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
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
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
_version_	1718391277158924288

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

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