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

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 sawdust and biochar was randomly distributed into plastic reactors and composted for 6 months. Pre-compost (biochar, sawdust, fresh dairy manure), 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 [3GC ^r ] 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 investigated bacteria. 3GC ^r - and ESBL- E. coli from fresh dairy manure were multidrug resistant and carried bla _CTX-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, virulence factor genes, and more bla _CTX-M genes (CTX-M-1, CTX-M-32, and CTX-M-55). However, those from experiment 2 (spring-summer) were clonal and carried bla _CTX-M-55 only. In conclusion, dairy manure composting effectively removes antibiotic resistant bacteria of public health importance, with no added effect of biochar amendment.

IMPORTANCE

Composting is a microbially mediated decomposition of organic matter into a nutrient-rich product for use as fertilizer. Biochar, obtained from the pyrolysis of biomass including animal manure, has been used for soil amendment. 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 bacteriologically “sterile,” and the sawdust used as a bulking agent had low concentrations of innocuous bacteria indicating that dairy manure was the main source of bacteria to the pre-compost mixture. Biochar did not have an extra effect on the bacterial load beyond composting alone. Composting during spring/summer is more effective than fall/winter. Furthermore, it is more effective against gram-negatives than gram-positive bacteria. Importantly, composting effectively eliminated multidrug-resistant bacteria of critical importance to public health for safer use of dairy manure.