Thakur MP, van der Putten WH, Cobben MMP, van Kleunen M, Geisen S. Microbial invasions in terrestrial ecosystems. Nat Rev Microbiol. 2019;17:621–31.
Google Scholar
Mooney HA, Cleland EE. The evolutionary impact of invasive species. Proc Natl Acad Sci USA. 2001;98:5446–51.
Google Scholar
Mallon CA, Elsas JDV, Salles JF. Microbial invasions: the process, patterns, and mechanisms. Trends Microbiol. 2015;23:719–29.
Google Scholar
O’Brien S, Hodgson DJ, Buckling A. Social evolution of toxic metal bioremediation in Pseudomonas aeruginosa. Proc R Soc B Biol Sci. 2014;281:20140858.
Walter J, Maldonado-Gómez MX, Martínez I. To engraft or not to engraft: an ecological framework for gut microbiome modulation with live microbes. Curr Opin Biotechnol. 2018;49:129–39.
Google Scholar
van der Goot E, van Spronsen FJ, Falcão Salles J, van der Zee EA. A microbial community ecology perspective on the gut-microbiome-brain axis. Front Endocrinol. 2020;11:611.
Google Scholar
Williamson M, Fitter A. The varying success of invaders. Ecology. 1996;77:1661–6.
Google Scholar
Catford JA, Jansson R, Nilsson C. Reducing redundancy in invasion ecology by integrating hypotheses into a single theoretical framework. Divers Distrib. 2009;15:22–40.
Google Scholar
Simberloff D. The role of propagule pressure in biological invasions. Annu Rev Ecol Evol Syst. 2009;40:81–102.
Google Scholar
Acosta F, Zamor RM, Najar FZ, Roe BA, Hambright KD. Dynamics of an experimental microbial invasion. Proc Natl Acad Sci USA. 2015;112:11594–9.
Google Scholar
Barney JN, Ho MW, Atwater DZ. Propagule pressure cannot always overcome biotic resistance: the role of density-dependent establishment in four invasive species. Weed Res. 2016;56:208–18.
Google Scholar
Ketola T, Saarinen K, Lindström L. Propagule pressure increase and phylogenetic diversity decrease community’s susceptibility to invasion. BMC Ecol. 2017;17:1–7.
Google Scholar
Vila JCC, Jones ML, Patel M, Bell T, Rosindell J. Uncovering the rules of microbial community invasions. Nat Ecol Evol. 2019;3:1162–71.
Google Scholar
Dressler MD, Conde J, Eldakar OT, Smith RP. Timing between successive introduction events determines establishment success in bacteria with an Allee effect. Proc R Soc B Biol Sci. 2019;286:20190598.
Google Scholar
Jones ML, Rivett DW, Pascual-Garria A, Bell T. Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms. eLife. 2021;10:e71811.
Google Scholar
Rivett DW, Jones ML, Ramoneda J, Mombrikotb SB, Ransome E, Bell T. Elevated success of multispecies bacterial invasions impacts community composition during ecological succession. Ecol Lett. 2018;21:516–24.
Google Scholar
Case TJ. Invasion resistance arises in strongly interacting species-rich model competition communities. Proc Natl Acad Sci USA. 1990;87:9610–4.
Google Scholar
Jousset A, Schulz W, Scheu S, Eisenhauer N. Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities. ISME J. 2011;5:1108–14.
Google Scholar
Eisenhauer N, Scheu S, Jousset A. Bacterial diversity stabilizes community productivity. PLoS ONE. 2012;7:e34517.
Wei Z, Yang T, Friman VP, Xu Y, Shen Q, Jousset A. Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health. Nat Comm. 2015;6:8413.
Google Scholar
Amalfitano S, Coci M, Corno G, Luna GM. A microbial perspective on biological invasions in aquatic ecosystems. Hydrobiologia. 2015;746:13–22.
Google Scholar
Li SP, Tan J, Yang X, Ma C, Jiang L. Niche and fitness differences determine invasion success and impact in laboratory bacterial communities. ISME J. 2019;13:402–12.
Google Scholar
Baumgartner M, Pfrunder-Cardozo KR, Hall AR. Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples. Proc R Soc B Biol Sci. 2021;288:20203106.
Google Scholar
Kurkjian HM, Akbari MJ, Momeni B. The impact of interactions on invasion and colonization resistance in microbial communities. PLoS Comp Biol. 2021;17:e1008643.
Google Scholar
Tilman D. Niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly. Proc Natl Acad Sci USA. 2004;101:10854–61.
Google Scholar
van Elsas JD, Chiurazzi M, Mallon CA, Elhottova D, Kristufek V, Salles JF. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proc Natl Acad Sci USA. 2012;109:1159–64.
Google Scholar
Foster KR, Bell T. Competition, not cooperation, dominates interactions among culturable microbial species. Curr Biol. 2012;22:1845–50.
Google Scholar
Mitri S, Foster KR. The genotypic view of social interactions in microbial communities. Annu Rev Microbiol. 2013;43:247–73.
Kehe J, Ortiz A, Kulesa A, Gore J, Blainey PC, Friedman J. Positive interactions are common among culturable bacteria. Sci Adv. 2021;7:7159.
Google Scholar
Connell JH, Slatyer RO. Mechanisms of succession in natural communities and their role in community stability and organization. Am Nat. 1977;111:1119–44.
Google Scholar
Debray R, Socolar Y, Kaulbach G, Guzman A, Hernandez CA, Curley R, et al. Priority effects in microbiome assembly. Nat Rev Microbiol. 2022;20:109–21.
Google Scholar
Datta MS, Sliwerska E, Gore J, Polz MF, Cordero OX. Microbial interactions lead to rapid micro-scale successions on model marine particles. Nat Commun. 2016;7:11965.
Google Scholar
Enke TN, Datta MS, Schwartzman J, Cermak N, Schmitz D, Barrere J, et al. Modular assembly of polysaccharide-degrading marine microbial communities. Curr Biol. 2019;29:1528–35.e6.
Google Scholar
Mazumdar V, Amar S, Segrè D. Metabolic proximity in the order of colonization of a microbial community. PLoS ONE. 2013;8:e77617.
Google Scholar
Gralka M, Szabo R, Stocker R, Cordero OX. Trophic interactions and the drivers of microbial community assembly. Curr Biol. 2020;30:R1176–88.
Google Scholar
Rickard AH, Gilbert P, High NJ, Kolenbrander PE, Handley PS. Bacterial coaggregation: an integral process in the development of multi-species biofilms. Trends Microbiol. 2003;11:94–100.
Google Scholar
Kolenbrander PE, Palmer RJ, Periasamy S, Jakubovics NS. Oral multispecies biofilm development and the key role of cell–cell distance. Nat Rev Microbiol. 2010;8:471–80.
Google Scholar
Monier JM, Lindow SE. Aggregates of resident bacteria facilitate survival of immigrant bacteria on leaf surfaces. Micro Ecol. 2005;49:343–52.
Google Scholar
Poza-Carrion C, Suslow T, Lindow S. Resident bacteria on leaves enhance survival of immigrant cells of Salmonella enterica. Phytopathology. 2013;103:341–51.
Google Scholar
Li M, Wei Z, Wang J, Jousset A, Friman V, Xu Y, et al. Facilitation promotes invasions in plant-associated microbial communities. Ecol Lett. 2019;22:149–58.
Google Scholar
Estrela S, Vila JCC, Lu N, Bajić D, Rebolleda-Gómez M, Chang CY, et al. Functional attractors in microbial community assembly. Cell Syst. 2022;13:29–42.e7.
Google Scholar
Bertness MD, Callaway R. Positive interactions in communities. Trends Ecol Evol. 1994;9:191–3.
Google Scholar
Zaneveld JR, McMinds R, Thurber RV. Stress and stability: applying the Anna Karenina principle to animal microbiomes. Nat Microbiol. 2017;2:1–8.
Google Scholar
de Vries FT, Griffiths RI, Bailey M, Craig H, Girlanda M, Gweon HS, et al. Soil bacterial networks are less stable under drought than fungal networks. Nat Commun. 2018;9:3033.
Google Scholar
Goldford JE, Lu N, Bajić D, Estrela S, Tikhonov M, Sanchez-Gorostiaga A, et al. Emergent simplicity in microbial community assembly. Science. 2018;361:469–74.
Google Scholar
Nguyen LTT, Broughton K, Osanai Y, Anderson IC, Bange MP, Tissue DT, et al. Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop. Sci Total Environ. 2019;675:81–9.
Google Scholar
Piccardi P, Vessman B, Mitri S. Toxicity drives facilitation between 4 bacterial species. Proc Natl Acad Sci USA. 2019;116:15979–84.
Google Scholar
Hernandez DJ, David AS, Menges ES, Searcy CA, Afkhami ME. Environmental stress destabilizes microbial networks. ISME J. 2021;15:1722–34.
Google Scholar
Urban MC, De Meester L. Community monopolization: Local adaptation enhances priority effects in an evolving metacommunity. Proc R Soc B Biol Sci. 2009;276:4129–38.
Google Scholar
Vanoverbeke J, Urban MC, De Meester L. Community assembly is a race between immigration and adaptation: eco-evolutionary interactions across spatial scales. Ecography. 2016;39:858–70.
Google Scholar
De Meester L, Vanoverbeke J, Kilsdonk LJ, Urban MC. Evolving perspectives on monopolization and priority effects. Trends Ecol Evol. 2016;31:136–46.
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
Nadeau CP, Farkas TE, Makkay AM, Papke RT, Urban MC. Adaptation reduces competitive dominance and alters community assembly. Proc R Soc B Biol Sci. 2021;288:20203133.
Google Scholar
Faillace CA, Morin PJ. Evolution alters the consequences of invasions in experimental communities. Nat Ecol Evol. 2017;1:0013.
Google Scholar
Castledine M, Sierocinski P, Padfield D, Buckling A. Community coalescence: an eco-evolutionary perspective. Philos Trans R Soc B Biol Sci. 2020;375:20190252.
Google Scholar
Amor DR, Ratzke C, Gore J. Transient invaders can induce shifts between alternative stable states of microbial communities. Sci Adv. 2020;6:eaay8676.
Google Scholar
van der Gast CJ, Thompson IP. Effects of pH amendment on metal working fluid wastewater biological treatment using a defined bacterial consortium. Biotechnol Bioeng. 2005;89:357–66.
Google Scholar
Saha R, Donofrio RS. The microbiology of metalworking fluids. Appl Microbiol Biotechnol. 2012;94:1119–30.
Google Scholar
Ratzke C, Barrere J, Gore J. Strength of species interactions determines biodiversity and stability in microbial communities. Nat Ecol Evol. 2020;4:376–83.
Google Scholar
Estrela S, Libby E, Van Cleve J, Débarre F, Deforet M, Harcombe WR, et al. Environmentally mediated social eilemmas. Trends Ecol Evol. 2019;34:6–18.
Google Scholar
Enke TN, Leventhal GE, Metzger M, Saavedra JT, Cordero OX. Microscale ecology regulates particulate organic matter turnover in model marine microbial communities. Nat Commun. 2018;9:2743.
Google Scholar
Furman O, Shenhav L, Sasson G, Kokou F, Honig H, Jacoby S, et al. Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics. Nat Commun. 2020;11:1–13.
Google Scholar
Coyte KZ, Rao C, Rakoff-Nahoum S, Foster KR. Ecological rules for the assembly of microbiome communities. PLoS Biol. 2021;19:e3001116.
Google Scholar
Molinero N, Ruiz L, Sánchez B, Margolles A, Delgado S. Intestinal bacteria interplay with bile and cholesterol metabolism: implications on host physiology. Front Physiol. 2019;10:185.
Google Scholar
Ruiz L, Margolles A, Sánchez B. Bile resistance mechanisms in Lactobacillus and Bifidobacterium. Front Microbiol. 2013;4:396.
Google Scholar
Gérard P. Metabolism of cholesterol and bile acids by the gut microbiota. Pathogens. 2013;3:14–24.
Google Scholar
Amarnath K, Narla AV, Pontrelli S, Dong J, Caglar T, Taylor BR, et al. Stress-induced cross-feeding of internal metabolites provides a dynamic mechanism of microbial cooperation. bioRxiv. 2021. https://doi.org/10.1101/2021.06.24.449802.
Fukami T, Beaumont HJ, Zhang XX, Rainey PB. Immigration history controls diversification in experimental adaptive radiation. Nature. 2007;446:436–9.
Google Scholar
Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK. The contribution of species richness and composition to bacterial services. Nature. 2005;436:1157–60.
Google Scholar
Ghoul M, Mitri S. The ecology and evolution of microbial competition. Trends Microbiol. 2016;24:833–45.
Google Scholar
Fukami T. Historical contingency in community assembly: integrating niches, species pools, and priority effects. Annu Rev Ecol Evol Syst. 2015;46:1–23.
Google Scholar
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