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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

Neighbor-joining tree of Actinobacteria. The frequency (%) of which a given branch was recovered in 1,000 bootstrap replicationsis shown above branches recovered in more than 65% of the bootstrap replicates.
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Figure 11: Neighbor-joining tree of Actinobacteria. The frequency (%) of which a given branch was recovered in 1,000 bootstrap replicationsis shown above branches recovered in more than 65% of the bootstrap replicates.

Mentions: OTUs classified as Actinobacteria (high G+C Gram-positive; Fig. 11) were represented in all libraries, with a range of relative abundances between 1.5 (T2S2) and 15.9% (T2S1) (Fig. 3). Firmicutes (low G+C Gram-positive; Fig. 12) and Bacteroidetes (Fig. 13) were represented by OTUs in 10 and 11 of the 12 libraries respectively (Fig. 3). Rarer OTUs that classified to the Chloroflexi/Thermomicrobia, Deferribacteres, Gemmatimonadetes, Nitrospira, OP10, Spirochaetes, and TM7 divisions were dispersed throughout the libraries (Fig. 10). For the Firmicutes-associated OTUs, approximately two-thirds (18 out of 29) classified to the order Clostridiales. For OTUs classified as Bacteroidetes, the majority (19 out of 39) classified as Sphingobacteriaceae.


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)

Neighbor-joining tree of Actinobacteria. The frequency (%) of which a given branch was recovered in 1,000 bootstrap replicationsis shown above branches recovered in more than 65% of the bootstrap replicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 11: Neighbor-joining tree of Actinobacteria. The frequency (%) of which a given branch was recovered in 1,000 bootstrap replicationsis shown above branches recovered in more than 65% of the bootstrap replicates.
Mentions: OTUs classified as Actinobacteria (high G+C Gram-positive; Fig. 11) were represented in all libraries, with a range of relative abundances between 1.5 (T2S2) and 15.9% (T2S1) (Fig. 3). Firmicutes (low G+C Gram-positive; Fig. 12) and Bacteroidetes (Fig. 13) were represented by OTUs in 10 and 11 of the 12 libraries respectively (Fig. 3). Rarer OTUs that classified to the Chloroflexi/Thermomicrobia, Deferribacteres, Gemmatimonadetes, Nitrospira, OP10, Spirochaetes, and TM7 divisions were dispersed throughout the libraries (Fig. 10). For the Firmicutes-associated OTUs, approximately two-thirds (18 out of 29) classified to the order Clostridiales. For OTUs classified as Bacteroidetes, the majority (19 out of 39) classified as Sphingobacteriaceae.

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