Composting dairy cattle manure significantly reduces antibiotic-resistant bacteria with no biochar impact

Authors: Agga, Getahun; NETTHISINGHE, ANNESLY - Western Kentucky University; WOOSLEY, PAUL - Western Kentucky University; STRUNK, WILLIAM - Western Kentucky University; Sistani, Karamat

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2026
Publication Date: 8/13/2026
Citation: Agga, G.E., Netthisinghe, A., Woosley, P., Strunk, W., Sistani, K.R. 2026. Composting dairy cattle manure significantly reduces antibiotic-resistant bacteria with no biochar impact. Applied and Environmental Microbiology. Article 0:e01258-26. https://doi.org/10.1128/aem.01258-26.
DOI: https://doi.org/10.1128/aem.01258-26

Interpretive Summary: Composting is a microbially mediated decomposition of organic matter. As animal manure treatment technology, it converts waste into a nutrient-rich product for use as organic fertilizer. Biochar, obtained from the pyrolysis of biomass including animal manure, has been used for soil amendment as a carbon-rich product. Beyond its nutrient stabilizing potential, composting has been shown to reduce bacterial load in animal manure. However, its effect with or without a biochar addition was not evaluated under a randomized controlled field trial. Biochar was nearly ‘sterile’ and the sawdust used as a bulking agent had low concentrations of innocuous bacteria. Thus, fresh dairy manure was the main source of bacteria to the pre-compost mixture. Biochar did not have extra effect on the bacterial load beyond composting alone. Composting during spring/summer is more effective than fall/winter. Composting is more effective against gram-negative bacteria than gram-positive bacteria. Importantly, composting eliminated multidrug resistant bacteria of critical importance to public health. This study showed that while composting is effective in complete elimination of bacteria that are resistant to critically important antibiotics for human health, further optimization and systems approach are required to make it free of any bacteria.

Technical Abstract: In two randomized controlled field studies, we investigated the effect of biochar amended dairy manure composting on the concentrations and prevalence of generic and antibiotic-resistant E. coli and enterococci. Fresh dairy manure mixed with saw dust and biochar were randomly distributed into plastic reactors and composted for six weeks. Pre-compost (biochar, sawdust, fresh dairy manure, and manure mixture) and final compost samples were cultured for enumeration and prevalence. While biochar and sawdust were not significant sources, fresh dairy manure was the major contributor of bacteria to the initial manure mixture. Biochar amendment did not significantly reduce bacterial load beyond that could be achieved by composting alone. Spring-summer composting was more effective than fall-winter composting. While E. coli was more prone, enterococci were more likely to survive composting. Dairy manure composting eliminated bacteria (3rd generation cephalosporin resistant [3GCr] and extended spectrum beta-lactamase-producing [ESBL]-E. coli) resistant to critically important and highest priority antibiotics for human health and significantly reduced the prevalence and concentrations of other bacteria. 3GCr- and ESBL-E. coli from fresh dairy manure were multidrug resistant and carried blaCTX-M genes, a widely distributed ESBL gene type. By whole genome sequencing, ESBL-E. coli from experiment 1 (fall-winter) had diverse resistance profiles, sequence types, plasmid profiles, and virulence factor genes, and more blaCTX-M genes (CTX-M-1, CTX-M-32, and CTX-M-55). However, those from experiment 2 (spring-summer) were clonal and carried blaCTX-M-55 only. In conclusion, dairy manure composting effectively removes antibiotic resistant bacteria of public health importance, with no added effect of biochar amendment.