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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Environmentally Integrated Dairy Management Research » Research » Publications at this Location » Publication #333396

Research Project: Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Location: Environmentally Integrated Dairy Management Research

Title: Opportunities for optimization: fate of manure-borne pathogens during anaerobic digestion and solids separation

item Burch, Tucker
item Spencer, Susan
item BORCHARDT, SPENCER - Us Geological Survey (USGS)
item LARSON, REBECCA - University Of Wisconsin
item Borchardt, Mark

Submitted to: Journal of Environmental Quality
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/18/2018
Publication Date: 2/8/2018
Publication URL:
Citation: Burch, T.R., Spencer, S.K., Borchardt, S.S., Larson, R.A., Borchardt, M.A. 2018. Opportunities for optimization: fate of manure-borne pathogens during anaerobic digestion and solids separation. Journal of Environmental Quality. 47:336-344.

Interpretive Summary: Anaerobic digestion is a waste treatment technology that can destroy zoonotic pathogens – those capable of infecting both livestock and humans – in cattle manure, and this technology is often paired with solids separation on large farms where separated solids are used as bedding for cattle. However, the extent of pathogen destruction achieved in full-scale digesters is not well-characterized, and the distribution of pathogens in the solid and liquid fractions of separated manure is not known. We studied seven full-scale digesters with separators over three seasons (winter, spring, summer) and measured pathogens in raw manure, digested manure, and separated manure. Pathogen measurements were based on genetic markers; such markers are often used as proxy measurements for live pathogens, because their levels correlate with live pathogens. Based on these genetic marker data, destruction of pathogens was suboptimal and highly variable among farms and seasons. We also found – again based on genetic marker data – that the majority of pathogens that survived anaerobic digestion and entered solids separators ultimately end up in the liquid fraction of separated manure. This research informs livestock producers that optimization of full-scale anaerobic digesters is required to maximize their public health benefits. Such optimization would also be likely to improve yields of biogas during anaerobic digestion, thereby improving the economic viability of these digesters on cattle and dairy farms.

Technical Abstract: Anaerobic digestion can inactivate zoonotic pathogens present in cattle manure, which reduces transmission of these pathogens from farms to humans through the environment. However, the variability in extent of inactivation across farms and over time is unknown because most studies have examined pathogen inactivation under ideal laboratory conditions or have focused on full-scale digesters at only 1 or 2 sites. In contrast, we sampled full-scale digesters treating cattle manure at 7 sites in Wisconsin for 9 months on a biweekly basis (n = 118 pairs of influent and effluent samples) and used real-time quantitative PCR to analyze these samples for 19 different microbial genetic markers. Overall, inactivation of pathogens and fecal indicators was highly variable. When aggregated across site and season, log-removal values for several representative microorganisms – bovine Bacteroides, Bacteroidales-like CowM3, and bovine polyomavirus – were 0.8 ± 0.3, 0.7 ± 0.5, and 0.5 ± 0.6, respectively (mean ± standard deviation). These log-removal values were also approximately 2 to 10 times lower than expectations based on the scientific literature. Thus, our study indicates that full-scale anaerobic digestion of cattle manure requires optimization with regard to pathogen inactivation. Future studies should focus on identifying the potential causes of this sub-optimal performance (e.g., overloading, poor mixing, poor temperature control). Our study also examined the fate of pathogens during manure separation and found that the majority of microbes entering solids separators ended up in the liquid fraction. This finding has important implications for the transmission of zoonotic pathogens through the environment to humans.