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 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. *

Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

“…We have previously shown that many of the properties of our experimental enrichment communities reflect the generic emergent behavior of consumer-resource models [14,17], and subsequent work extended this finding to complex natural communities [18]. We thus sought to ask whether our observations regarding the assembly of communities in pairs of resources are similarly reflecting a generic emergent property of consumer-resource models.…”

The Community Simulator: A Python package for microbial ecology

“…More recently, the convex optimization approach has made it possible to perform more than 100,000 independent simulations in a reinterpretation and extension of Robert May's classic work on diversity and stability [32,33]. We have also employed the package to reproduce large-scale patterns in microbial biodiversity from the Human Microbiome Project, Earth Microbiome Project, and similar surveys [34]. Finally, the random matrix approach implemented in this package is amenable to analytic calculation in the limit of large numbers of species and resources, using cavity methods from the physics of disordered systems [35,36].…”

Positive interactions are common among culturable bacteria

“…Quantifying the prevalence of positive interactions and determining the conditions in which they occur could significantly improve our ability to predict and control the ecology of microbial communities (23,24). Positive interactions are predicted to enhance a community's diversity and productivity but decrease its stability (6,25,26).…”