Abstract
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function.This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
Highlights
Microbial communities underpin all major biological and biogeochemical processes [1]
Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose as sole carbon source
Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed
Summary
Microbial communities underpin all major biological and biogeochemical processes [1]. New strategies for investigation are required that are process-focused [11] Such approaches will provide knowledge on the complex interconnections between community members, their combined effects, including feedbacks that shape the evolution of community members [12,13,14,15]. Recent advances draw upon new strategies for linking patterns of sequence diversity in metagenomic datasets to population genetic processes [16,17,18,19]. Knowledge of such processes provides a link between variation and the likelihood that particular traits fix. We show—in a proof-of-principle experiment—that this can be achieved via an experimental strategy that combines theory governing the behaviour of selfish genetic elements [20,21,22,23] (SGEs) and expected effects on horizontal gene transfer (HGT), with approaches from experimental evolution [24,25], comparative metagenomics [26] and functional assay
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