Project ID



Through soil sampling pre- and post-manure application and sampling the manure, the project analyzed the bacterial community present in each sample. DNA was extracted individually from each sample in triplicate for qPCR analysis.Reproducible qPCR results for ermB, sulI, intI, ermC, strB and incWrepA were collected and for each reaction the amount of DNA present was determined based on standard control. All samples were normalized for 16S rRNA. For more information on the project, see published jounal article: Lopatto E, Choi J, Colina A, Ma L, Howe A, et al. (2019) Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application. PLOS ONE 14(8): e0220770.

Key Question

What impact does the application of swine manure as fertilizer have on the bacterial community structure and abundance of antibiotic resistance and genetic mobility in the soil?


The manure community were found 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. Significant differences were observed in the soil microbiome between all time points, except between the spring samples. However, by tracking manure associated taxa, the addition of the manure microbiome was determined 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.

Principal Investigator(s)

Shannon Hinsa-Leasure

Year of Grant Completion


Link to Published Article