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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.


Venn Diagram showing the shared and unique closest match taxa of 286 total OTUs between the combined above water table (AWT) and taiga samples (combined as AK), Hawaii (HI), Utah (UT), and Florida (FL) with the criteria that a certain closest-match taxa is present in at least 50% of all samples in a site.
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Figure 6: Venn Diagram showing the shared and unique closest match taxa of 286 total OTUs between the combined above water table (AWT) and taiga samples (combined as AK), Hawaii (HI), Utah (UT), and Florida (FL) with the criteria that a certain closest-match taxa is present in at least 50% of all samples in a site.

Mentions: The majority of differences between the AK and Florida, Utah, and Hawaii sites were not due to changes in relative abundances, but rather to absence in the AK sites of specific OTUs (Figure 6). Taxa most associated with AK included several halophiles, aquatic species and those associated with respiration of alternate electron acceptors, reflecting ecosystem pressures on the proliferation or the exclusion of certain lineages. Halophiles have been found to be a feature of permafrost samples (Steven et al., 2007), due to the distribution of brine channel habitats. Comparisons between our AK AWT samples and the AK taiga site revealed that presence-absence drove differences between these more similar habitats within the rarer (<0.1%) members while the more abundant OTUs varied in relative abundances.


NifH -Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient
Venn Diagram showing the shared and unique closest match taxa of 286 total OTUs between the combined above water table (AWT) and taiga samples (combined as AK), Hawaii (HI), Utah (UT), and Florida (FL) with the criteria that a certain closest-match taxa is present in at least 50% of all samples in a site.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 6: Venn Diagram showing the shared and unique closest match taxa of 286 total OTUs between the combined above water table (AWT) and taiga samples (combined as AK), Hawaii (HI), Utah (UT), and Florida (FL) with the criteria that a certain closest-match taxa is present in at least 50% of all samples in a site.
Mentions: The majority of differences between the AK and Florida, Utah, and Hawaii sites were not due to changes in relative abundances, but rather to absence in the AK sites of specific OTUs (Figure 6). Taxa most associated with AK included several halophiles, aquatic species and those associated with respiration of alternate electron acceptors, reflecting ecosystem pressures on the proliferation or the exclusion of certain lineages. Halophiles have been found to be a feature of permafrost samples (Steven et al., 2007), due to the distribution of brine channel habitats. Comparisons between our AK AWT samples and the AK taiga site revealed that presence-absence drove differences between these more similar habitats within the rarer (<0.1%) members while the more abundant OTUs varied in relative abundances.

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.