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Article
Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application
PLoS ONE
  • Edward Lopatto, Grinnell College
  • Jinlyung Choi, Iowa State University
  • Alfredo Colina, Grinnell College
  • Lanying Ma, Iowa State University
  • Adina Howe, Iowa State University
  • Shannon Hinsa-Leasure, Grinnell College
Document Type
Article
Publication Version
Published Version
Publication Date
8-19-2019
DOI
10.1371/journal.pone.0220770
Abstract

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.

Comments

This article is published as Lopatto, Edward, Jinlyung Choi, Alfredo Colina, Lanying Ma, Adina Howe, and Shannon Hinsa-Leasure. "Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application." PLoS One 14, no. 8 (2019): e0220770. DOI: 10.1371/journal.pone.0220770. Posted with permission.

Access
Open
Creative Commons License
Creative Commons Attribution 4.0
Copyright Owner
Lopatto et al.
Language
en
File Format
application/pdf
Citation Information
Edward Lopatto, Jinlyung Choi, Alfredo Colina, Lanying Ma, et al.. "Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application" PLoS ONE Vol. 14 Iss. 8 (2019) p. e0220770
Available at: http://works.bepress.com/adina/39/