Vellend M. Conceptual synthesis in community ecology. Q Rev Biol. 2010;85:183–206.
Google Scholar
Leibold MA. Chase JM Metacommunity Ecology. Levin SA, Horn HS, editors: Princeton University Press, Princeton; 2018.
Logue JB, Mouquet N, Peter H, Hillebrand H, Declerck P, Flohre A, et al. Empirical approaches to metacommunities: A review and comparison with theory. Trends Ecol Evol. 2011;26:482–91.
Google Scholar
Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JB. Beyond biogeographic patterns: Processes shaping the microbial landscape. Nat Rev Microbiol. 2012;10:497–506.
Google Scholar
Lindström ES, Langenheder S. Local and regional factors influencing bacterial community assembly. Environ Microbiol Rep. 2012;4:1–9.
Google Scholar
Langenheder S, Lindström ES. Factors influencing aquatic and terrestrial bacterial community assembly. Environ Microbiol Rep. 2019;11:306–15.
Google Scholar
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.
Vass M, Langenheder S. The legacy of the past: Effects of historical processes on microbial metacommunities. Aquat Micro Ecol. 2017;79:13–9.
Fukami T. Historical contingency in community assembly: Integrating niches, species pools, and priority effects. Annu Rev Ecol Evol Syst. 2015;46:1–23.
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. 2015;112:E1326–32.
Google Scholar
Zhang FG, Zhang QG. Patterns in species persistence and biomass production in soil microcosms recovering from a disturbance reject a neutral hypothesis for bacterial community assembly. PLoS One. 2015;10:e0126962.
Google Scholar
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. 2014;111:E836–45.
Google Scholar
Ferrenberg S, O’Neill SP, Knelman JE, Todd B, Duggan S, Bradley D, et al. Changes in assembly processes in soil bacterial communities following a wildfire disturbance. ISME J. 2013;7:1102–11.
Google Scholar
Jiang L, Morin PJ. Temperature fluctuation facilitates coexistence of competing species in experimental microbial communities. J Anim Ecol. 2007;76:660–8.
Google Scholar
Tucker CM, Fukami T. Environmental variability counteracts priority effects to facilitate species coexistence: evidence from nectar microbes. Proc Biol Sci. 2014;281:20132637.
Google Scholar
Grainger TN, Letten AD, Gilbert B, Fukami T. Applying modern coexistence theory to priority effects. Proc Natl Acad Sci. 2019;116:6205–10.
Google Scholar
Jiang L, Patel SN. Community assembly in the presence of disturbance: A microcosm experiment. Ecology 2008;89:1931–40.
Google Scholar
Loeuille N, Leibold MA. Evolution in metacommunities: On the relative importance of species sorting and monopolization in structuring communities. Am Nat. 2008;171:788–99.
Google Scholar
Shade A, Jones SE, McMahon KD. The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics. Environ Microbiol. 2008;10:1057–67.
Google Scholar
Pereira CL, Araújo MB, Matias MG. Interplay between productivity and regional species pool determines community assembly in aquatic microcosms. Aquat Sci. 2018;80:45.
Herlemann DP, 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.
Google Scholar
Neubauer SC, Piehler MF, Smyth AR, Franklin RB. Saltwater intrusion modifies microbial community structure and decreases denitrification in tidal freshwater marshes. Ecosystems. 2018;22:912–28.
Rath KM, Fierer N, Murphy DV, Rousk J. Linking bacterial community composition to soil salinity along environmental gradients. ISME J. 2019;13:836–46.
Google Scholar
Tang X, Xie G, Shao K, Tian W, Gao G, Qin B. Aquatic bacterial diversity, community composition and assembly in the semi-arid Inner Mongolia Plateau: combined effects of salinity and nutrient levels. Microorganisms. 2021;9:208.
Google Scholar
Xia LC, Steele JA, Cram JA, Cardon ZG, Simmons SL, Vallino JJ, et al. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst Biol. 2011;5:S15.
Google Scholar
Langenheder S, Comte J, Zha Y, Samad MS, Sinclair L, Eiler A, et al. Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin. Environ Microbiol Rep. 2016;8:479–85.
Google Scholar
Comte J, Lindström ES, Eiler A, Langenheder S. Can marine bacteria be recruited from freshwater sources and the air? ISME J. 2014;8:2423–30.
Google Scholar
Comte J, Langenheder S, Berga M, Lindström ES. Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change. Environ Microbiol. 2017;19:251–60.
Google Scholar
Langenheder S, Ragnarsson H. The role of environmental and spatial factors for the composition of aquatic bacterial communities. Ecology 2007;88:2154–61.
Google Scholar
del Giorgio PA, Bird DF, Prairie YT, Planas D. Flow cytometric determination of bacterial abundance in lakeplankton with the green nucleid acid stain SYTO 13. Limnol Oceanogr. 1996;41:783–9.
Blazewicz SJ, Barnard RL, Daly RA, Firestone MK. Evaluating rRNA as an indicator of microbial activity in environmental communities: Limitations and uses. ISME J. 2013;7:2061–8.
Google Scholar
Székely AJ, Berga M, Langenheder S. Mechanisms determining the fate of dispersed bacterial communities in new environments. ISME J. 2013;7:61–71.
Google Scholar
Apprill A, McNally S, Parsons R, Weber L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat Micro Ecol. 2015;75:129–37.
Hugerth LW, Wefer HA, Lundin S, Jakobsson HE, Lindberg M, Rodin S, et al. DegePrime, a program for degenerate primer design for broad- taxonomic-range PCR in microbial ecology studies. Appl Environ Microbiol. 2014;80:5116–23.
Google Scholar
Martin M. Cutadapt removes adapter sequences from high- throughput sequencing reads. EMBnet J. 2011;17:10–2.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Google Scholar
Chao A, Jost L. Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size. Ecology 2012;93:2533–47.
Google Scholar
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.
Google Scholar
R-Core-Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2020.
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. Vegan: Community Ecology Package. R package version 2.5-7. ed 2020.
Bier RL Field and chemistry data from 2016 Fluctuations Project Data sets. In: DiVA, editor. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3517382016.
Noguchi K, Gel YR, Brunner E, Konietschke F. nparLD: An R software package for the nonparametric analysis of longitudinal data in factorial experiments. J Stat Softw. 2012;50:1–23.
Willis A, Martin BD, Trinh P, Teichman S, Barger K, Bunge J. Breakaway: Species Richness Estimation and Modeling. R package version 4.7.3. ed. 2020.
Baselga A, Orme D, Villeger S, De Bortoli J, Leprieur F, Logez M. Betapart: Partitioning beta diversity into turnover and nestedness components. R package version 1.5.2 ed. 2020.
Anderson MJ. Permutational multivariate analysis of variance (PERMANOVA). In: Balakrishnan N, Colton T, Everitt B, Piegorsch W, Ruggeri F, Teugels JL, editors. Wiley StatsRef: Statistics Reference Online: John Wiley & Sons, Inc; 2017. p. 1–15.
Jabot F, Laroche F, Massol F, Arthaud F, Crabot J, Dubart M, et al. Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition. Ecol Lett. 2020;23:1330–9.
Google Scholar
Rosseel Y. Lavaan: An R Package for Structural Equation Modeling. J Stat Softw. 2012;48:1–36.
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.
Google Scholar
Assenov Y, Ramirez F, Schelhorn SE, Lengauer T, Albrecht M. Computing topological parameters of biological networks. Bioinformatics 2008;24:282–4.
Google Scholar
Drake JA. Community-assembly mechanics and the structure of an experimental species ensemble. Am Nat. 1991;137:1–26.
Orrock JL, Fletcher RL Jr. Changes in community size affect the outcome of competition. Am Nat. 2005;166:107–11.
Google Scholar
Fukami T. Community assembly along a species pool gradient: implications for multiple‐scale patterns of species diversity. Popul Ecol. 2004;46:137–47.
Lozupone CA, Hamady M, Kelley ST, Knight R. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol. 2007;73:1576–85.
Google Scholar
Werba JA, Stucy AL, Peralta AL, McCoy MW. Effects of diversity and coalescence of species assemblages on ecosystem function at the margins of an environmental shift. PeerJ. 2020;8:e8608.
Google Scholar
Logares R, Brate J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K. Infrequent marine-freshwater transitions in the microbial world. Trends Microbiol. 2009;17:414–22.
Google Scholar
Logares R, Lindström ES, Langenheder S, Logue JB, Paterson H, Laybourn-Parry J, et al. Biogeography of bacterial communities exposed to progressive long-term environmental change. ISME J. 2013;7:937–48.
Google Scholar
Muylaert K, Van Der Gucht K, Vloemans N, Meester LD, Gillis M, Vyverman W. Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes. Appl Environ Microbiol. 2002;68:4740–50.
Google Scholar
Lee AM, Sæther B-E, Engen S. Spatial covariation of competing species in a fluctuating environment. Ecology 2020;101:e02901.
Google Scholar
Liu J, Fu B, Yang H, Zhao M, He B, Zhang XH. Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients. Front Microbiol. 2015;6:64.
Google Scholar
Guiry MD, Guiry GM. AlgaeBase. World-wide electronic publication: National University of Ireland, Galway; 2022.
Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, et al. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio 2014;5:e01371–14.
Google Scholar
Andersson MGI, Berga M, Lindström ES, Langenheder S. The spatial structure of bacterial communities is influenced by historical environmental conditions. Ecology 2014;95:1134–40.
Google Scholar
Ai D, Gravel D, Chu C, Wang G. Spatial structures of the environment and of dispersal impact species distribution in competitive metacommunities. PLoS One. 2013;8:e68927.
Google Scholar
Maloufi S, Catherine A, Mouillot D, Louvard C, Couté A, Bernard C, et al. Environmental heterogeneity among lakes promotes hyper β-diversity across phytoplankton communities. Freshw Biol. 2016;61:633–45.
Firkowski CR, Thompson PL, Gonzalez A, Cadotte MW, Fortin M-J. Multi-trophic metacommunity interactions mediate asynchrony and stability in fluctuating environments. Ecol Monogr. n/a:e1484.
Lennon JT, Jones SE. Microbial seed banks: The ecological and evolutionary implications of dormancy. Nat Rev Microbiol. 2011;9:119–30.
Google Scholar
Knope ML, Forde SE, Fukami T. Evolutionary history, immigration history, and the extent of diversification in community assembly. Front Microbiol. 2011;2:273.
Google Scholar
Fukami T. Assembly history interacts with ecosystem size to influence species diversity. Ecology 2004;85:3234–42.
Orrock JL, Watling JI. Local community size mediates ecological drift and competition in metacommunities. Proc Biol Sci. 2010;277:2185–91.
Google Scholar
Chase JM. Community assembly: When should history matter? Oecologia 2003;136:489–98.
Google Scholar
Ron R, Fragman-Sapir O, Kadmon R. Dispersal increases ecological selection by increasing effective community size. Proc Natl Acad Sci. 2018;115:11280–5.
Google Scholar
Siqueira T, Saito VS, Bini LM, Melo AS, Petsch DK, Landeiro VL, et al. Community size can affect the signals of ecological drift and niche selection on biodiversity. Ecology 2020;101:e03014.
Google Scholar
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;10:2455.
Google Scholar
Shen D, Langenheder S, Jürgens K. Dispersal modifies the diversity and composition of active bacterial communities in response to a salinity disturbance. Front Microbiol. 2018;9:2188.
Google Scholar
Cunze S, Heydel F, Tackenberg O. Are plant species able to keep pace with the rapidly changing climate? PLoS One. 2013;8:e67909.
Google Scholar
Source: Ecology - nature.com