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Microbial community structure across a wastewater-impacted riparian buffer zone in the southeastern coastal plain.

Ducey TF, Johnson PR, Shriner AD, Matheny TA, Hunt PG - Open Microbiol J (2013)

Bottom Line: Clone libraries of the 16S rDNA gene were generated from each of twelve sites across the riparian buffer with a total of 986 partial sequences grouped into 654 operational taxonomic units (OTUs).The Proteobacteria were the dominant group (49.8% of all OTUs), with the Acidobacteria also well represented (19.57% of all OTUs).Analysis of qPCR results identified spatial relationships between soil series, site location, and gene abundance, which could be used to infer both incomplete and total DEA rates.

View Article: PubMed Central - PubMed

Affiliation: Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, USDA, Florence SC.

ABSTRACT
Riparian buffer zones are important for both natural and developed ecosystems throughout the world because of their ability to retain nutrients, prevent soil erosion, protect aquatic environments from excessive sedimentation, and filter pollutants. Despite their importance, the microbial community structures of riparian buffer zones remains poorly defined. Our objectives for this study were twofold: first, to characterize the microbial populations found in riparian buffer zone soils; and second, to determine if microbial community structure could be linked to denitrification enzyme activity (DEA). To achieve these objectives, we investigated the microbial populations of a riparian buffer zone located downslope of a pasture irrigated with swine lagoon effluent, utilizing DNA sequencing of the 16S rDNA, DEA, and quantitative PCR (qPCR) of the denitrification genes nirK, nirS, and nosZ. Clone libraries of the 16S rDNA gene were generated from each of twelve sites across the riparian buffer with a total of 986 partial sequences grouped into 654 operational taxonomic units (OTUs). The Proteobacteria were the dominant group (49.8% of all OTUs), with the Acidobacteria also well represented (19.57% of all OTUs). Analysis of qPCR results identified spatial relationships between soil series, site location, and gene abundance, which could be used to infer both incomplete and total DEA rates.

No MeSH data available.


Related in: MedlinePlus

Taxonomic breakdown of classified 16S rDNA gene sequences from riparian buffer zone.
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Figure 3: Taxonomic breakdown of classified 16S rDNA gene sequences from riparian buffer zone.

Mentions: The dominant bacterial division represented in the libraries was the Proteobacteria that accounted for 42.8% (280 of 654) of all OTUs (Fig. 3). When the Proteobacteria were categorized by subclass, the α- and γ- subclasses were the major constituents, accounting for 19.42% (127 OTUs; Fig. 4) and 13.00% (85 OTUs; Fig. 5) of all OTUs respectively. The β- (37 OTUs, 5.66%; Fig. 6) and δ- (24 OTUs, 3.67%; Fig. 7) proteobacterial OTUs were represented in lesser proportions. The identification of a large number of OTUs classified as α-Proteobacteria has been demonstrated in previous studies of acidic soils. Rheims et al. showed a high proportion of α-Proteobacteria from a peat bog [29], while McCaig et al. demonstrated a predominance of α-Proteobacteria in mildly acidic grasslands [30]. These results are consistent with the riparian buffers acidic soils. Of the 127 OTUs classifiable to the α- subclass, 41 and 46 OTUs belonged to the orders Rhizobiales and Rhodospirillales respectively. Clones that composed OTUs with these classifications were found in 11 of the 12 sites, with T1S3 as the exception. Species within these orders have a wide range of phenotypic characteristics, from nitrogen fixation, to methanotrophy, to phototrophy [31].


Microbial community structure across a wastewater-impacted riparian buffer zone in the southeastern coastal plain.

Ducey TF, Johnson PR, Shriner AD, Matheny TA, Hunt PG - Open Microbiol J (2013)

Taxonomic breakdown of classified 16S rDNA gene sequences from riparian buffer zone.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3722543&req=5

Figure 3: Taxonomic breakdown of classified 16S rDNA gene sequences from riparian buffer zone.
Mentions: The dominant bacterial division represented in the libraries was the Proteobacteria that accounted for 42.8% (280 of 654) of all OTUs (Fig. 3). When the Proteobacteria were categorized by subclass, the α- and γ- subclasses were the major constituents, accounting for 19.42% (127 OTUs; Fig. 4) and 13.00% (85 OTUs; Fig. 5) of all OTUs respectively. The β- (37 OTUs, 5.66%; Fig. 6) and δ- (24 OTUs, 3.67%; Fig. 7) proteobacterial OTUs were represented in lesser proportions. The identification of a large number of OTUs classified as α-Proteobacteria has been demonstrated in previous studies of acidic soils. Rheims et al. showed a high proportion of α-Proteobacteria from a peat bog [29], while McCaig et al. demonstrated a predominance of α-Proteobacteria in mildly acidic grasslands [30]. These results are consistent with the riparian buffers acidic soils. Of the 127 OTUs classifiable to the α- subclass, 41 and 46 OTUs belonged to the orders Rhizobiales and Rhodospirillales respectively. Clones that composed OTUs with these classifications were found in 11 of the 12 sites, with T1S3 as the exception. Species within these orders have a wide range of phenotypic characteristics, from nitrogen fixation, to methanotrophy, to phototrophy [31].

Bottom Line: Clone libraries of the 16S rDNA gene were generated from each of twelve sites across the riparian buffer with a total of 986 partial sequences grouped into 654 operational taxonomic units (OTUs).The Proteobacteria were the dominant group (49.8% of all OTUs), with the Acidobacteria also well represented (19.57% of all OTUs).Analysis of qPCR results identified spatial relationships between soil series, site location, and gene abundance, which could be used to infer both incomplete and total DEA rates.

View Article: PubMed Central - PubMed

Affiliation: Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, USDA, Florence SC.

ABSTRACT
Riparian buffer zones are important for both natural and developed ecosystems throughout the world because of their ability to retain nutrients, prevent soil erosion, protect aquatic environments from excessive sedimentation, and filter pollutants. Despite their importance, the microbial community structures of riparian buffer zones remains poorly defined. Our objectives for this study were twofold: first, to characterize the microbial populations found in riparian buffer zone soils; and second, to determine if microbial community structure could be linked to denitrification enzyme activity (DEA). To achieve these objectives, we investigated the microbial populations of a riparian buffer zone located downslope of a pasture irrigated with swine lagoon effluent, utilizing DNA sequencing of the 16S rDNA, DEA, and quantitative PCR (qPCR) of the denitrification genes nirK, nirS, and nosZ. Clone libraries of the 16S rDNA gene were generated from each of twelve sites across the riparian buffer with a total of 986 partial sequences grouped into 654 operational taxonomic units (OTUs). The Proteobacteria were the dominant group (49.8% of all OTUs), with the Acidobacteria also well represented (19.57% of all OTUs). Analysis of qPCR results identified spatial relationships between soil series, site location, and gene abundance, which could be used to infer both incomplete and total DEA rates.

No MeSH data available.


Related in: MedlinePlus