Decoupling function and taxonomy in the global ocean microbiome

Abstract

Microbial metabolism powers biogeochemical cycling in Earth's ecosystems. The taxonomic composition of microbial communities varies substantially between environments, but the ecological causes of this variation remain largely unknown. We analyzed taxonomic and functional community profiles to determine the factors that shape marine bacterial and archaeal communities across the global ocean. By classifying >30,000 marine microorganisms into metabolic functional groups, we were able to disentangle functional from taxonomic community variation. We find that environmental conditions strongly influence the distribution of functional groups in marine microbial communities by shaping metabolic niches, but only weakly influence taxonomic composition within individual functional groups. Hence, functional structure and composition within functional groups constitute complementary and roughly independent "axes of variation" shaped by markedly different processes.

Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

“…In addition, it is challenging to measure multiple functional traits of thousands of species. Although omics data could allow identifying traits at the community level (Louca et al, 2016), more research is still needed to assign functional traits to sequences, especially for eukaryotic plankton. Despite these methodological issues, traitbased approach of marine communities opens new opportunities for a better understanding of ecosystem functioning and for the development of ecological indicators (Beauchard et al, 2017).…”

“…Complementary to a "bulk" screening of marine biodiversity, single-cell genomics approaches allow matching of phenotype and genotype, and have been used to investigate the phylogenetic affinities of microbial dark matter (i.e., currently unculturable microbial organisms; Rinke et al, 2013;Hug et al, 2016) and to uncover niche partitioning within globally distributed lineages of marine microbes (Kashtan et al, 2014). In combination, bulk and targeted approaches could unravel the taxonomic composition of planktonic organisms, as well as aspects of their ecological function (Thrash et al, 2014;Louca et al, 2016) and genome evolution to new environments (Mock et al, 2017).…”

On the role, ecology, phylogeny, and structure of dual-family immunophilins

“…None of the DFI organisms were found in this particular niche. A more recent and comprehensive study of >30,000 marine microorganisms from global ocean waters allowed a clearer decoupling of function and taxonomy (Louca et al 2016) and revealed that the environmental conditions, not taxonomy, dictate the metabolic profile of the organisms, thus defining a common Bmetabolic niche.Î nterestingly, the marine microbial population in this study included two CFBP phyla (Bacteroidetes, Spirochetes) and shared several metabolic functions (Louca et al 2016). This is again consistent with our hypothesis that environmentrelated metabolic needs, rather than phylogeny per se, resulted in the creation and evolution of the DFI sequences, and therefore, the DFI organisms define a new OTU.…”

“…Acknowledgements I am deeply indebted to two research groups for generously sharing their raw datasets: Professor Lynne Regan (Yale University, New Haven, CT) and her associate, Dr. Jieming Chen (currently in the Institute for Computational Health Sciences, University of California, San Francisco), for sharing the TPR sequence collection used in their analysis (Sawyer et al 2013), and Dr. Stilianos Louca (University of British Columbia, Canada) for sharing the list of the organisms from their OTU studies (Louca et al 2016). I thank Professor Andreas Teske (Marine Sciences, University of North Carolina, Chapel Hill, NC) for helpful discussions on the phylogeny and ecology of DFI organisms.…”

Environmental Predictors of Indole Acetic Acid Producing Rhizobacteria at Fly Ash Dumps: Nature-Based Solution for Sustainable Restoration

“…The microbes produce different levels of IAA and form different functional types or functional guilds (Wilson, 1999). Microenvironmental conditions rather than the taxonomic composition is responsible for the variation in the level of each functional trait exhibited by microbial communities (Petchey and Gaston, 2002;Loucas et al, 2016).…”