Journal Article

Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application

Howe, Adina, Choi, Jinlyung, Hinsa-Leasure, Shannon, Lopatto, Edward, Colina, Alfredo, Ma, Lanying

2019

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Abundance / Agricultural chemicals / Agricultural industry / Agricultural land / Agricultural management / Agricultural research / Agriculture / Animal feeding and feeds / Animal manures / Animal wastes / Animals / Anti-Bacterial Agents - pharmacology / Antibiotic resistance / Antibiotics / Antimicrobial agents / Bacteria / Bacteria - drug effects / Bacteria - genetics / Bacteria - isolation & purification / Biology / Biology and Life Sciences / Communities / Concentrated animal feeding operations / Drug resistance / Drug Resistance, Microbial / Earth Sciences / Ecology and Environmental Sciences / Environmental aspects / Factory farming / Factory farms / Farm buildings / Fertilizers / Genes / Genes, Bacterial / Genetic aspects / Health / Hogs / Intensive farming / Livestock / Loam soils / Manure - microbiology / Manures / Medicine and Health Sciences / Microbial drug resistance / Microbiomes / Microbiota (Symbiotic organisms) / Next-generation sequencing / Organic fertilizers / Penicillin / RNA / rRNA 16S / Soil dynamics / Soil fertility / Soil Microbiology / Soils / Spring / Swine / Swine - microbiology