A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns

Abstract Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping micr...

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Autores principales: Robert Marsland, Wenping Cui, Pankaj Mehta
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Publicado: Nature Portfolio 2020
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Acceso en línea:https://doaj.org/article/be866e48d82c43889fcb24c5e6c2947a
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spelling oai:doaj.org-article:be866e48d82c43889fcb24c5e6c2947a2021-12-02T14:28:22ZA minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns10.1038/s41598-020-60130-22045-2322https://doaj.org/article/be866e48d82c43889fcb24c5e6c2947a2020-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-60130-2https://doaj.org/toc/2045-2322Abstract Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promising approach is to use minimal models that can relate mechanistic assumptions at the microbe scale to community-level patterns. Here, we demonstrate the utility of this approach by showing that the Microbial Consumer Resource Model (MiCRM) – a minimal model for microbial communities with resource competition, metabolic crossfeeding and stochastic colonization – can qualitatively reproduce patterns found in survey data including compositional gradients, dissimilarity/overlap correlations, richness/harshness correlations, and nestedness of community composition. By using the MiCRM to generate synthetic data with different environmental and taxonomical structure, we show that large scale patterns in the EMP can be reproduced by considering the energetic cost of surviving in harsh environments and HMP patterns may reflect the importance of environmental filtering in shaping competition. We also show that recently discovered dissimilarity-overlap correlations in the HMP likely arise from communities that share similar environments rather than reflecting universal dynamics. We identify ecologically meaningful changes in parameters that alter or destroy each one of these patterns, suggesting new mechanistic hypotheses for further investigation. These findings highlight the promise of minimal models for microbial ecology.Robert MarslandWenping CuiPankaj MehtaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-17 (2020)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Robert Marsland
Wenping Cui
Pankaj Mehta
A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
description Abstract Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promising approach is to use minimal models that can relate mechanistic assumptions at the microbe scale to community-level patterns. Here, we demonstrate the utility of this approach by showing that the Microbial Consumer Resource Model (MiCRM) – a minimal model for microbial communities with resource competition, metabolic crossfeeding and stochastic colonization – can qualitatively reproduce patterns found in survey data including compositional gradients, dissimilarity/overlap correlations, richness/harshness correlations, and nestedness of community composition. By using the MiCRM to generate synthetic data with different environmental and taxonomical structure, we show that large scale patterns in the EMP can be reproduced by considering the energetic cost of surviving in harsh environments and HMP patterns may reflect the importance of environmental filtering in shaping competition. We also show that recently discovered dissimilarity-overlap correlations in the HMP likely arise from communities that share similar environments rather than reflecting universal dynamics. We identify ecologically meaningful changes in parameters that alter or destroy each one of these patterns, suggesting new mechanistic hypotheses for further investigation. These findings highlight the promise of minimal models for microbial ecology.
format article
author Robert Marsland
Wenping Cui
Pankaj Mehta
author_facet Robert Marsland
Wenping Cui
Pankaj Mehta
author_sort Robert Marsland
title A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
title_short A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
title_full A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
title_fullStr A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
title_full_unstemmed A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
title_sort minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
publisher Nature Portfolio
publishDate 2020
url https://doaj.org/article/be866e48d82c43889fcb24c5e6c2947a
work_keys_str_mv AT robertmarsland aminimalmodelformicrobialbiodiversitycanreproduceexperimentallyobservedecologicalpatterns
AT wenpingcui aminimalmodelformicrobialbiodiversitycanreproduceexperimentallyobservedecologicalpatterns
AT pankajmehta aminimalmodelformicrobialbiodiversitycanreproduceexperimentallyobservedecologicalpatterns
AT robertmarsland minimalmodelformicrobialbiodiversitycanreproduceexperimentallyobservedecologicalpatterns
AT wenpingcui minimalmodelformicrobialbiodiversitycanreproduceexperimentallyobservedecologicalpatterns
AT pankajmehta minimalmodelformicrobialbiodiversitycanreproduceexperimentallyobservedecologicalpatterns
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