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Abstract
<p class="first" id="P3">A major unresolved question in microbiome research is whether
the complex taxonomic
architectures observed in surveys of natural communities can be explained and predicted
by fundamental, quantitative principles. Bridging theory and experiment is hampered
by the multiplicity of ecological processes that simultaneously affect community assembly
in natural ecosystems. We addressed this challenge by monitoring the assembly of hundreds
of soil- and plant-derived microbiomes in well-controlled minimal synthetic media.
Both the community-level function and the coarse-grained taxonomy of the resulting
communities are highly predictable and governed by nutrient availability, despite
substantial species variability. By generalizing classical ecological models to include
widespread nonspecific cross-feeding, we show that these features are all emergent
properties of the assembly of large microbial communities, explaining their ubiquity
in natural microbiomes.
</p>
The remarkable differences that have been detected by metagenomics in the genomes of strains of the same bacterial species are difficult to reconcile with the widely accepted paradigm that periodic selection within bacterial populations will regularly purge genomic diversity by clonal replacement. We have found that many of the genes that differ between strains affect regions that are potential phage recognition targets. We therefore propose the constant-diversity dynamics model, in which the diversity of prokaryotic populations is preserved by phage predation. We provide supporting evidence for this model from metagenomics, mathematical analysis and computer simulations. Periodic selection and phage predation dynamics are not mutually exclusive; we compare their predictions to shed light on the ecological circumstances under which each type of dynamics could predominate.
The tremendous diversity of species in ecological communities has motivated a century of research into the mechanisms that maintain biodiversity. However, much of this work examines the coexistence of just pairs of competitors. This approach ignores those mechanisms of coexistence that emerge only in diverse
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