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

Abstract

Growing evidence suggests that livestock manure used as organic fertilizer in agriculture may lead to the potential propagation of antibiotic resistance genes (ARGs) from “farm to fork.” However, little is known about the impacts of manure fertilization on the incidence of ARGs in the plant-associated microbiomes (including rhizosphere, endosphere, and phyllosphere), which hampers our ability to assess the dissemination of antibiotic resistance in the soil-plant system. Here, we constructed a pot experiment to explore the effects of poultry and cattle manure applications on the shifts in the resistome in the plant microbiome of harvested cherry radish. A total of 144 ARGs conferring resistance to eight major classes of antibiotics were detected among all the samples. Rhizosphere and phyllosphere microbiomes harbored significantly higher diversity and abundance of ARGs than did root endophytic microbiomes of cherry radish. Manure application significantly increased the abundance of ARGs in the rhizosphere and phyllosphere but not in the endophytes of the root, which is the edible part of cherry radish. Soil and plant microbiomes changed dramatically after manure applications and clustered separately according to different sample types and treatments. Structural equation modeling revealed that bacterial abundance was the most important factor modulating the distribution patterns of soil and plant resistomes after accounting for multiple drivers. Taken together, we provide evidence that enrichment of the resistome in the rhizosphere and phyllosphere of cherry radish is more obvious than with the endosphere after manure application, suggesting that manure amendment might not enhance the dissemination of ARGs into the root of vegetables in the pot experiment. IMPORTANCE Our study provides important evidence that manure application increased the occurrence of ARGs in the rhizosphere and phyllosphere of cherry radish, compared with that in the endophytic bacterial microbiota of root, which is the edible part of cherry radish. Our findings suggest that although manure amendment is a significant route of ARGs entering agricultural soils, these manure-derived ARGs may be at low risk of migrating into the endophytes of root vegetables.

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

“…The abundance of MGE was found to be positively correlated with individual ARGs coding for resistance to aminoglycoside, fluoroquinolone, quinolone, florfenicol-chloramphenicol-amphenicol, sulfonamide and tetracycline, and MDR determinants including MLSB. The results suggest that manure application significantly increased the abundance of ARGs in the rhizosphere and phyllosphere but not in the endophytes of the root, i.e., the edible part ( Zhang et al, 2020 ).…”

“…A considerable number of studies have reported the presence of significant numbers of ARB on consumer-ready vegetables, such as lettuce and spinach leaves ( Abriouel et al, 2008 ; Bezanson et al, 2008 ). Zhang et al (2020) constructed a pot experiment to determine the effect of poultry and cattle manure application on resistome shifts in the plant microbiome of harvested cherry radish. A total of 144 ARGs conferring resistance to eight major classes of antibiotics were detected across all samples.…”

“…However, although the ARB involved in the transfer colonize as root endophytes, they demonstrate very little transfer to plant tissues; this suggests that the risk of transmitting external ARGs to the food chain is low. Therefore, root vegetables like cherry radish might be at a lower risk of ARGs contamination than leafy vegetables like lettuce ( Zhang et al, 2019 , 2020 ).…”

Effect of Chicken Manure-Based Fertiliser on Bacterial Communities and Diversity of Tomato Endosphere Microbiota

“…A pot experiment was performed in flower pots with 25 cm in height and 15 cm in diameter. The first treatment contained a total of 1.5 kg of soil with chicken manure (1 kg soil + 0.5 kg chicken manure) as a treated sample (CMR), and the other contained 1.5 kg soil without chicken manure as a control (OR) (Zhang et al 2020b). Each treatment was performed with three replicates.…”

Compostagem de resíduos agropecuários: seguridade ambiental, ciclagem de nutrientes e eficácia agronômica

“…Estudos mostram que a disseminação de GRAs ocorre de forma intensa na rizosfera e filosfera das plantas, mas ocorre de forma mais fraca na comunidade endofítica das plantas (ZHANG et al, 2020e).…”