Manure-Based Amendments Influence Surface-Associated Bacteria and Markers of Antibiotic Resistance on Radishes Grown in Soils with Different Textures

• Published in: Applied and environmental microbiology Vol. 87; no. 10
• Main Authors: Guron, Giselle K P, Chen, Chaoqi, Du, Pang, Pruden, Amy, Ponder, Monica A
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 27-04-2021
• Subjects: Abundance; Agricultural practices; Agricultural research; Agrochemicals; Animal manures; Antibiotic resistance; Antibiotics; Bacteria; Beef; Cattle; Clay loam; Composting; Composts; Dairy cattle; Drug resistance; Erythromycin; Fertilizers; Food Microbiology; Gene sequencing; Greenhouses; Indicators; Integrase; Manures; Markers; Microbiota; Multiantibiotic resistance; Radishes; Raphanus; Relative abundance; rRNA 16S; Soil amendment; Soil chemistry; Soil fertility; Soil microorganisms; Soil properties; Soil texture; Soils; Sulfamethazine; Texture; Vancomycin; manure; antibiotic resistance; compost; greenhouse; beef; soil microbiology; antibiotics; dairy; vegetables
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.02753-20

A controlled greenhouse study was performed to determine the effect of manure or compost amendments, derived during or in the absence of antibiotic treatment of beef and dairy cattle, on radish taproot-associated microbiota and indicators of antibiotic resistance when grown in different soil textures. Bacterial beta diversity, determined by 16S rRNA gene amplicon sequencing, bifurcated according to soil texture (
 < 0.001,
 = 0.501). There was a striking cross-effect in which raw manure from antibiotic-treated and antibiotic-free beef and dairy cattle added to loamy sand (LS) elevated relative (16S rRNA gene-normalized) (by 0.9 to 1.9 log
) and absolute (per-radish) (by 1.1 to 3.0 log
) abundances of
(an integrase gene and indicator of mobile multiantibiotic resistance) on radishes at harvest compared to chemical fertilizer-only control conditions (
 < 0.001). Radishes tended to carry fewer copies of
and
when grown in silty clay loam than LS. Composting reduced relative abundance of
on LS-grown radishes (0.6 to 2.4 log
decrease versus corresponding raw manure;
 < 0.001). Effects of antibiotic use were rarely discernible. Heterotrophic plate count bacteria capable of growth on media containing tetracycline, vancomycin, sulfamethazine, or erythromycin tended to increase on radishes grown in turned composted antibiotic-treated dairy or beef control (no antibiotics) manures relative to the corresponding raw manure in LS (0.8- to 2.3-log
increase;
 < 0.001), suggesting that composting sometimes enriches cultivable bacteria with phenotypic resistance. This study demonstrates that combined effects of soil texture and manure-based amendments influence the microbiota of radish surfaces and markers of antibiotic resistance, illuminating future research directions for reducing agricultural sources of antibiotic resistance.
In working toward a comprehensive strategy to combat the spread of antibiotic resistance, potential farm-to-fork routes of dissemination are gaining attention. The effects of preharvest factors on the microbiota and corresponding antibiotic resistance indicators on the surfaces of produce commonly eaten raw is of special interest. Here, we conducted a controlled greenhouse study, using radishes as a root vegetable grown in direct contact with soil, and compared the effects of manure-based soil amendments, antibiotic use in the cattle from which the manure was sourced, composting of the manure, and soil texture, with chemical fertilizer only as a control. We noted significant effects of amendment type and soil texture on the composition of the microbiota and genes used as indicators of antibiotic resistance on radish surfaces. The findings take a step toward identifying agricultural practices that aid in reducing carriage of antibiotic resistance and corresponding risks to consumers.