Patterns and Processes of Microbial Community Assembly

Nemergut, Diana R.; Schmidt, Steven K.; Fukami, Tadashi; O’Neill, Sean; Bilinski, Teresa; Stanish, Lee F.; Knelman, Joseph E.; Darcy, John L.; Lynch, Ryan C.; Wickey, Phillip; Ferrenberg, Scott

doi:10.1128/mmbr.00051-12

Cited by 1,458 publications

(1,318 citation statements)

References 156 publications

(188 reference statements)

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“…Probability of dispersing is not linked to other traits in the model (for example, competitive ability), and did not vary among taxa in any deterministic way. Although studies have found that some microbial life forms are more easily dispersed than others (for example, spores), most microorganisms are likely to disperse passively over large areas (Martiny et al, 2006;Nemergut et al, 2013).…”

Section: Dispersalmentioning

confidence: 99%

“…Because microbes have high dispersal rates, large population sizes, fast growth rates and a propensity for dormancy, communities were traditionally thought to assemble deterministically. However, recent characterizations of microbial communities provide evidence that in addition to environmental selection, stochastic processes can be important drivers of microbial community assembly (Ferrenberg et al, 2013;Nemergut et al, 2013;Zhou et al, 2013;Fukami, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Some mechanisms of microbial community assembly (Vellend, 2010) map easily onto the stochastic-deterministic framework: demographic drift, or fluctuation in population size due to random birth and death events, is a stochastic process, whereas selection, equivalent to environmental filtering or species sorting, can be considered deterministic. In contrast, dispersal can be deterministic-when certain species are better dispersers than others-or stochastic, occurring through passive processes like wind (Nemergut et al, 2013;Lowe and McPeek, 2014). Low or limited dispersal can also introduce stochasticity in microbial communities (Martiny et al, 2006;Bell, 2010;Lindström and Östman, 2011), potentially through increased drift (Hanson et al, 2012;Stegen et al, 2013), whereas high rates of dispersal can induce mass effects.…”

Section: Introductionmentioning

confidence: 99%

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Effects of dispersal and selection on stochastic assembly in microbial communities

2016

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Stochastic processes can play an important role in microbial community assembly. Dispersal limitation is one process that can increase stochasticity and obscure relationships between environmental variables and microbial community composition, but the relationship between dispersal, selection and stochasticity has not been described in a comprehensive way. We examine how dispersal and its interactions with drift and selection alter the consistency with which microbial communities assemble using a realistic, individual-based model of microbial decomposers. Communities were assembled under different environmental conditions and dispersal rates in repeated simulations, and we examined the compositional difference among replicate communities colonizing the same type of leaf litter ('within-group distance'), as well as between-group deterministic selection. Dispersal rates below 25% turnover per year resulted in high within-group distance among communities and no significant environmental effects. As dispersal limitation was alleviated, both within-and between-group distance decreased, but despite this homogenization, deterministic environmental effects remained significant. In addition to direct effects of dispersal rate, stochasticity of community composition was influenced by an interaction between dispersal and selection strength. Specifically, communities experiencing stronger selection (less favorable litter chemistries) were more stochastic, possibly because lower biomass and richness intensified drift or priority effects. Overall, we show that dispersal rate can significantly alter patterns of community composition. Partitioning the effects of dispersal, selection and drift based on static patterns of microbial composition will be difficult, if not impossible. Experiments will be required to tease apart these complex interactions between assembly processes shaping microbial communities.

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Section: Dispersalmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Effects of dispersal and selection on stochastic assembly in microbial communities

2016

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“…Community assembly processes could be divided into four main forces: dispersal, diversification, ecological drift and selection (Nemergut et al 2013). Recently, many research groups have investigated the importance of selection in determining community assembly in the rhizosphere and the phyllosphere (Bulgarelli et al 2013;Müller et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Assembly of seed-associated microbial communities within and across successive plant generations

et al. 2017

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Background and aims Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.Methods Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model. Results Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota. Conclusions These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.

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“…Microbial community assembly, like all ecological community assembly, is mediated by the forces of selection, dispersal, diversification, and drift (Nemergut et al., 2013; Vellend, 2010). In many ways, microbial assembly resembles plant primary succession (Fierer, Nemergut, Knight, & Craine, 2010), but the impact of dormancy and rapid evolution, as well as the immense diversity of microbes, can elicit unique patterns.…”

Section: Discussionmentioning

confidence: 99%

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms

Reese

Lulow

David

et al. 2017

Ecology and Evolution

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Soils harbor large, diverse microbial communities critical for local and global ecosystem functioning that are controlled by multiple and poorly understood processes. In particular, while there is observational evidence of relationships between both biotic and abiotic conditions and microbial composition and diversity, there have been few experimental tests to determine the relative importance of these two sets of factors at local scales. Here, we report the results of a fully factorial experiment manipulating soil conditions and plant cover on old‐field mesocosms across a latitudinal gradient. The largest contributor to beta diversity was site‐to‐site variation, but, having corrected for that, we observed significant effects of both plant and soil treatments on microbial composition. Separate phyla were associated with each treatment type, and no interactions between soil and plant treatment were observed. Individual soil characteristics and biotic parameters were also associated with overall beta‐diversity patterns and phyla abundance. In contrast, soil microbial diversity was only associated with site and not experimental treatment. Overall, plant community treatment explained more variation than soil treatment, a result not previously appreciated because it is difficult to dissociate plant community composition and soil conditions in observational studies across gradients. This work highlights the need for more nuanced, multifactorial experiments in microbial ecology and in particular indicates a greater focus on relationships between plant composition and microbial composition during community assembly.

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Patterns and Processes of Microbial Community Assembly

Cited by 1,458 publications

References 156 publications

Effects of dispersal and selection on stochastic assembly in microbial communities

Effects of dispersal and selection on stochastic assembly in microbial communities

Assembly of seed-associated microbial communities within and across successive plant generations

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms

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