Development and comparison of SYBR Green quantitative real-time PCR assays for detection and enumeration of sulfate-reducing bacteria in stored swine manure.
OBJECTIVE
To develop and evaluate primer sets targeted to the dissimilatory sulfite reductase gene (dsrA) for use in quantitative real-time PCR detection of sulfate-reducing bacteria (SRB) in stored swine manure.


RESULTS
Degenerate primer sets were developed to detect SRB in stored swine manure. These were compared with a previously reported primer set, DSR1F+ and DSR-R, for their coverage and ability to detect SRB communities in stored swine manure. Sequenced clones were most similar to Desulfovibrio sp. and Desulfobulbus sp., and these SRB populations differed within different manure ecosystems. Sulfur content of swine diets was shown to affect the population of Desulfobulbus-like Group 1 SRB in manure.


CONCLUSIONS
The newly developed assays were able to enumerate and discern different groups of SRB, and suggest a richly diverse and as yet undescribed population of SRB in swine manure.


CONCLUSIONS
The PCR assays described here provide improved and efficient molecular tools for quantitative detection of SRB populations. This is the first study to show population shifts of SRB in swine manure, which are a result of either the effects of swine diets or the maturity of the manure ecosystem.
Spence
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Fermentation Biotechnology Research Unit, National Center for Agricultural Research, USDA, Agricultural Research Service, Peoria, IL 61604, USA. cheryl.spence@ars.usda.gov
Whitehead
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Cotta
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D000818:Animals; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis; D008372:Manure / Q000382:microbiology*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D017422:Sequence Analysis, DNA; D016999:Sulfur-Reducing Bacteria / Q000235:genetics / Q000302:isolation & purification*; D013552:Swine
D017931:DNA Primers; D004269:DNA, Bacterial; D008372:Manure; D012336:RNA, Ribosomal, 16S