Location: Northwest Irrigation and Soils Research
Project Number: 5368-63000-001-03
Start Date: Jan 01, 2011
End Date: Dec 31, 2013
During year 1, samples will be collected from as many as 10 dairy lagoons. At each lagoon, a total of 8 samples (250 mL) will be aseptically collected from the perimeter of each lagoon and composited. Samples will be collected by the researcher, unless it is deemed necessary to collect the samples using a single- or double-blind method. In either case, the samples will be transported to our laboratory in coolers, then stored at 5oC for no longer than 48 hours. Prior to DNA extraction, the composite samples will be thoroughly homogenized and 100-mL aliquots will be filtered through 0.2 'm filters. The filters will then be placed into bead beating tubes and processed to extract the DNA from the microbial community. The DNA will be amplified using universal primer sets (BA8F and UN1492R) and the subsequent PCR product will be cloned into pGEM-T Easy Vector. One hundred clones from each plate will be randomly selected, then grown in appropriate media. Afterwards, the plasmid from each clone will be isolated and sent to a commercial laboratory for sequencing. The 16S rDNA sequences will be identified using the BLAST database at the National Center for Biotechnology Information. In the subsequent year, samples will be collected from the same lagoons using the procedures described above. Based on the information collected during year 1, up to five bacterial pathogens will be selected for further study. The suspected targets are Campylobacter jejuni, Escherichia coli O157:H7, Salmonella, Clostridium perfringens, and Mycobacterium bovis. These pathogens will be quantified using standard culture-based methods and quantitative PCR. In addition to these bacterial pathogens, the following indicator organisms of fecal pollution will be cultivated: Escherichia coli, total coliforms, fecal streptococci, and somatic coliphage (bacterial virus). In CY2013, samples will be collected from 10 dairy wastewater ponds with and without purple sulfur bacteria during the spring and summer months. Purple sulfur bacteria will be characterized after isolation using PCR analysis of 16S ribosomal DNA. The wastewater samples will also be analyzed for a full sweep of chemical properties, such as pH, total ammoniacal nitrogen, total Kjeldahl nitrogen, total and volatile solids, electrical conductivity, and chemical oxygen demand. The data will then be analyzed to determine which wastewater properties, if any, control the presence and abundance of purple sulfur bacteria.