Limits...
NifH -Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

View Article: PubMed Central - PubMed

ABSTRACT

Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.

No MeSH data available.


Neighbor joining tree based on 116 comparable NifH amino acid positions using reference sequences obtained from the hand-curated NifH database used for BLASTp assignment. Cluster representative sequences representing those clusters that constituted the SIMPER results were chosen. Bootstrap values >50% are indicated by branch symbols. Group names (e.g., 3E) indicated are based upon the ARB database. The innermost two data fields indicate the relative abundances for each OTU in the above water table (AWT-red) and below water table (BWT-blue). The outermost field indicates significant differences (t-test, p < 0.05) between the BWT and AWT relative abundances (black bar = significant, no bar = not significant).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5121533&req=5

Figure 2: Neighbor joining tree based on 116 comparable NifH amino acid positions using reference sequences obtained from the hand-curated NifH database used for BLASTp assignment. Cluster representative sequences representing those clusters that constituted the SIMPER results were chosen. Bootstrap values >50% are indicated by branch symbols. Group names (e.g., 3E) indicated are based upon the ARB database. The innermost two data fields indicate the relative abundances for each OTU in the above water table (AWT-red) and below water table (BWT-blue). The outermost field indicates significant differences (t-test, p < 0.05) between the BWT and AWT relative abundances (black bar = significant, no bar = not significant).

Mentions: Significant changes in the composition of the diazotroph community were found based on position above (AWT) and below (BWT) the water table (PERMANOVA; F = 2.19 P < 0.001, ANOSIM; P < 0.001), roughly corresponding to the thaw depth at time of sampling. Chao richness estimators were significantly higher in the BWT samples versus AWT (ANOVA; F = 4.78, P = 0.03) (Supplementary Figure S2). A neighbor-joining tree was constructed to visualize the differences in relative abundances between the AWT and BWT layers (Figure 2). Two distinct clades of the group III and one clade of group 1A nifH-harboring taxa consisting of Delta Proteobacteria were most associated with the deeper layers while group I (especially 1 K) containing Alpha Proteobacteria were higher in abundance in the samples above the water table. NifH sequences associated with the Delta Proteobacteria were clearly separated from the other groups. Tree branch length differences were smaller between the Alpha-, Beta-, and Gamma-Proteobacteria that may affect the confidence in assigning finer taxonomic resolution.


NifH -Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient
Neighbor joining tree based on 116 comparable NifH amino acid positions using reference sequences obtained from the hand-curated NifH database used for BLASTp assignment. Cluster representative sequences representing those clusters that constituted the SIMPER results were chosen. Bootstrap values >50% are indicated by branch symbols. Group names (e.g., 3E) indicated are based upon the ARB database. The innermost two data fields indicate the relative abundances for each OTU in the above water table (AWT-red) and below water table (BWT-blue). The outermost field indicates significant differences (t-test, p < 0.05) between the BWT and AWT relative abundances (black bar = significant, no bar = not significant).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121533&req=5

Figure 2: Neighbor joining tree based on 116 comparable NifH amino acid positions using reference sequences obtained from the hand-curated NifH database used for BLASTp assignment. Cluster representative sequences representing those clusters that constituted the SIMPER results were chosen. Bootstrap values >50% are indicated by branch symbols. Group names (e.g., 3E) indicated are based upon the ARB database. The innermost two data fields indicate the relative abundances for each OTU in the above water table (AWT-red) and below water table (BWT-blue). The outermost field indicates significant differences (t-test, p < 0.05) between the BWT and AWT relative abundances (black bar = significant, no bar = not significant).
Mentions: Significant changes in the composition of the diazotroph community were found based on position above (AWT) and below (BWT) the water table (PERMANOVA; F = 2.19 P < 0.001, ANOSIM; P < 0.001), roughly corresponding to the thaw depth at time of sampling. Chao richness estimators were significantly higher in the BWT samples versus AWT (ANOVA; F = 4.78, P = 0.03) (Supplementary Figure S2). A neighbor-joining tree was constructed to visualize the differences in relative abundances between the AWT and BWT layers (Figure 2). Two distinct clades of the group III and one clade of group 1A nifH-harboring taxa consisting of Delta Proteobacteria were most associated with the deeper layers while group I (especially 1 K) containing Alpha Proteobacteria were higher in abundance in the samples above the water table. NifH sequences associated with the Delta Proteobacteria were clearly separated from the other groups. Tree branch length differences were smaller between the Alpha-, Beta-, and Gamma-Proteobacteria that may affect the confidence in assigning finer taxonomic resolution.

View Article: PubMed Central - PubMed

ABSTRACT

Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.

No MeSH data available.