Human nutrition, the gut microbiome and the immune system

Nature, Journal Year: 2011, Volume and Issue: 474(7351), P. 327 - 336

Published: June 14, 2011

Language: Английский

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Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist

Ecology Letters, Journal Year: 2010, Volume and Issue: 14(1), P. 19 - 28

Published: Nov. 11, 2010

Ecology Letters (2011) 14: 19–28 A recent increase in studies of β diversity has yielded a confusing array concepts, measures and methods. Here, we provide roadmap the most widely used ecologically relevant approaches for analysis through series mission statements. We distinguish two types diversity: directional turnover along gradient vs. non-directional variation. Different emphasize different properties ecological data. Such include degree emphasis on presence/absence relative abundance information inclusion exclusion joint absences. Judicious use multiple concert can uncover underlying nature patterns given dataset. case study Indonesian coral assemblages shows utility multi-faceted approach. advocate careful consideration questions, matched by appropriate analyses. The rigorous application null models will also help to reveal potential processes driving observed diversity.

Language: Английский

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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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Quantifying community assembly processes and identifying features that impose them

The ISME Journal, Journal Year: 2013, Volume and Issue: 7(11), P. 2069 - 2079

Published: June 6, 2013

Language: Английский

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Stochastic and deterministic assembly processes in subsurface microbial communities

The ISME Journal, Journal Year: 2012, Volume and Issue: 6(9), P. 1653 - 1664

Published: March 29, 2012

Language: Английский

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Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

Annual Review of Ecology Evolution and Systematics, Journal Year: 2015, Volume and Issue: 46(1), P. 1 - 23

Published: Aug. 5, 2015

The order and timing of species immigration during community assembly can affect abundances at multiple spatial scales. Known as priority effects, these effects cause historical contingency in the structure function communities, resulting alternative stable states, transient or compositional cycles. mechanisms fall into two categories, niche preemption modification, conditions for by be organized groups, those regarding regional pool properties local population dynamics. Specifically, requirements must satisfied to occur: contains that together dynamics are rapid enough early-arriving preempt modify niches before other arrive. Organizing current knowledge this way reveals an outstanding key question: How pools yield generated maintained?

Language: Английский

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Disentangling the importance of ecological niches from stochastic processes across scales

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2011, Volume and Issue: 366(1576), P. 2351 - 2363

Published: July 18, 2011

Deterministic theories in community ecology suggest that local, niche-based processes, such as environmental filtering, biotic interactions and interspecific trade-offs largely determine patterns of species diversity composition. In contrast, more stochastic emphasize the importance chance colonization, random extinction ecological drift. The schisms between deterministic perspectives, which date back to earliest days ecology, continue fuel contemporary debates (e.g. niches versus neutrality). As illustrated by pioneering studies Robert H. MacArthur co-workers, resolution these requires consideration how local processes changes across scales. Here, we develop a framework for disentangling relative generating site-to-site variation composition (β-diversity) along gradients (disturbance, productivity interactions) among biogeographic regions differ size regional pool. We illustrate discern using null-model approaches explicitly account factors inherently create turnover. By embracing scales, can build synthetic understanding structure biodiversity face emerge from factors.

Language: Английский

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Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

Proceedings of the National Academy of Sciences, Journal Year: 2015, Volume and Issue: 112(11)

Published: March 2, 2015

Significance Across ecology, and particularly within microbial there is limited understanding of the mechanisms governing relative influences stochastic deterministic processes. Filling this knowledge gap a major challenge that requires development novel conceptual paradigms, experiments, ecological models. Here we ( i ) present model couples stochastic/deterministic balance to primary secondary succession, thereby integrating previously isolated domains; ii evaluate over 105 years ecosystem development, revealing systematic shift in type strength selection; iii couple empirical data with new simulation elucidate underlying characterize their scale dependency. The insights framework provided here represent nexus for cross-system integration.

Language: Английский

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Rethinking Community Assembly through the Lens of Coexistence Theory

Annual Review of Ecology Evolution and Systematics, Journal Year: 2012, Volume and Issue: 43(1), P. 227 - 248

Published: Aug. 30, 2012

Although research on the role of competitive interactions during community assembly began decades ago, a recent revival interest has led to new discoveries and opportunities. Using contemporary coexistence theory that emphasizes stabilizing niche differences relative fitness differences, we evaluate three empirical approaches for studying assembly. We show experimental manipulations abiotic or biotic environment, assessments trait-phylogeny-environment relationships, investigations frequency-dependent population growth all suggest strong influences outcome plant Nonetheless, due limitations these applied in isolation, still have poor understanding which axes traits determine competition structure. Combining current represents our best chance achieving this goal, is fundamental conceptual ecology management communities under global change.

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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