Abstract
Lateral bays of the lower Columbia River estuary are areas of enhanced water retention that influence net ecosystem metabolism through activities of their diverse microbial communities. Metagenomic characterization of sediment microbiota from three disparate sites in two brackish lateral bays (Baker and Youngs) produced ∼100 Gbp of DNA sequence data analyzed subsequently for predicted SSU rRNA and peptide-coding genes. The metagenomes were dominated by Bacteria. A large component of Eukaryota was present in Youngs Bay samples, i.e., the inner bay sediment was enriched with the invasive New Zealand mudsnail, Potamopyrgus antipodarum, known for high ammonia production. The metagenome was also highly enriched with an archaeal ammonia oxidizer closely related to Nitrosoarchaeum limnia. Combined analysis of sequences and continuous, high-resolution time series of biogeochemical data from fixed and mobile platforms revealed the importance of large-scale reciprocal particle exchanges between the mainstem estuarine water column and lateral bay sediments. Deposition of marine diatom particles in sediments near Youngs Bay mouth was associated with a dramatic enrichment of Bacteroidetes (58% of total Bacteria) and corresponding genes involved in phytoplankton polysaccharide degradation. The Baker Bay sediment metagenome contained abundant Archaea, including diverse methanogens, as well as functional genes for methylotrophy and taxonomic markers for syntrophic bacteria, suggesting that active methane cycling occurs at this location. Our previous work showed enrichments of similar anaerobic taxa in particulate matter of the mainstem estuarine water column. In total, our results identify the lateral bays as both sources and sinks of biogenic particles significantly impacting microbial community composition and biogeochemical activities in the estuary.
Highlights
Coastal zones worldwide receive significant nutrient inputs from land through rivers
Standard curves were generated by serial dilutions of linearized plasmids from sediment samples collected on the Washington bank of the Columbia River estuary (105–101 template copies)
Sampling Site Characteristics Sediment samples were collected from three locations within two lateral bays of the tidally dominated lower Columbia River estuary (Figure 1)
Summary
Coastal zones worldwide receive significant nutrient inputs from land through rivers. Organic matter inputs to estuaries are provided by terrigenous sources (runoff from watersheds transported by rivers), submerged aquatic vegetation of fresh/salt water marshes, and planktonic organisms developing in the river-toocean continuum (Crump et al, 2012). These inputs consist of labile dissolved and more recalcitrant particulate organic matter (DOM and POM, respectively; Simon et al, 2002; Jiao et al, 2010). Multiple studies have indicated that particle-associated microorganisms are distinct in characteristics related to growth and activities from those in freeliving fractions (DeLong et al, 1993; Crump et al, 1999; Simon et al, 2002, 2014; Smith et al, 2013; Satinsky et al, 2014)
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