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Contrasting Genomic Properties of Free-living and Particle-attached Microbial Assemblages within a Coastal Ecosystem

TitleContrasting Genomic Properties of Free-living and Particle-attached Microbial Assemblages within a Coastal Ecosystem
Publication TypeJournal Article
Year of Publication2013
AuthorsSmith MW, Zeigler_Allen L, Allen A, Herfort L, Simon HM
Journal TitleFrontiers in Microbiology
Keywordscoastal margins, Columbia River, environmental, metagenome, microbes, microorganism detection

The Columbia River (CR) is a powerful economic and environmental driver in the US Pacific  Northwest. To characterize the dominant microorganisms and metabolisms contributing to  coastal biogeochemistry, 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 or DNA isolation and 454 sequencing, resulting in 12 metagenomes of >5 million reads (>1.6 Gbp). 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. Metabolic profiling supported this conclusion. Results from this study provide a metagenome perspective on ecosystem-scale metabolism in an upwelling-influenced river-dominated coastal margin.