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.

Highlights

  • 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 challenge for contemporary microbial ecology is to understand and identify the ecological origins of these patterns. This problem is especially difficult because it involves what in the ecology literature has been called the “problem of pattern and scale”[4]: explaining ecological patterns requires connecting processes that occur at very different scales of spatial, temporal, and taxonomical organization

  • The Microbial Consumer Resource Model (MiCRM) provides a systematic way of exploring the effect of stochastic colonization, resource competition, and metabolic crossfeeding on large-scale observables

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Summary

Introduction

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. 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. 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. The MiCRM incorporates stochastic dispersal by seeding new environments through random sampling of a larger regional species pool (Fig. 1b)

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