Abstract
Linking microbial community structure to ecological processes requires understanding of the functional roles among individual populations and the factors that influence their distributions. These structure-function relationships are particularly difficult to disentangle in estuaries, due to highly variable physico-chemical conditions. Yet, examining microbe-mediated turnover of resources in these "bioreactor" ecosystems is critical for understanding estuarine ecology. In this study, a combined metagenomics and metaproteomics approach was used to show that the unequal distribution of microbial populations across the Yaquina Bay estuary led to a habitat-specific taxonomic and functional structure and a clear spatial distribution in microbe-mediated capacities for cycling of carbon and nitrogen. For example, size-fractionation revealed that communities inhabiting suspended particulate material encoded more diverse types of metabolisms (e.g., fermentation and denitrification) than those with a planktonic lifestyle, suggesting that the metabolic reactions can differ between size fractions of the same parcel of an estuarine water column. Similarly, communities inhabiting oligotrophic conditions in the lower estuary were enriched in genes involved in central carbon metabolism (e.g., TCA cycle), while communities in the upper estuary were enriched in genes typical of copiotrophic populations (e.g., cell growth, cell division). Integrating gene and protein data revealed that abundant populations of Flavobacteriales and Rhodobacterales encoded similar genomic functions, yet differed significantly in protein expression, dedicating a large proportion of their respective proteomes to rapid growth and division versus metabolic versatility and resource acquisition. This suggested potentially distinct life-strategies between these two co-occurring lineages and was concomitant with differing patterns of positive evolutionary selection on their encoded genes. Microbial communities and their functions across Yaquina Bay appear to be structured by population-level habitat preferences, resulting in spatially distinct elemental cycling, while within each community, forces such as competitive exclusion and evolutionary selection influence species life-strategies and may help maintain microbial diversity.
Original language | English |
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Article number | 1282 |
Journal | Frontiers in Microbiology |
Volume | 9 |
Issue number | JUN |
DOIs | |
State | Published - Jun 14 2018 |
Funding
We thank the Oregon State University Center for Genomic Research and Biocomputing and for their support in data collection and analysis. Hatfield Marine Science Center staffand facilities were instrumental in sample collection and processing. We also thank the reviewers of the manuscript, whose comments and suggestions significantly improved the presentation of this research. This work was funded by the Gordon and Betty Moore Foundation Marine Microbiology Initiative (Grant Id: GBMF3302). Part of this work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Oak Ridge National Laboratory resources, including the Oak Ridge Leadership Computing Facility, were used in the research and are supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. BC was supported by National Science Foundation grant OCE-0424602.
Funders | Funder number |
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Oregon State University Center for Genomic Research and Biocomputing | |
National Science Foundation | OCE-0424602 |
U.S. Department of Energy | |
Directorate for Geosciences | 0424602 |
Gordon and Betty Moore Foundation | GBMF3302 |
Office of Science | DE-AC05-00OR22725 |
Lawrence Livermore National Laboratory | DE-AC52-07NA27344 |
Oak Ridge National Laboratory | |
National Science Foundation |
Keywords
- Biogeochemical cycling
- Estuary
- Free-living
- Metagenomics
- Metaproteomics
- Particle-attached
- Yaquina Bay