Bacterial carbon processing by generalist species in the coastal ocean

Metagenomics, or environmental genomics, has revolutionized our picture of microorganisms in the real world — as opposed to how they behave in laboratory cultivated 'clonal' cultures. A novel example of 'experimental metagenomics' is now reported, involving the creation of a 20-litre microcosm of sea water collected off Sapelo Island in the US state of Georgia. Manipulation of the system shows that this coastal microbial community is dominated by metabolic generalists capable of utilizing a wide variety of organic compounds, rather than by bacterial species that specialize in metabolizing a specific component of the dissolved organic carbon pool. This finding has important implications for identifying taxon–function relationships for carbon cycle-relevant processes and the construction of predictive models of ocean biogeochemistry. Experimental metagenomics is used to show that coastal communities are populated by taxa capable of metabolizing a wide variety of organic carbon compounds. It is concluded that metabolic generalists dominate coastal microbial communities, with important implications for identifying taxon–function relationships for carbon cycle-relevant processes and the construction of predictive models of ocean biogeochemistry. The assimilation and mineralization of dissolved organic carbon (DOC) by marine bacterioplankton is a major process in the ocean carbon cycle1. However, little information exists on the specific metabolic functions of participating bacteria and on whether individual taxa specialize on particular components of the marine DOC pool2. Here we use experimental metagenomics to show that coastal communities are populated by taxa capable of metabolizing a wide variety of organic carbon compounds. Genomic DNA captured from bacterial community subsets metabolizing a single model component of the DOC pool (either dimethylsulphoniopropionate or vanillate) showed substantial overlap in gene composition as well as a diversity of carbon-processing capabilities beyond the selected phenotypes. Our direct measure of niche breadth for bacterial functional assemblages indicates that, in accordance with ecological theory, heterogeneity in the composition and supply of organic carbon to coastal oceans may favour generalist bacteria. In the important interplay between microbial community structure and biogeochemical cycling, coastal heterotrophic communities may be controlled less by transient changes in the carbon reservoir that they process and more by factors such as trophic interactions and physical conditions.