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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.


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Principal-component analysis of genus-level taxonomic annotations (A) and subsystems-level functional annotations (B) between each site and creek.
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Figure 2: Principal-component analysis of genus-level taxonomic annotations (A) and subsystems-level functional annotations (B) between each site and creek.

Mentions: Taxonomic annotations showed great similarity in composition between the two creeks, with a high degree of concordance in the frequencies of the most abundant genera (see Fig. S2A in the supplemental material). In both creeks, Geobacter, Bacteroides, Pseudomonas, Desulfovibrio, and Burkholderia were among the most abundant genera. Furthermore, PCA plots based on class-, order-, and genus-level classifications all revealed similar patterns, with the sample site along the creek separating samples along principal component axis 1 (PC1) but with no clear separation by creek type (Fig. 2A). Both creeks also showed similarities based on PCA analysis of KEGG functional subsystems (Fig. 2B), with identical rankings of the top 10 most abundant subsystems (see Fig. S2B in the supplemental material). In contrast, a PCA plot of functional subsystems data did indicate some separation along PC1 by creek, particularly at site 13, which is the closest to the outfall (Fig. 2B).


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)

Principal-component analysis of genus-level taxonomic annotations (A) and subsystems-level functional annotations (B) between each site and creek.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Principal-component analysis of genus-level taxonomic annotations (A) and subsystems-level functional annotations (B) between each site and creek.
Mentions: Taxonomic annotations showed great similarity in composition between the two creeks, with a high degree of concordance in the frequencies of the most abundant genera (see Fig. S2A in the supplemental material). In both creeks, Geobacter, Bacteroides, Pseudomonas, Desulfovibrio, and Burkholderia were among the most abundant genera. Furthermore, PCA plots based on class-, order-, and genus-level classifications all revealed similar patterns, with the sample site along the creek separating samples along principal component axis 1 (PC1) but with no clear separation by creek type (Fig. 2A). Both creeks also showed similarities based on PCA analysis of KEGG functional subsystems (Fig. 2B), with identical rankings of the top 10 most abundant subsystems (see Fig. S2B in the supplemental material). In contrast, a PCA plot of functional subsystems data did indicate some separation along PC1 by creek, particularly at site 13, which is the closest to the outfall (Fig. 2B).

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