Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Zhou, Jizhong; Ning, Daliang

doi:10.1128/mmbr.00002-17

Cited by 1,739 publications

(1,604 citation statements)

References 273 publications

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“…βMNTD values can be larger, smaller or equal to the values expected when selection is not affecting community turnover (i.e., expected under a random distribution [null model]). βMNTD values higher than expected indicate that communities are under heterogeneous selection (Zhou and Ning, ). In contrast, βMNTD values which are lower than expected indicate that communities are experiencing homogeneous selection.…”

Section: Methodsmentioning

confidence: 90%

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes

Logares

Tesson

Canbäck³

et al. 2018

Environmental Microbiology

175

138

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Whether or not communities of microbial eukaryotes are structured in the same way as bacteria is a general and poorly explored question in ecology. Here, we investigated this question in a set of planktonic lake microbiotas in Eastern Antarctica that represent a natural community ecology experiment. Most of the analysed lakes emerged from the sea during the last 6000 years, giving rise to waterbodies that originally contained marine microbiotas and that subsequently evolved into habitats ranging from freshwater to hypersaline. We show that habitat diversification has promoted selection driven by the salinity gradient in bacterial communities (explaining ∼ 72% of taxa turnover), while microeukaryotic counterparts were predominantly structured by ecological drift (∼72% of the turnover). Nevertheless, we also detected a number of microeukaryotes with specific responses to salinity, indicating that albeit minor, selection has had a role in the structuring of specific members of their communities. In sum, we conclude that microeukaryotes and bacteria inhabiting the same communities can be structured predominantly by different processes. This should be considered in future studies aiming to understand the mechanisms that shape microbial assemblages.

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Section: Methodsmentioning

confidence: 90%

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes

Logares

Tesson

Canbäck³

et al. 2018

Environmental Microbiology

175

138

View full text Add to dashboard Cite

show abstract

“…Our capacity to predict the moose gut microbial community at the population scale increased when we included spatial information, indicating that either stochastic events such as microbial dispersal, host social structure or spatial similarities in diet may be important in structuring associations between gut microbes. Dispersal of microbes is thought to be passive (Nemergut et al, ); however, these microbial species are often in high abundance and have broad distributions making dispersal challenging to quantify (Evans et al, ; Zhou & Ning, ). Biogeographical studies have shown that dispersal limitation is important for structuring microbial communities including those of the gut (Evans et al, ; Hanson, Fuhrman, Horner‐Devine, & Martiny, ; Moeller et al, ), but rarely over a relatively small area within a host population.…”

Section: Discussionmentioning

confidence: 99%

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Fountain-Jones

Clark

Kinsley

et al. 2020

Journal of Animal Ecology

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Microbial communities are increasingly recognized as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free‐living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison with other factors such as host characteristics or spatial proximity of hosts. Here, we ask how gut microbial communities are structured in a population of North American moose Alces alces. We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition. We sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information. We found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with ~90% accuracy. Collectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping gut microbial communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non‐model hosts.

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“…All possible communities were simulated with 100 replicate regional species pools such that all possible combination of parameters were used once with each regional species pool. Equation (2) simplifies dispersal as a probabilistic function without regard to phylogeny, although we acknowledge that the ability of organisms to disperse is not phylogenetically random in natural settings [17]. In our view of community assembly (and in our simulation model), both selection and dispersal are probabilistic.…”

Section: Community Assemblymentioning

confidence: 99%

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

2017

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Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal rates high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community's biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.

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Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Cited by 1,739 publications

References 273 publications

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

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