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Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River.

Smith MW, Davis RE, Youngblut ND, Kärnä T, Herfort L, Whitaker RJ, Metcalf WW, Tebo BM, Baptista AM, Simon HM - Front Microbiol (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA.

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.

No MeSH data available.


Contour map of the lower Columbia River estuary. The shore locations of three sediment sampling sites in Baker Bay and Youngs Bay are shown as black triangles, BB, Baker Bay; YB-M, Youngs Bay mouth, and YB-B, Youngs Bay back. The white triangles show locations of the SATURN endurance stations providing continuous flow-through biogeochemical measurements (including salinity, chl a concentrations, etc.).
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Figure 1: Contour map of the lower Columbia River estuary. The shore locations of three sediment sampling sites in Baker Bay and Youngs Bay are shown as black triangles, BB, Baker Bay; YB-M, Youngs Bay mouth, and YB-B, Youngs Bay back. The white triangles show locations of the SATURN endurance stations providing continuous flow-through biogeochemical measurements (including salinity, chl a concentrations, etc.).

Mentions: Our sampling sites were selected to reflect differences in the origin and character of the sediments, as well as in the degree of tidal forcing and salt water intrusion that are observed in these regions. Baker Bay (BB) is a shallow, intertidal inlet located between river miles 3 and 9, with insignificant local tributary inflow (Figure 1). It is connected to the North Channel of the main estuary by three conduits, each with dramatic differences in the phase and magnitude of water exchange (Simenstad et al., 1984). The shallow bay interior (including our sampling site) experiences maximum salinities well below ocean values (Simenstad et al., 1984). Youngs Bay is another large, shallow, oligohaline lateral bay, with the mouth located between river miles 11 and 17 at the confluence of the Youngs and Columbia Rivers (Figure 1). The Youngs, and Lewis and Clark Rivers provide significant annual local tributary runoff, two-thirds of which occurs in winter, with less than 5% of the total flow occurring in July–September (Simenstad et al., 1984). Salinities at Youngs Bay mouth (at the YB-M sampling location) range from fresh under high river flow, to more than 20 PSU under low-flow summer conditions (Simenstad et al., 1984). Historically, drainage of 1000s of acres of tidal marsh and swamp around Youngs Bay led to enhanced flushing of organic material, silt, and nutrients by the rivers into the bay (Lev et al., 2008). Compared to BB, Youngs Bay is more organic matter rich, supporting a higher abundance of prey for invertebrates, macroinvertebrates, and fish (Bottom et al., 2005).


Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River.

Smith MW, Davis RE, Youngblut ND, Kärnä T, Herfort L, Whitaker RJ, Metcalf WW, Tebo BM, Baptista AM, Simon HM - Front Microbiol (2015)

Contour map of the lower Columbia River estuary. The shore locations of three sediment sampling sites in Baker Bay and Youngs Bay are shown as black triangles, BB, Baker Bay; YB-M, Youngs Bay mouth, and YB-B, Youngs Bay back. The white triangles show locations of the SATURN endurance stations providing continuous flow-through biogeochemical measurements (including salinity, chl a concentrations, etc.).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4589670&req=5

Figure 1: Contour map of the lower Columbia River estuary. The shore locations of three sediment sampling sites in Baker Bay and Youngs Bay are shown as black triangles, BB, Baker Bay; YB-M, Youngs Bay mouth, and YB-B, Youngs Bay back. The white triangles show locations of the SATURN endurance stations providing continuous flow-through biogeochemical measurements (including salinity, chl a concentrations, etc.).
Mentions: Our sampling sites were selected to reflect differences in the origin and character of the sediments, as well as in the degree of tidal forcing and salt water intrusion that are observed in these regions. Baker Bay (BB) is a shallow, intertidal inlet located between river miles 3 and 9, with insignificant local tributary inflow (Figure 1). It is connected to the North Channel of the main estuary by three conduits, each with dramatic differences in the phase and magnitude of water exchange (Simenstad et al., 1984). The shallow bay interior (including our sampling site) experiences maximum salinities well below ocean values (Simenstad et al., 1984). Youngs Bay is another large, shallow, oligohaline lateral bay, with the mouth located between river miles 11 and 17 at the confluence of the Youngs and Columbia Rivers (Figure 1). The Youngs, and Lewis and Clark Rivers provide significant annual local tributary runoff, two-thirds of which occurs in winter, with less than 5% of the total flow occurring in July–September (Simenstad et al., 1984). Salinities at Youngs Bay mouth (at the YB-M sampling location) range from fresh under high river flow, to more than 20 PSU under low-flow summer conditions (Simenstad et al., 1984). Historically, drainage of 1000s of acres of tidal marsh and swamp around Youngs Bay led to enhanced flushing of organic material, silt, and nutrients by the rivers into the bay (Lev et al., 2008). Compared to BB, Youngs Bay is more organic matter rich, supporting a higher abundance of prey for invertebrates, macroinvertebrates, and fish (Bottom et al., 2005).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA.

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.

No MeSH data available.