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A strong link between marine microbial community composition and function challenges the idea of functional redundancy

Abstract

Marine microbes have tremendous diversity, but a fundamental question remains unanswered: why are there so many microbial species in the sea? The idea of functional redundancy for microbial communities has long been assumed, so that the high level of richness is often explained by the presence of different taxa that are able to conduct the exact same set of metabolic processes and that can readily replace each other. Here, we refute the hypothesis of functional redundancy for marine microbial communities by showing that a shift in the community composition altered the overall functional attributes of communities across different temporal and spatial scales. Our metagenomic monitoring of a coastal northwestern Mediterranean site also revealed that diverse microbial communities harbor a high diversity of potential proteins. Working with all information given by the metagenomes (all reads) rather than relying only on known genes (annotated orthologous genes) was essential for revealing the similarity between taxonomic and functional community compositions. Our finding does not exclude the possibility for a partial redundancy where organisms that share some specific function can coexist when they differ in other ecological requirements. It demonstrates, however, that marine microbial diversity reflects a tremendous diversity of microbial metabolism and highlights the genetic potential yet to be discovered in an ocean of microbes.

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Acknowledgements

Raw sequences were archived in the EBI repository under accession number PRJEB26919. The work of PEG was supported by the Agence Nationale de la Recherche (ANR) through the projects EUREKA (ANR-14-CE02-0004-01). We thank the captain and crew of the Nereis II, Eric Maria, and Louise Oriol for assisting with the collection and analysis of samples over the time series. We extend our acknowledgments to all the researchers that were involved in working with the time series over the years.

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Conflict of interest

The authors declare that they have no conflict of interest.

Correspondence to Pierre E. Galand.

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Supplementary Table S1, Table S2, Table S3 and Table S4

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