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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

Bootstrapped neighbor-joining phylogeny of 158 nosZ sequence clusters from our original 240-reference NCBI-based database, representing 80 distinct bacterial and 3 archaeal genera. Clusters of >93% similarities were formed to reduce the total spread of the tree using UCLUST (47). Sequences in this tree had at least 1 hit from our creek sediment metagenomic data with an alignment bit score greater than 80. The number of hits from enriched and reference creeks to each cluster is shown by the length of the bar at the terminal node of each branch. Branches are colored by typical (gray) versus atypical (violet) genera according to categorization of atypical and typical genera by Sanford et al. in 2012 (17).
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Figure 4: Bootstrapped neighbor-joining phylogeny of 158 nosZ sequence clusters from our original 240-reference NCBI-based database, representing 80 distinct bacterial and 3 archaeal genera. Clusters of >93% similarities were formed to reduce the total spread of the tree using UCLUST (47). Sequences in this tree had at least 1 hit from our creek sediment metagenomic data with an alignment bit score greater than 80. The number of hits from enriched and reference creeks to each cluster is shown by the length of the bar at the terminal node of each branch. Branches are colored by typical (gray) versus atypical (violet) genera according to categorization of atypical and typical genera by Sanford et al. in 2012 (17).

Mentions: Our metagenomic analyses revealed dramatic differences in the frequency of nitrous oxide reductase (nosZ) between the two creeks, with substantially greater frequencies found in the enriched versus the reference creek (Table 1; Fig. 3). The frequency of sequences from our metagenomic libraries with high-quality hits to our curated set of nosZ reference sequences was again higher in the enriched creek (2.4 × 10−5) (3,875 total reads) than in the reference creek (1.2 × 10−5) (2,355 total reads), confirming our conclusions based on MG-RAST–generated KEGG annotations that the gene is more prevalent in the enriched creek. The taxonomic distributions of nosZ were similar between the two creeks (Fig. 4; see also Fig. S5 in the supplemental material), suggesting that the increased abundance of nosZ was spread over a broad taxonomic distribution of nosZ-harboring microorganisms.


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)

Bootstrapped neighbor-joining phylogeny of 158 nosZ sequence clusters from our original 240-reference NCBI-based database, representing 80 distinct bacterial and 3 archaeal genera. Clusters of >93% similarities were formed to reduce the total spread of the tree using UCLUST (47). Sequences in this tree had at least 1 hit from our creek sediment metagenomic data with an alignment bit score greater than 80. The number of hits from enriched and reference creeks to each cluster is shown by the length of the bar at the terminal node of each branch. Branches are colored by typical (gray) versus atypical (violet) genera according to categorization of atypical and typical genera by Sanford et al. in 2012 (17).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Bootstrapped neighbor-joining phylogeny of 158 nosZ sequence clusters from our original 240-reference NCBI-based database, representing 80 distinct bacterial and 3 archaeal genera. Clusters of >93% similarities were formed to reduce the total spread of the tree using UCLUST (47). Sequences in this tree had at least 1 hit from our creek sediment metagenomic data with an alignment bit score greater than 80. The number of hits from enriched and reference creeks to each cluster is shown by the length of the bar at the terminal node of each branch. Branches are colored by typical (gray) versus atypical (violet) genera according to categorization of atypical and typical genera by Sanford et al. in 2012 (17).
Mentions: Our metagenomic analyses revealed dramatic differences in the frequency of nitrous oxide reductase (nosZ) between the two creeks, with substantially greater frequencies found in the enriched versus the reference creek (Table 1; Fig. 3). The frequency of sequences from our metagenomic libraries with high-quality hits to our curated set of nosZ reference sequences was again higher in the enriched creek (2.4 × 10−5) (3,875 total reads) than in the reference creek (1.2 × 10−5) (2,355 total reads), confirming our conclusions based on MG-RAST–generated KEGG annotations that the gene is more prevalent in the enriched creek. The taxonomic distributions of nosZ were similar between the two creeks (Fig. 4; see also Fig. S5 in the supplemental material), suggesting that the increased abundance of nosZ was spread over a broad taxonomic distribution of nosZ-harboring microorganisms.

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