Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and Resistomes

Abstract

Dairy cattle are routinely treated with antibiotics, and the resulting manure or composted manure is commonly used as a soil amendment for crop production, raising questions regarding the potential for antibiotic resistance to propagate from “farm to fork.” The objective of this study was to compare the microbiota and “resistomes” (i.e., carriage of antibiotic resistance genes [ARGs]) associated with lettuce leaf and radish taproot surfaces grown in different soils amended with dairy manure, compost, or chemical fertilizer only (control). Manure was collected from antibiotic-free dairy cattle (DC) or antibiotic-treated dairy cattle (DA), with a portion composted for parallel comparison. Amendments were applied to loamy sand or silty clay loam, and lettuce and radishes were cultivated to maturity in a greenhouse. Metagenomes were profiled via shotgun Illumina sequencing. Radishes carried a distinct ARG composition compared to that of lettuce, with greater relative abundance of total ARGs. Taxonomic species richness was also greater for radishes by 1.5-fold. The resistomes of lettuce grown with DC compost were distinct from those grown with DA compost, DC manure, or fertilizer only. Further, compost applied to loamy sand resulted in twofold-greater relative abundance of total ARGs on lettuce than when applied to silty clay loam. The resistomes of radishes grown with biological amendments were distinct from the corresponding fertilizer controls, but effects of composting or antibiotic use were not measureable. Cultivation in loamy sand resulted in higher species richness for both lettuce and radishes than when grown in silty clay loam by 2.2-fold and 1.2-fold, respectively, when amended with compost. IMPORTANCE A controlled, integrated, and replicated greenhouse study, along with comprehensive metagenomic analysis, revealed that multiple preharvest factors, including antibiotic use during manure collection, composting, biological soil amendment, and soil type, influence vegetable-borne resistomes. Here, radishes, a root vegetable, carried a greater load of ARGs and species richness than lettuce, a leafy vegetable. However, the lettuce resistome was more noticeably influenced by upstream antibiotic use and composting. Network analysis indicated that cooccurring ARGs and mobile genetic elements were almost exclusively associated with conditions receiving raw manure amendments, suggesting that composting could alleviate the mobility of manure-derived resistance traits. Effects of preharvest factors on associated microbiota and resistomes of vegetables eaten raw are worthy of further examination in terms of potential influence on human microbiomes and spread of antibiotic resistance. This research takes a step toward identifying on-farm management practices that can help mitigate the spread of agricultural sources of antibiotic resistance.

Dose effect of Zn and Cu in sludge-amended soils on vegetable uptake of trace elements, antibiotics, and antibiotic resistance genes: Human health implications

“…Radish may pose a higher ARG risk, except in the case of bla TEM . This finding is consistent with prior studies showing radishes had a greater load of ARGs than lettuce (Guron et al, 2019;Tien et al, 2017). Both growth time and vegetable species could affect the occurrence of ARGs in vegetable tissues.…”

Antibiotics and Antibiotic Resistance Genes in Animal Manure – Consequences of Its Application in Agriculture

“…The soil may well represent the main source of ARGs to the plant, as indicted by the large degree of overlap between ARGs in the plant microbiome and those in the soil resistome ( Yang et al, 2018 ). ARB associated with soil and manure may enter the plant microbiome by colonizing the roots, which are in direct contact with soil, or the aboveground parts, potentially through air particulates or the motility of root endophytes ( Zhu et al, 2017 ; Guron et al, 2019 ). In addition, plants have been found to take up antibiotic residues from manure-amended soil; this may exert long-term pressure in the plant, facilitating the acquisition of drug resistance and its spread across the plant resistome ( Chen et al, 2019a ).…”

Manure Application Did Not Enrich Antibiotic Resistance Genes in Root Endophytic Bacterial Microbiota of Cherry Radish Plants

“…ARGs in the plant microbiome considerably overlapped the soil resistome, indicating that soil might be a major origin of plant-associated resistome (19). Soil-and manure-associated antibiotic-resistant bacteria may find their way to the plant microbiome through colonization on vegetable roots, which are in direct contact with soil, or on aboveground parts of vegetables potentially through air particulates or motility of root endophytes (20,21). Moreover, plants can take up antibiotic residues from manure-amended soil, which may impose long-term selective pressure on the emergence and spread of the plant resistome (22).…”