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Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment.

Graves CJ, Makrides EJ, Schmidt VT, Giblin AE, Cardon ZG, Rand DM - Appl. Environ. Microbiol. (2016)

Bottom Line: Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone.Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities.In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance.

View Article: PubMed Central - PubMed

Affiliation: Brown University, Department of Ecology and Evolutionary Biology, Providence, Rhode Island, USA.

No MeSH data available.


Related in: MedlinePlus

Plots showing the frequency of annotations corresponding to enzymes associated with various steps in the denitrification pathway. Each panel represents the abundance of annotations corresponding to a given enzyme across all 5 sites in both the enriched and reference creeks. Multiple points at each site represent replicate samples.
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Figure 3: Plots showing the frequency of annotations corresponding to enzymes associated with various steps in the denitrification pathway. Each panel represents the abundance of annotations corresponding to a given enzyme across all 5 sites in both the enriched and reference creeks. Multiple points at each site represent replicate samples.

Mentions: We hypothesized that increased concentrations of nitrate in the enriched creek would lead to increases in denitrifying bacteria and, correspondingly, to increases in the frequency of annotations linked to denitrification. Annotations that were labeled as nitrate reductase, nitrite reductase, nitrous oxide reductase, and nitric oxide reductase were strongly increased in sites from the enriched creek compared to the reference creek (see Fig. S3 in the supplemental material). Since these broadly defined groups likely included some annotations unrelated to denitrification, we also focused on subsets of annotations that corresponded to more specific steps in the denitrification pathway. Among them, annotations associated with respiratory nitrate reductase, copper-containing nitrite reductase, cytochrome cd1 nitrite reductase, nitric oxide reductase, and nitrous oxide reductase showed significantly higher frequencies in the enriched creek than in the reference creek (Table 1; Fig. 3). Importantly, both nutrient concentration (% C) and creek were significant factors in most of our analyses, demonstrating that differences in annotation abundances between the creeks are at least partly related to nutrient enrichment from the sewage effluent (Table 1).


Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment.

Graves CJ, Makrides EJ, Schmidt VT, Giblin AE, Cardon ZG, Rand DM - Appl. Environ. Microbiol. (2016)

Plots showing the frequency of annotations corresponding to enzymes associated with various steps in the denitrification pathway. Each panel represents the abundance of annotations corresponding to a given enzyme across all 5 sites in both the enriched and reference creeks. Multiple points at each site represent replicate samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836423&req=5

Figure 3: Plots showing the frequency of annotations corresponding to enzymes associated with various steps in the denitrification pathway. Each panel represents the abundance of annotations corresponding to a given enzyme across all 5 sites in both the enriched and reference creeks. Multiple points at each site represent replicate samples.
Mentions: We hypothesized that increased concentrations of nitrate in the enriched creek would lead to increases in denitrifying bacteria and, correspondingly, to increases in the frequency of annotations linked to denitrification. Annotations that were labeled as nitrate reductase, nitrite reductase, nitrous oxide reductase, and nitric oxide reductase were strongly increased in sites from the enriched creek compared to the reference creek (see Fig. S3 in the supplemental material). Since these broadly defined groups likely included some annotations unrelated to denitrification, we also focused on subsets of annotations that corresponded to more specific steps in the denitrification pathway. Among them, annotations associated with respiratory nitrate reductase, copper-containing nitrite reductase, cytochrome cd1 nitrite reductase, nitric oxide reductase, and nitrous oxide reductase showed significantly higher frequencies in the enriched creek than in the reference creek (Table 1; Fig. 3). Importantly, both nutrient concentration (% C) and creek were significant factors in most of our analyses, demonstrating that differences in annotation abundances between the creeks are at least partly related to nutrient enrichment from the sewage effluent (Table 1).

Bottom Line: Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone.Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities.In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance.

View Article: PubMed Central - PubMed

Affiliation: Brown University, Department of Ecology and Evolutionary Biology, Providence, Rhode Island, USA.

No MeSH data available.


Related in: MedlinePlus