Bacterial community shifts in decomposing cowpats and the subsequent impacts on fecal source indicators for water quality monitoring

Abstract The intensification of dairy farming on the agricultural landscape in New Zealand has raised concerns about pollution sources from dairy fecal runoff into waterways. An important step for mitigation of pollution is the identification of the sources of fecal contamination. An amplicon-based metagenomic assay of the bacterial community mobilised into runoff from decomposing cowpats revealed shifts in the community composition over five and a half months of on-field decomposition. Mobilised fractions from the cowpats showed major bacterial community shifts from the anaerobic bacteria (Clostridiales and Bacteroidales) that dominate the cow rumen and fresh cowpat, to the bacterial Orders of the Actinomycetales, Sphingobacteriales and Flavobacteriales. These bacterial community shifts were in conjunction with summertime conditions of low rainfall and high sunshine hours coupled with reduced water availability. The impacts of these bacterial shifts is discussed in terms of their effects on the indicators used for water quality monitoring: the fecal indicator bacterium, Escherichia coli, and fecal source tracking (FST) markers (host-associated quantitative polymerase chain reaction (qPCR) markers and fecal steroids). The hypothesis that these bacterial community shifts would impact on the steroid ratios used as FST signatures was disproved. The fecal steroids were, therefore, reliable indicators of fecal sources from cowpats, which had been decomposing for up to five and a half months post-deposition. Consistent with the noted bacterial community changes, there were, however, concentration decreases in the bacterial groups targeted by the faecal source qPCR markers, and the E. coli mobilised from decomposing cowpats.