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

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.

Presence and abundance of antibiotic resistance genes at an organic goat dairy farm

“…We compared the abundance of intI1, sul1 and tetG in the goat bedding and goat pellet samples with the literature, expecting our results would have a lower prevalence of ARGs compared to reported quantities of ARGs in conventional farms, also known as concentrated animal feeding operations (CAFOs). Instead, we found that our results were on the same order of magnitude of 10 -3 gene copies per 16S rRNA gene for intI1 and tetG in pellets, and a greater order of magnitude for sul1 (Lopatto et al, 2019;Cheng et al, 2013). Since our samples were not actively influenced by antibiotics, but have comparable values to many studies that did use soil influenced by antibiotics, this raises the question of whether antibiotic usage promotes ARGs in microbial populations.…”

Integrated Metagenomic Assessment of Multiple Pre-harvest Control Points on Lettuce Resistomes at Field-Scale

“…Further microbial community analyses are needed to connect microbial community diversity and ARG attenuation or proliferation, and deeper taxonomic analysis than the genera level may provide insight to potential pathogenicity which will allow for bacterial host identification across the preharvest vegetable production chain. Other studies have indicated need to examine this more closely specifically in agricultural soils (Cycoń et al, 2019;Lopatto et al, 2019) and on vegetable surfaces Shen et al, 2021).…”

Antibiotic resistance gene dissipation in soil microcosms amended with antibiotics and swine manure

“…However, this use of manure creates a pathway for ARGs to be introduced into the environment (Ruuskanen et al, 2016). Previous work has shown that field application of manure leads to elevated levels of antibiotic-resistant bacteria and to the spread of resistance genes between bacteria within agricultural soils and their downstream waters (Garder et al, 2014;Ghosh & LaPara, 2007;Hsu et al, 2014;Joy et al, 2013;Lopatto et al, 2019;Marti et al, 2013).…”