Original Research ARTICLE

Front. Microbiol., 30 May 2013 | doi: 10.3389/fmicb.2013.00120

Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem

Maria W. Smith1, Lisa Zeigler Allen2, Andrew E. Allen2, Lydie Herfort1 and Holly M. Simon1,3*
  • 1Center for Coastal Margin Observation and Prediction, Oregon Health and Science University, Beaverton, OR, USA
  • 2Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, USA
  • 3Division of Environmental and Biomolecular Systems, Department of Science and Engineering, Oregon Health and Science University, Beaverton, OR, USA

The Columbia River (CR) is a powerful economic and environmental driver in the US Pacific Northwest. Microbial communities in the water column were analyzed from four diverse habitats: (1) an estuarine turbidity maximum (ETM), (2) a chlorophyll maximum of the river plume, (3) an upwelling-associated hypoxic zone, and (4) the deep ocean bottom. Three size fractions, 0.1–0.8, 0.8–3, and 3–200 μm were collected for each habitat in August 2007, and used for DNA isolation and 454 sequencing, resulting in 12 metagenomes of >5 million reads (>1.6 Gbp). To characterize the dominant microorganisms and metabolisms contributing to coastal biogeochemistry, we used predicted peptide and rRNA data. The 3- and 0.8-μm metagenomes, representing particulate fractions, were taxonomically diverse across habitats. The 3-μm size fractions contained a high abundance of eukaryota with diatoms dominating the hypoxic water and plume, while cryptophytes were more abundant in the ETM. The 0.1-μm metagenomes represented mainly free-living bacteria and archaea. The most abundant archaeal hits were observed in the deep ocean and hypoxic water (19% of prokaryotic peptides in the 0.1-μm metagenomes), and were homologous to Nitrosopumilus maritimus (ammonia-oxidizing Thaumarchaeota). Bacteria dominated metagenomes of all samples. In the euphotic zone (estuary, plume and hypoxic ocean), the most abundant bacterial taxa (≥40% of prokaryotic peptides) represented aerobic photoheterotrophs. In contrast, the low-oxygen, deep water metagenome was enriched with sequences for strict and facultative anaerobes. Interestingly, many of the same anaerobic bacterial families were enriched in the 3-μm size fraction of the ETM (2–10X more abundant relative to the 0.1-μm metagenome), indicating possible formation of anoxic microniches within particles. Results from this study provide a metagenome perspective on ecosystem-scale metabolism in an upwelling-influenced river-dominated coastal margin.

Keywords: metagenome analysis, Columbia River coastal margin, environmental water, microbial communities, particle-attached and free-living microbes

Citation: Smith MW, Zeigler Allen L, Allen AE, Herfort L and Simon HM (2013) Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Front. Microbiol. 4:120. doi: 10.3389/fmicb.2013.00120

Received: 16 January 2013; Accepted: 29 April 2013;
Published online: 30 May 2013.

Edited by:

Hongyue Dang, Xiamen University, China

Reviewed by:

Zhe-Xue Quan, Fudan University, China
Shawn R. Campagna, University of Tennessee, USA;
Craig E. Nelson, University of Hawaii at Manoa, USA

Copyright © 2013 Smith, Zeigler Allen, Allen, Herfort and Simon. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.

*Correspondence: Holly M. Simon, Division of Environmental and Biomolecular Systems, Department of Science and Engineering, School of Medicine, Oregon Health and Science University, 20000 NW Walker Road, Beaverton, OR 97006-8921, USA. e-mail: simonh@ebs.ogi.edu

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