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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.


Related in: MedlinePlus

Inferred phylogenetic tree showing archaeal 16S rRNA contigs from the lateral bay sediment metagenomes (UPGMA, bootstrap analysis with 100 replicates). Only contigs with at least 4X coverage that were >1 kb in length are shown. Gray circles (BB), gray diamonds (YB-M), and open diamonds (YB-B) indicate contigs from Baker Bay, Youngs Bay mouth, and Youngs Bay back, respectively. Phylogenetic clades were anchored using both rRNA sequences from fully sequenced archaeal genomes (shown with organism names) and selected environmental rRNA clones (most closely related to our sequences and shown with GenBank accession numbers). Numbers represent bootstrap values corresponding to each branch.
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Figure 10: Inferred phylogenetic tree showing archaeal 16S rRNA contigs from the lateral bay sediment metagenomes (UPGMA, bootstrap analysis with 100 replicates). Only contigs with at least 4X coverage that were >1 kb in length are shown. Gray circles (BB), gray diamonds (YB-M), and open diamonds (YB-B) indicate contigs from Baker Bay, Youngs Bay mouth, and Youngs Bay back, respectively. Phylogenetic clades were anchored using both rRNA sequences from fully sequenced archaeal genomes (shown with organism names) and selected environmental rRNA clones (most closely related to our sequences and shown with GenBank accession numbers). Numbers represent bootstrap values corresponding to each branch.

Mentions: The highest abundance of Archaea, constituting ∼9% of all SSU rRNA and predicted peptides, was observed in the BB metagenome (Table 3). In YB-M and YB-B, respectively, 0.8 and 1.5% of the archaeal sequences were identified from SSU rRNA analysis, and 1–5.7% from predicted peptides (Table 3). Differences in results from these approaches likely reflect a number of issues including: (i) variation in copy numbers of rRNA genes, (ii) relative scarcity of annotated peptide references available for Archaea, and (iii) annotation of archaeal genes as bacterial due to sequence similarities (Lloyd et al., 2013). Some archaeal groups, such as Thaumarchaeota and Methanomicrobia, showed consistency between the two approaches (Figure 9). In contrast, Methanobacteria were observed mainly from predicted peptide data, and the “Miscellaneous Crenarchaeotal Group” (Kubo et al., 2012) was identified only in SSU rRNA data (Figure 9). To classify the predominant Archaea present in the sediment metagenomes, we analyzed the most abundant archaeal SSU rRNA sequences represented by long contigs (using selection criteria of ≥4X coverage and ≥1 Kb length; Figure 10). The highest number of contigs (6) meeting these criteria was observed in the BB metagenome, followed by YB-M (3) and YB-B (1).


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)

Inferred phylogenetic tree showing archaeal 16S rRNA contigs from the lateral bay sediment metagenomes (UPGMA, bootstrap analysis with 100 replicates). Only contigs with at least 4X coverage that were >1 kb in length are shown. Gray circles (BB), gray diamonds (YB-M), and open diamonds (YB-B) indicate contigs from Baker Bay, Youngs Bay mouth, and Youngs Bay back, respectively. Phylogenetic clades were anchored using both rRNA sequences from fully sequenced archaeal genomes (shown with organism names) and selected environmental rRNA clones (most closely related to our sequences and shown with GenBank accession numbers). Numbers represent bootstrap values corresponding to each branch.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 10: Inferred phylogenetic tree showing archaeal 16S rRNA contigs from the lateral bay sediment metagenomes (UPGMA, bootstrap analysis with 100 replicates). Only contigs with at least 4X coverage that were >1 kb in length are shown. Gray circles (BB), gray diamonds (YB-M), and open diamonds (YB-B) indicate contigs from Baker Bay, Youngs Bay mouth, and Youngs Bay back, respectively. Phylogenetic clades were anchored using both rRNA sequences from fully sequenced archaeal genomes (shown with organism names) and selected environmental rRNA clones (most closely related to our sequences and shown with GenBank accession numbers). Numbers represent bootstrap values corresponding to each branch.
Mentions: The highest abundance of Archaea, constituting ∼9% of all SSU rRNA and predicted peptides, was observed in the BB metagenome (Table 3). In YB-M and YB-B, respectively, 0.8 and 1.5% of the archaeal sequences were identified from SSU rRNA analysis, and 1–5.7% from predicted peptides (Table 3). Differences in results from these approaches likely reflect a number of issues including: (i) variation in copy numbers of rRNA genes, (ii) relative scarcity of annotated peptide references available for Archaea, and (iii) annotation of archaeal genes as bacterial due to sequence similarities (Lloyd et al., 2013). Some archaeal groups, such as Thaumarchaeota and Methanomicrobia, showed consistency between the two approaches (Figure 9). In contrast, Methanobacteria were observed mainly from predicted peptide data, and the “Miscellaneous Crenarchaeotal Group” (Kubo et al., 2012) was identified only in SSU rRNA data (Figure 9). To classify the predominant Archaea present in the sediment metagenomes, we analyzed the most abundant archaeal SSU rRNA sequences represented by long contigs (using selection criteria of ≥4X coverage and ≥1 Kb length; Figure 10). The highest number of contigs (6) meeting these criteria was observed in the BB metagenome, followed by YB-M (3) and YB-B (1).

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.


Related in: MedlinePlus