Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Microbiology and Molecular Biology Reviews, Journal Year: 2017, Volume and Issue: 81(4)

Published: Oct. 12, 2017

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly microbial ecology. Although stochastic processes are believed to play nonnegligible roles shaping structure, their importance relative deterministic hotly debated. The of ecological stochasticity structure far less appreciated. Some main reasons for such heavy debates difficulty defining diverse methods used delineating stochasticity. Here, we provide critical review synthesis data from most recent studies on assembly We then describe both components embedded various processes, including selection, dispersal, diversification, drift. also different approaches inferring observational diversity patterns highlight experimental communities. In addition, research challenges, gaps, future directions research.

Language: Английский

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A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Sept. 18, 2020

Abstract Unraveling the drivers controlling community assembly is a central issue in ecology. Although it generally accepted that selection, dispersal, diversification and drift are major processes, defining their relative importance very challenging. Here, we present framework to quantitatively infer mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93–0.99), precision (0.80–0.94), sensitivity (0.82–0.94), specificity (0.95–0.98) on simulated communities, which 10–160% higher than those from entire community-based approach. Application of grassland microbial communities response experimental warming reveals dominant roles homogeneous selection (38%) ‘drift’ (59%). Interestingly, decreases over time, enhances primarily imposed Bacillales. In addition, has correlations with drought plant productivity under control. provides an effective robust tool quantify should also be useful for animal

Language: Английский

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Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

The ISME Journal, Journal Year: 2018, Volume and Issue: 12(4), P. 1072 - 1083

Published: March 1, 2018

Little is known about the factors affecting relative influences of stochastic and deterministic processes that govern assembly microbial communities in successional soils. Here, we conducted a meta-analysis bacterial using six different soil datasets distributed across regions. Different relationships between pH age these allowed us to separate (i.e., time) from pH. We found extreme acidic or alkaline conditions lead phylogenetically more clustered through processes, whereas close neutral less with stochasticity. suggest influence pH, rather than age, main driving force producing trends phylogenetic bacteria, also balance along Given had much stronger association community did evaluated whether inferred was maintained when studying globally samples collected without regard for age. This dataset confirmed strong suggesting on occurs globally. Extreme likely exert stringent limits survival fitness, imposing selective pressures ecological evolutionary time. Taken together, findings degree which vs. shape consequence

Language: Английский

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Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

The ISME Journal, Journal Year: 2019, Volume and Issue: 14(1), P. 202 - 216

Published: Oct. 14, 2019

Language: Английский

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A general framework for quantitatively assessing ecological stochasticity

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(34), P. 16892 - 16898

Published: Aug. 7, 2019

Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it generally accepted that both deterministic and stochastic processes play important roles assembly, quantifying their relative importance challenging. Here we propose general mathematical framework to quantify ecological stochasticity under different situations which factors drive communities more similar or dissimilar than null expectation. An index, normalized ratio (NST), was developed with 50% as boundary point between (<50%) (>50%) assembly. NST tested simulated by considering abiotic filtering, competition, environmental noise, spatial scales. All approaches showed limited performance at large scales very high noise. However, all of other scenarios, accuracy (0.90 1.00) precision (0.91 0.99), averages 0.37 higher (0.1 0.7) 0.33 (0.0 1.8) previous approaches. also applied estimate succession groundwater microbial response organic carbon (vegetable oil) injection. Our results shifted from (NST = 21%) 70%) right after input. As vegetable oil consumed, gradually returned be 27%). In addition, our demonstrated model algorithms similarity metrics had strong effects on stochasticity.

Language: Английский

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Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: Oct. 22, 2019

Abstract Background The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes shaping riverine microeukaryotic biogeography is still poorly understood. Here, we compared spatiotemporal and biogeographical patterns using high-throughput sequencing 18S rRNA gene multivariate statistical analyses from subtropical river during wet dry seasons. Results Our results provide first description communities Tingjiang River, largest west Fujian province, southeastern China. showed that microeukaryotes both seasons exhibited contrasting compositions, which might be owing to planktonic having seasonal succession patterns. Further, all components (including total, dominant, always rare, conditionally rare taxa) significant distance-decay pattern seasons, had stronger relationship season, especially for taxa. Although several variables influence on communities, environmental spatial factors minor roles communities. Importantly, were strongly driven by processes, with 89.9%, 88.5%, 89.6% variation explained neutral model wet, dry, respectively. also large fraction across different taxonomic groups levels. Additionally, taxa, above below prediction, ecologically taxonomically distinct groups, interactively structured deterministic processes. Conclusions This study demonstrated sufficient substantial metacommunity hydrographic regimes, thereby providing better understanding patterns, waters.

Language: Английский

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Microbial interactions lead to rapid micro-scale successions on model marine particles

Nature Communications, Journal Year: 2016, Volume and Issue: 7(1)

Published: June 17, 2016

Abstract In the ocean, organic particles harbour diverse bacterial communities, which collectively digest and recycle essential nutrients. Traits like motility exo-enzyme production allow individual taxa to colonize exploit particle resources, but it remains unclear how community dynamics emerge from these traits. Here we track taxon trait of bacteria attached model marine demonstrate that particle-attached communities undergo rapid, reproducible successions driven by ecological interactions. Motile, particle-degrading are selected for during early successional stages. However, this selective pressure is later relaxed when secondary consumers invade, unable use resource but, instead, rely on carbon primary degraders. This creates a trophic chain shifts metabolism away substrate. These results suggest may shape in ocean rapid community-wide metabolic could limit rates degradation.

Language: Английский

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Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes

The ISME Journal, Journal Year: 2018, Volume and Issue: 12(9), P. 2198 - 2210

Published: June 7, 2018

Unraveling the relative importance of ecological processes regulating microbial community structure is a central goal in ecology. Here, we used high-throughput sequencing to examine contribution selective and neutral assembly abundant rare subcommunities from three subtropical bays China. We found that bacterial taxa were distinctly different diversity, despite similar biogeographic patterns strong distance-decay relationships, but dispersal was more limited than taxa. Furthermore, environmental (selective processes) spatial (neutral factors seemed govern biogeography subcommunities, although both explained only small fraction variation within subcommunity. More importantly, partitioning (based on adjusted R2 redundancy analysis) showed exhibited slightly greater influence compared selection; however, subcommunity had much stronger response (17.3% pure variance explained) shown by bacteria (3.5%). These results demonstrate selection large proportion unexplained (91.1%) implies complex mechanisms may exist shape assemblages bays.

Language: Английский

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Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

Nature Communications, Journal Year: 2016, Volume and Issue: 7(1)

Published: April 7, 2016

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex temporally dynamic, making development of predictive models challenging. Spatial temporal variations zone communities a key, but understudied, component riverine function. Here, investigate the coupling among groundwater–surface mixing, biogeochemistry, we apply ecological theory, aqueous DNA sequencing ultra-high-resolution organic carbon profiling field samples collected across times locations representing broad range mixing conditions. Our results indicate stimulates heterotrophic respiration, alters composition, causes processes shift from stochastic deterministic is associated elevated abundances taxa may degrade suite compounds. Groundwater-surface zones link critical ecosystem domains, attendant microbe-biogeochemistry-hydrology interactions poorly known. authors show groundwater-surface shifts ecology deterministic.

Language: Английский

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Effects of dispersal and selection on stochastic assembly in microbial communities

The ISME Journal, Journal Year: 2016, Volume and Issue: 11(1), P. 176 - 185

Published: Aug. 5, 2016

Language: Английский

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