Bacterial carbon processing by generalist species in the coastal ocean

Abstract

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.

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Figure 1: Apparent taxonomic distribution of 16S rRNA-like gene sequences recovered from metagenomes.
Figure 2: Estimated genome equivalents in experimental metagenomic data sets based on homologue counts for single-copy genes.

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Data deposits

Metagenomic sequences are deposited in the Genome Projects Database (http://www.ncbi.nlm.nih.gov/Genomes) under accession number 19145. 16S rRNA gene sequences are deposited in GenBank under accession numbers DQ880941DQ881441 and EU167151EU167496.

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Acknowledgements

We thank W. Whitman, C. Lasher, B. Rodriguez-Brito, C. Reisch, J. Henriksen, E. Biers and W. Sheldon for advice or assistance with experimental or bioinformatic analyses; C. English for graphics; and J. T. Hollibaugh for discussions. This project was funded by grants from the National Science Foundation and the Gordon and Betty Moore Foundation.

Author Contributions X.M. and M.A.M. planned the project; X.M. conducted the experimental work; S.S. and R.A.E. conducted the bioinformatic and statistical analyses; X.M., R.E.H. and M.A.M. interpreted results; M.A.M. directed the project and wrote the paper.

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Correspondence to Mary Ann Moran.

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This file contains Supplementary Tables S1-S3 and Supplementary Figures S1-S13 with Legends. (PDF 1698 kb)

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Mou, X., Sun, S., Edwards, R. et al. Bacterial carbon processing by generalist species in the coastal ocean. Nature 451, 708–711 (2008). https://doi.org/10.1038/nature06513

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