Summary
This study investigates the impact of swine concentrated animal feeding operation (CAFO) manure fertilization on the soil microbiome and the abundance of antibiotic resistance genes (ARGs) over the fall and spring. Results indicate that while manure application may not be a significant factor in altering the soil community, it does affect the gene abundance of select antibiotic resistance genes. Taking manure, manure line (i.e. spatial applications of manure lined parallel to the field), and field soil from a swine CAFO farm in Iowa, the study performed DNA extraction, rRNA sequencing, and qPCR to characterize the soil’s response to application types and levels of manure, as well as test ARG levels. A strength of the study is the authors’ acknowledgment that the response of the soil microbiome to manure can depend heavily on outside factors (i.e. regional soil characteristics, weather) beyond manure application. A limitation of the study is the five month assessment period, as the authors themselves acknowledge that measured alterations of the soil microbiome may occur over a much longer time span. The findings related to the levels of ARGs have important implications for human health, as dissemination of ARGs into the environment can contribute to the increasing public health threat of antibiotic resistance through horizontal gene transfer.
As agriculture industrializes, concentrated animal feeding operations (CAFOs) are becoming more common. Feces from CAFOs is often used as fertilizer on fields. However, little is known about the effects manure has on the soil microbiome, which is an important aspect of soil health and fertility. In addition, due to the subtherapeutic levels of antibiotics necessary to keep the animals healthy, CAFO manure has elevated levels of antibiotic resistant bacteria. Using 16s rRNA high-throughput sequencing and qPCR, this study sought to determine the impact of swine CAFO manure application on both the soil microbiome and abundance of select antibiotic resistance genes (ARGs) and mobile element genes (erm(B), erm(C), sul1, str(B), intI1, IncW repA) in agricultural soil over the fall and spring seasons. We found the manure community to be distinct from the soil community, with a majority of bacteria belonging to Bacteroidetes and Firmicutes. The soil samples had more diverse communities dominated by Acidobacteria, Actinobacteria, Proteobacteria, Verrucomicrobia, and unclassified bacteria. We observed significant differences in the soil microbiome between all time points, except between the spring samples. However, by tracking manure associated taxa, we found the addition of the manure microbiome to be a minor driver of the shift. Of the measured genes, manure application only significantly increased the abundance of erm(B) and erm(C) which remained elevated in the spring. These results suggest bacteria in the manure do not survive well in soil and that ARG dynamics in soil following manure application vary by resistance gene.