Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/5/2004
Publication Date: 7/20/2004
Citation: McGarvey, J.A., Miller, W., Sanchez, S., Stanker, L.H. 2004. Identification of bacterial populations in dairy wastewaters by use of 16S rRNA gene sequences and other genetic markers. Applied and Environmental Microbiology. 70(7):4267-4275. Interpretive Summary: Dairy farms produce large amounts of animal waste that must be treated to ensure good animal and human health. Many dairy farms use particle separators to segregate the solid from the liquid portion of the waste and pump the liquid into treatment lagoons where the liquid is processed. Little is know about the types of bacteria that live in these systems. In order to gain information about these bacteria we used microbiological and genetic techniques to identify them. We were able to determine the major groups of bacteria that inhabit these systems. We also were able to find some bacteria that are able to cause disease in humans and livestock, but were unable to find any of the common disease causing pathogens like Salmonella and pathogenic E. coli. The data from this work is useful to determine if rivers, streams or ground water is contaminated with dairy waste water. It also adds to the collective knowledge of the types of bacteria that inhabit these systems.
Technical Abstract: Hydraulic flush waste removal systems coupled to solid/liquid separators and circulated treatment lagoons are commonly utilized to manage the large amounts of animal waste produced on high-intensity dairy farms. Although these systems are common, little is know about the microbial populations that inhabit them or how they change as they traverse the system. Using culture (plate counting) and nonculture based (16S rDNA sequencing and pathogen specific PCR assays) methods we characterized the microbial community structure of manure, water from the first separator pit, and water from the treatment lagoon from a large dairy in the San Joaquin valley of California. Our results show that both total bacterial numbers and bacterial diversity are highest in manure, followed by the first separator pit water and the lagoon water. The most prevalent phylum in all locations was the Firmicutes (low G+C Gram positive bacteria). The most commonly occurring operational taxonomic unit (OUT) had a 16S rDNA sequence 96-99% similar to Clostridium lituseburense and represented approximately 6% of the manure derived sequences, 14% of the first separator pit derived sequences and 20% of the lagoon derived sequences. Also highly prevalent was an OTU with a 16S rDNA sequence 97-100% similar to Eubacterium tenue, comprising ca. 3% of the manure derived sequences, 6% of the separator pit derived sequences and 9% of the lagoon derived sequences. Taken together these sequences represent approximately one third of the total organisms in the lagoon waters and may be of use as indicator organisms for dairy waste water contamination and source tracking. We also identified several potential pathogens using our 16S rDNA method; however, our pathogen specific PCR assays did not detect any of the common livestock associated pathogens such as E. coli O157:H7, Salmonella, or Mycobacterium avium subsp. paratuberculosis indicating that these organisms were either not present or were in such low numbers that they were undetectable.