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ARS Home » Plains Area » Lincoln, Nebraska » Agroecosystem Management Research » Research » Publications at this Location » Publication #406085
Research Project: Managing Manure as a Soil Resource for Improved Biosecurity, Nutrient Availability, and Soil Sustainability

Location: Agroecosystem Management Research

Title: Changes in the antibiotic resistome over 71 years in soils of the U.S. plains

Author
item QIAN, XUN - Northwest A&f University
item Durso, Lisa
item VASCO, KARLA - University Of Michigan
item LI, BINTAO - University Of Michigan
item LIM, MARK - University Of Michigan
item HASHSHAM, SYED - University Of Michigan
item TIEDJE, JAMES - University Of Michigan

Submitted to: ASA-CSSA-SSSA Annual Meeting Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 8/8/2023
Publication Date: 10/31/2023
Citation: Qian, X., Durso, L.M., Vasco, K., Li, B., Lim, M., Hashsham, S., Tiedje, J. 2023. Changes in the antibiotic resistome over 71 years in soils of the U.S. plains. ASA-CSSA-SSSA Annual Meeting Abstracts. Available: https://scisoc.confex.com/scisoc/2023am/meetingapp.cgi/Paper/154134.

Interpretive Summary:

Technical Abstract: Soils are the largest reservoir of antibiotic resistance genes (ARGs) and play important roles in the evolution and dissemination of ARGs. To understand changes of soil resistomes in agriculture ecosystems, we used soil samples from the Hass soil archive, which contains plains soils collected in 1947 (pre-antibiotic era) from Montana to Texas, with three locations resampled in 2018. The antibiotic resistant communities were enriched by incubations with five individual antibiotics, and community composition and resistome were analyzed using shotgun metagenomic sequencing. High diversity of ARGs (176-202 subtypes) were detected in all soils, and yr-2018 had significantly higher functional ARG diversity than yr-1947. Class A betalactamase genes, tetK and tetL, norB were representative enriched ARGs corresponding to beta-lactam, tetracycline, and quinolone antibiotic resistance. The core ARGs which dominated resistome abundance were highly similar in the two years and across the three sites, with bacA, bcrA, mexF, mexT, mexW, vanR and vanS accounting for over 88% of resistome abundance. Some ARGs found only in 2018 have sequences that correspond with resistance to clinically important antibiotics. The previously proposed proxy for anthropogenic pollution, class 1 integron gene (intI1), was not detected in these soils, but significant correlation was observed between insertion sequence abundance and resistome abundance. Procrustes analysis suggested that the changes in resistome profiles were mainly driven by the variations of soil community structure. The same antibiotic selected similar ARGs in all soils, and some ARGs were enriched in multiple antibiotic incubations, especially in ampicillin, ceftiofur and tetracycline enrichments, suggesting the natural and persistent co-occurrence of their corresponding ARGs. While providing novel insights on antibiotic resistance, interpretation has limitations based on short read data and the inability to identify intrinsic resistance. We propose criteria and define the functional, non-functional and ubiquitous ARGs in the soils based on the enrichment experiments (with/without antibiotic).