Leibold, M. A. & Chase, J. M. Metacommunity ecology. 59 (Princeton University Press, 2017).
Stegen, J. C., Lin, X., Konopka, A. E. & Fredrickson, J. K. Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. 6, 1653–1664 (2012).
Yeh, Y. C. et al. Determinism of bacterial metacommunity dynamics in the southern East China Sea varies depending on hydrography. Ecography. 38, 198–212 (2015).
Dini-Andreote, F., Stegen, J. C., van Elsas, J. D. & Salles, J. F. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc. Natl. Acad. Sci. 112, E1326–E1332 (2015).
Langenheder, S., Berga, M., Östman, Ö. & Székely, A. J. Temporal variation of β-diversity and assembly mechanisms in a bacterial metacommunity. ISME J. 6, 1107–1114 (2012).
Veach, A. M., Stegen, J. C., Brown, S. P., Dodds, W. K. & Jumpponen, A. Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem. Mol. Ecol., https://doi.org/10.1111/mec.13784 (2016).
Wojciechowski, J., Heino, J., Bini, L. M. & Padial, A. A. Temporal variation in phytoplankton beta diversity patterns and metacommunity structures across subtropical reservoirs. Freshw. Biol. 62, 751–766 (2017).
Langenheder, S. & Lindström, E. S. Factors influencing aquatic and terrestrial bacterial community assembly. Environ. Microbiol. Rep. 00 (2019).
Viana, D. S. et al. Assembly mechanisms determining high species turnover in aquatic communities over regional and continental scales. Ecography (Cop.). 39, 281–288 (2016).
Hawkes, C. V. & Keitt, T. H. Resilience vs. historical contingency in microbial responses to environmental change. Ecol. Lett. 18, 612–625 (2015).
Fukami, T. Historical contingency in community assembly: integrating niches, species pools, and priority effects. Annu. Rev. Ecol. Evol. Syst. 46, 1–23 (2015).
Vass, M. & Langenheder, S. The legacy of the past: effects of historical processes on microbial metacommunities. Aquat. Microb. Ecol. 79, 13–19 (2017).
Andersson, M. G. I., Berga, M., Lindström, E. S. & Langenheder, S. The spatial structure of bacterial communities is influenced by historical environmental conditions. Ecology 95, 1134–1140 (2014).
Lindström, E. S. & Östman, Ö. The importance of dispersal for bacterial community composition and functioning. PLoS One, https://doi.org/10.1371/journal.pone.0025883 (2011).
Stegen, J. C., Lin, X., Fredrickson, J. K. & Konopka, A. E. Estimating and mapping ecological processes influencing microbial community assembly. Front. Microbiol. 6, 1–15 (2015).
Tripathi, B. M. et al. Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. ISME J. 12, 1072–1083 (2018).
Zhang, X., Johnston, E. R., Liu, W., Li, L. & Han, X. Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes. Glob. Chang. Biol. 22, 198–207 (2016).
Chase, J. M. Stochastic Community Assembly Causes Higher Biodiversity in More Productive Environments. Science (80-.). 328, 1388–1391 (2010).
Liu, L., Yang, J., Yu, X., Chen, G. & Yu, Z. Patterns in the composition of microbial communities from a subtropical river: effects of environmental, spatial and temporal factors. PLoS One 8, e81232 (2013).
Zhao, D. et al. The heterogeneity of composition and assembly processes of the microbial community between different nutrient loading lake zones in Taihu Lake. Appl. Microbiol. Biotechnol. 1–11, https://doi.org/10.1007/s00253-017-8327-0 (2017).
Logares, R. et al. Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes. Environ. Microbiol. 20, 2231–2240 (2018).
Wu, W. et al. Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities. ISME J. 1–10, https://doi.org/10.1038/ismej.2017.183 (2017).
Brislawn, C. J. et al. Forfeiting the priority effect: turnover defines biofilm community succession. ISME J. 1865–1877, https://doi.org/10.1038/s41396-019-0396-x (2019).
Beisner, B. E., Peres-Neto, P. R., Lindström, E. S., Barnett, A. & Longhi, M. L. The role of environmental and spatial processes in structuring lake communities from bacteria to fish. Ecology 87, 2985–91 (2006).
De Bie, T. et al. Body size and dispersal mode as key traits determining metacommunity structure of aquatic organisms. Ecol. Lett. 15, 740–747 (2012).
Gotelli, N. J. Research frontiers in null model analysis. Glob. Ecol. Biogeogr. 10, 337–343 (2001).
Stegen, J. C. et al. Quantifying community assembly processes and identifying features that impose them. ISME J. 7, 2069–2079 (2013).
Leibold, M. A. & Mikkelson, G. M. Coherence, species turnover, and boundary clumping: elements of meta-community structure. Oikos 97, 237–250 (2002).
Presley, S. J., Higgins, C. L. & Willig, M. R. A comprehensive framework for the evaluation of metacommunity structure. Oikos 119, 908–917 (2010).
Raup, D. M. & Crick, R. E. Measurement of faunal similarity in paleontology. J. Paleontol. 53, 1213–1227 (1979).
Chase, J. M., Kraft, N. J. B., Smith, K. G., Vellend, M. & Inouye, B. D. Using null models to disentangle variation in community dissimilarity from variation in α-diversity. Ecosphere 2, art24 (2011).
Gerhold, P., Cahill, J. F., Winter, M., Bartish, I. V. & Prinzing, A. Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better). Funct. Ecol. 29, 600–614 (2015).
Cavender-Bares, J., Kozak, K. H., Fine, P. V. A. & Kembel, S. W. The merging of community ecology and phylogenetic biology. Ecol. Lett. 12, 693–715 (2009).
Jespersen, A.-M. & Christoffersen, K. Measurements of chlorophyll-a from phytoplankton using ethanol as extraction solvent. Arch. für Hydrobiol., https://doi.org/10.1093/nar/26.14.3392 (1987).
Székely, A. J., Berga, M. & Langenheder, S. Mechanisms determining the fate of dispersed bacterial communities in new environments. ISME J. 7, 61–71 (2013).
Herlemann, D. P. et al. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5, 1571–1579 (2011).
Hugerth, L. W. et al. Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS One 9, e95567 (2014).
Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41 (2013).
R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna Austria https://www.R-project.org (2015).
Dormann, C. F. et al. Collinearity: a review of methods to deal with it and a simulation study evaluating their performance. Ecography (Cop.). 36, 27–46 (2013).
Oksanen, J., Blanchet, F., Kindt, R., Legendre, P. & O’Hara, R. Vegan: community ecology package. R package 2, 3–3 (2016).
Dallas, T. Metacom: An R package for the analysis of metacommunity structure. Ecography (Cop.). 37, 402–405 (2014).
Soininen, J., Korhonen, J. J. & Luoto, M. Stochastic species distributions are driven by organism size. Ecology 94, 660–670 (2013).
Székely, A. J. & Langenheder, S. The importance of species sorting differs between habitat generalists and specialists in bacterial communities. FEMS Microbiol. Ecol. 87, 102–112 (2014).
Langenheder, S. & Ragnarsson, H. The role of environmental and spatial factors for the composition of aquatic bacterial communities. Ecology 88, 2154–2161 (2007).
Castillo-Escrivà, A., Aguilar-Alberola, J. A. & Mesquita-Joanes, F. Spatial and environmental effects on a rock-pool metacommunity depend on landscape setting and dispersal mode. Freshw. Biol. 62, 1004–1011 (2017).
Ulrich, W. & Gotelli, N. J. Null model analysis of species associations using abundance data. Ecology 91, 3384–3397 (2010).
Tucker, C. M., Shoemaker, L. G., Davies, K. F., Nemergut, D. R. & Melbourne, B. A. Differentiating between niche and neutral assembly in metacommunities using null models of β-diversity. Oikos 125, 778–789 (2016).
Modenutti, B. E., Balseiro, E. G., Callieri, C. & Bertoni, R. Light versus food supply as factors modulating niche partitioning in two pelagic mixotrophic ciliates. Limnol. Oceanogr., https://doi.org/10.4319/lo.2008.53.2.0446 (2008).
Crane, K. W. & Grover, J. P. Coexistence of mixotrophs, autotrophs, and heterotrophs in planktonic microbial communities. J. Theor. Biol., https://doi.org/10.1016/j.jtbi.2009.10.027 (2010).
Leibold, M. A. & Chase, J. M. Metacommunity Patterns in Space. In Metacommunity Ecology 90–130 (Princeton Univ. Press, 2017).
Parks, D. H. & Beiko, R. G. Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities. ISME J. 7, 173–183 (2013).
Pontarp, M., Canbäck, B., Tunlid, A. & Lundberg, P. Phylogenetic Analysis Suggests That Habitat Filtering Is Structuring Marine Bacterial Communities Across the Globe. Microb. Ecol. 64, 8–17 (2012).
García-García, N., Tamames, J., Linz, A. M., Pedrós-Alió, C. & Puente-Sánchez, F. Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions. ISME J. 2969–2983, https://doi.org/10.1038/s41396-019-0487-8 (2019).
Martiny, J. B. H., Eisen, J. A., Penn, K., Allison, S. D. & Horner-Devine, M. C. Drivers of bacterial beta-diversity depend on spatial scale. Proc. Natl. Acad. Sci. USA 108, 7850–4 (2011).
van der Gast, C. J. Microbial biogeography: The end of the ubiquitous dispersal hypothesis? Environ. Microbiol. 17, 544–546 (2015).
Langenheder, S. et al. Bacterial metacommunity organization in a highly connected aquatic system. FEMS Microbiol. Ecol. 93, 1–9 (2017).
Zhou, J. & Ning, D. Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiol. Mol. Biol. Rev. 81, 1–32 (2017).
Martiny, J. B. H. et al. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4, 102–112 (2006).
Source: Ecology - nature.com
