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Nonpoint sources of fecal contamination are a significant detriment to waterquality and impose risks to aquatic ecosystems and human health. Over the past fourdecades, the swine industry has become an increasing environmental concern worldwide,due to augmented production and concentration of farming operations. Despite attempts to reduce fecal loading into aquatic environments, the problemendures, in part as a result of the inability to routinely identify the origin of fecalpollution. This study evaluated the specificity, distribution, and sensitivity of available pig-specific assaystargeting the Bacteroidales 16S rRNA gene and the methanogen mcrA gene. The assayswere tested against DNA extracts derived from 88 pig fecal samples (OH, DE, TX, andWV), 98 non-target mammalian fecal samples (NE, WV, TX), and 47 groundwater andsurface water samples (IL). The study also investigated the phylogenetic diversity of 1200Bacteroidales 16S rRNA gene sequences derived from swine feces, lagoons, manure pits,and waters adjacent to swine operations. PCR results indicated that 95.5% and 87.5% ofswine fecal DNA extracts were positive with the general and pig-specific Bacteroidalesassay, respectively. However, the pig-specific Bacteroidales PCR assay was also positivefor sheep (i.e. 2 of 8) and horse (i.e. 4 of 12) fecal DNA, suggesting potential issues withhost-specificity. The mcrA gene marker was detected in less than one-third of all swinefecal samples, indicating lower detection limits when compared to the Bacteroidalesassay. Only 17% of the water samples tested with the pig-specific Bacteroidales yieldedpositive PCR results. Phylogenetic analysis of swine fecal clones revealed that approximately 40% of the sequences were shared by previously identified Bacteroidalesclones derived from mammals other than swine. In contrast, 23 pig fecal clones closelyrelated to Prevotella populations showed pig-specific distributions. While Bacteroidalespopulations may be promising targets for swine fecal source tracking, further sequencinganalysis of environmental clones is needed to better discriminate pig-fecal specificpopulations in contaminated watersheds from other potential fecal pollution sources. Includes abstract only.

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Edition: Vol. - No. Published: 11/01/2008 Number of Pages: 2 File Size: 1 file , 700 KB