplain system. Wetlands. 2013;33:837–45.
José de Paggi SB, Devercelli M, Molina FR. Zooplankton and their driving factors in a large subtropical river during low water periods. Fundam Appl Limnol/Arch für Hydrobiol. 2014;184:125–39.
Fernandez Zenoff V, Sineriz F, Farias ME. Diverse responses to UV-B radiation and repair mechanisms of bacteria isolated from high-altitude aquatic environments. Appl Environ Microbiol. 2006;72:7857–63.
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.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–4.
Logares R. Workflow for analysing MiSeq amplicons based on Uparse v1.5.: https://github.com/ramalok/amplicon_processing. 2017. https://doi.org/10.5281/zenodo.259579.
Edgar RC. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. 2016;081257. https://doi.org/10.1101/081257.
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, et al. Vegan: community ecology package. R package version 2.0-9. 2013. http://CRAN.R-project.org/package=vegan.
R Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2015. https://www.R-project.org/.
Ranjard L, Dequiedt S, Chemidlin Prévost-Bouré N, Thioulouse J, Saby NPA, Lelievre M, et al. Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity. Nat Commun. 2013;4:1–10.
Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26:32–46.
Anderson MJ. Distance-based tests for homogeneity of multivariate dispersions. Biometrics. 2006;62:245–53.
Anderson MJ, Walsh DCI, Robert Clarke K, Gorley RN, Guerra-Castro E. Some solutions to the multivariate Behrens–Fisher problem for dissimilarity-based analyses. Aust N Zeal J Stat. 2017;59:57–79.
Pedrós-Alió C. The rare bacterial biosphere. Ann Rev Mar Sci. 2012;4:449–66.
Zhou J, Ning D. Stochastic community assembly: does it matter in microbial ecology? Microbiol Mol Biol Rev. 2017;81:1–32.
Fine PVA, Kembel SW. Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities. Ecography. 2011;34:552–65.
Webb CO, Ackerly DD, McPeek MA, Donoghue MJ. Phylogenies and community ecology. Annu Rev Ecol Syst. 2002;33:475–505.
Webb CO, Ackerly DD, Kembel SW. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics. 2008;24:2098–2100.
Kembel SW. Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecol Lett. 2009;12:949–60.
Oden NL, Sokal RR. Directional autocorrelation: an extension of spatial correlograms to two dimensions. Syst Zool. 1986;35:608–17.
Diniz-Filho JAF, Terribile LC, Da Cruz MJR, Vieira LCG. Hidden patterns of phylogenetic non-stationarity overwhelm comparative analyses of niche conservatism and divergence. Glob Ecol Biogeogr. 2010;19:916–26.
Stegen JC, Lin X, Konopka AE, Fredrickson JK. Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. 2012;6:1653–64.
Andersson AF, Riemann L, Bertilsson S. Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities. ISME J. 2010;4:171–81.
Chase JM, Myers JA. Disentangling the importance of ecological niches from stochastic processes across scales. Philos Trans R Soc B Biol Sci. 2011;366:2351–63.
Chase JM. Picante: R tools for integrating phylogenies and ecology. Oecologia 2003;136:489–98.
Dray S, Legendre P, Peres-Neto PR. Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM). Ecol Modell. 2006;196:483–93.
Braak CJF ter, Šmilauer P. CANOCO reference manual and CanoDraw for Windows user’s guide: software for canonical community ordination (Version 5). Ithaca, NY: Section on Permutation Methods Microcomputer Power; 2012.
Legendre P, Legendre L. Numerical ecology. Oxford, U.K.: Elsevier Scientific; 1998.
Faust K, Lima-Mendez G, Lerat JS, Sathirapongsasuti JF, Knight R, Huttenhower C, et al. Cross-biome comparison of microbial association networks. Front Microbiol. 2015;6:1–13.
Faust K, Raes J. CoNet app: inference of biological association networks using Cytoscape. F1000Research. 2016;5:1–16.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.
Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, et al. Microbial co-occurrence relationships in the Human Microbiome. PLoS Comput Biol. 2012;8. https://doi.org/10.1371/journal.pcbi.1002606.
Volterra V. Variazioni flultuazioni del numero d’invididui in specie convirenti. Men Acad Lincei. 1926;2:31–113.
Assenov Y, Ramírez F, Schelhorn SESE, Lengauer T, Albrecht M. Computing topological parameters of biological networks. Bioinformatics. 2008;24:282–4.
Banerjee S, Walder F, Büchi L, Meyer M, Held AY, Gattinger A, et al. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J. 2019;13:1722–36.
Cao X, Zhao D, Xu H, Huang R, Zeng J, Yu Z. Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: a network analysis. Sci Rep. 2018;8:1–11.
Newman MEJ. The structure and function of complex networks. Soc Ind Appl Math Rev. 2003;45:167–256.
Barabási AL, Oltvai ZN. Network biology: understanding the cell’s functional organization. Nat Rev Genet. 2004;5:101–13.
Newman MEJ. A measure of betweenness centrality based on random walks. Soc Netw. 2005;27:39–54.
Brandes U. A faster algorithm for betweenness centrality. J Math Sociol. 2001;25:163–77.
Powell JR, Karunaratne S, Campbell CD, Yao H, Robinson L, Singh BK. Deterministic processes vary during community assembly for ecologically dissimilar taxa. Nat Commun. 2015;6:1–10.
Weilhoefer CL, Pan Y, Eppard S. The effects of river floodwaters on floodplain wetland water quality and diatom assemblages. Wetlands. 2008;28:473–86.
Unrein F. Changes in phytoplankton community along a transversal section of the lower Paraná floodplain, Argentina. Hydrobiologia. 2002;468:123–34.
Vass M, Székely AJ, Lindström ES, Langenheder S. Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions. Sci Rep. 2020;10:1–13.
Wagg C, Schlaeppi K, Banerjee S, Kuramae EE, van der Heijden MGA. Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nat Commun. 2019;10:4841.
Barberán A, Bates ST, Casamayor EO, Fierer N. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 2012;6:343–51.
Fuhrman JA. Microbial community structure and its functional implications. Nature. 2009;459:193–9.
Newman MEJ. The structure and function of networks. Comput Phys Commun. 2002;147:40–47.
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