Abstract
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.
Highlights
Our study site encompasses an upwelling-influenced riverdominated coastal margin of the Pacific Northwest region of the United States
Results from the alignment of 16S ribosomal RNA (rRNA) hits to the N. maritimus 16S rRNA gene were consistent with the amoA protein recruitment data (Figure 3B), indicating that close relatives of N. maritimus from both the deep ocean and hypoxic water habitats are capable of ammonia oxidation
When normalized by the total number of corresponding Marine Group I (MGI) 16S rRNA hits, the resultant OTU values indicated that the diversity of N. maritimus-like organisms was ∼50% higher in the deep ocean compared to the hypoxic water habitat
Summary
The CR estuary has been characterized as a “bioreactor” for microbially driven transformations of organic carbon and nitrogen from both the river and the coastal ocean. These activities are enhanced by development of large and welldefined estuarine turbidity maxima (ETM) (Small et al, 1990; Baross et al, 1994; Crump et al, 1998, 1999; Small and Prahl, 2004). Bacterial carbon production measurements indicated much higher activities for particle-attached, compared to free-living, microbiota (both freshwater and estuarine samples) (Crump et al, 1998). Smaller (3–10 μm in size), slowsettling particles were the most bacterially active, and are thought to be retained in the estuary through processes in the water column leading to larger, rapidly-settling macro-aggregates (Crump and Baross, 2000b)
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