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Background: Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts. Results: In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86–99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting. Conclusions: Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs. [ABSTRACT FROM AUTHOR]

Many TGA transcription factors participate in immune responses in the SA‐mediated signaling pathway in Arabidopsis. This study identified a transcription factor OsTGAL1, which is induced upon infection by Xoo. Overexpression of OsTGAL1 increased the susceptibility of rice to Xoo. Plants overexpressing OsTGAL1 could affect the expression of many SA signaling‐related genes. OsTGAL1 was able to interact with the promoter of OsSGT1, which encodes a key enzyme for SA metabolism. The transcript of OsSGT1 was induced by Xoo and this responsive expression was further increased in plants overexpressing OsTGAL1. OsSGT1 knockout lines had enhanced resistance to Xoo, and knocking out OsSGT1 in plants overexpressing OsTGAL1 blocked the susceptibility caused by OsTGAL1. Altered expression levels of several OsPRs in all the transgenic plants demonstrated that SA‐mediated signaling had been affected. Furthermore, we identified an oxidoreductase of CC‐type glutaredoxin, OsGRX17, which interacted with OsTGAL1. OsGRX17 reduced the regulation of OsTGAL1 on OsSGT1, and this may be due to its redox modulation. Thus, our results demonstrate that OsTGAL1 negatively regulates resistance to Xoo by its effects on SA metabolism via the activation of OsSGT1, which provides valuable targets for plant breeders in developing new cultivars that are resistant to Xoo. Summary statement: OsTGAL1 negatively regulates the resistance of rice to Xoo by activating the transcription of OsSGT1. OsGRX17 interacts with OsTGAL1 to reduces the regulation of OsTGAL1 on OsSGT1. This study provides valuable targets for breeders in developing new cultivars that are resistant to Xoo. [ABSTRACT FROM AUTHOR]

As the number of people in the world increases, people's demand for food becomes greater. In order to reduce reliance on pesticides that maintain crop yields, plant disease resistance is gaining increasing attention. As a near-isogenic line with high resistance to bacterial blight, transcriptional regulation of Y73 on disease resistance has aroused our great interest. To comprehend how Y73 plants defend themselves against bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) and how their disease resistance is executed at the transcriptional level, a time series transcriptional profiles of the local leaves and systemic leaves of Y73 and its recurrent parent Dalixiang (DLX) were obtained after inoculation with Xoo strain PXO341. Transcriptome data showed that the differences between incompatible (Y73 to Xoo) and compatible (DLX to Xoo) interactions were greater in the systemic leaves than in the inoculated ones. In contrast to compatible interactions, incompatible interactions were able to generate a sustained systemic acquired resistance (SAR) response, groups of genes like PR3 (chitinase 5) and PR1 had been up-regulated in systemic leaves. These results provide evidence that a robust and sustained SAR response in Y73 plays an important role in its broad-spectrum and high resistance to bacterial blight. [ABSTRACT FROM AUTHOR]

Animal manure is an important source of antibiotics and antibiotic resistance genes (ARGs) in the environment. However, the difference of antibiotic residues and ARG profiles in layer and broiler manure as well as their compost remains unexplored. In this study, we investigated the profiles of twelve antibiotics, seventeen ARGs, and class 1 integrase gene (intI1) in layer and broiler manure, and the corresponding compost at large-scale. Compared with layer manure, broiler manure exhibited approximately six times more residual tetracyclines, especially chlortetracycline. The relative abundances of qnrS and ermA genes in broiler manure were significantly higher than those in layer manure. The concentration of tetracyclines not only had a significantly positive correlation with tetracycline resistance genes (tetA and tetC) but was also positively correlated with quinolone resistance (qepA, qnrB, and qnrS) and macrolide resistance (ermA and ermT). Most ARGs in manure were reduced after composting. However, the relative abundance of sulfonamide resistance gene sul1 increased up to 2.41% after composting, which was significantly higher than that of broiler (0.41%) and layer (0.62%) manure. The associated bacterial community was characterized by high-throughput 16S rRNA gene sequencing. The relative abundances of thermophilic bacteria had significant positive correlations with the abundance of sul1 in compost. The composting has a significant impact on the ARG-associated gut microbes in poultry manure. Variation partitioning analysis indicated that the change of bacterial community compositions and antibiotics contributed partially to the shift in ARG profiles. The results indicate that at industry-scale production broiler manure had more antibiotics and ARGs than layer manure did, and composting decreased most ARG abundances in poultry manure except for sulfonamide resistance genes. [ABSTRACT FROM AUTHOR]

Pot experiments were set up to simulate the soil contamination by three initial concentrations of sulfamethoxazole (SMX) (S1, 100 mg/kg; S2, 200 mg/kg; S3, 300 mg/kg). The content of SMX in soil and its accumulation in lettuce were analysed. Additionally, the effects of SMX on soil microorganisms and antibiotic resistance genes were studied by Illumina high-throughput sequencing and droplet digital polymerase chain reaction (ddPCR). The results demonstrated that the SMX content in soil reduced by 97%, 86% and 75% in the S1, S2 and S3 treatment groups after 120 days, respectively. The accumulated SMX in lettuce was positively correlated with the initial concentration of SMX in soil. SMX contamination significantly reduced the bacterial diversity and altered the composition of bacterial and fungal communities in soil. The dominant bacterial and fungal genera in the SMX-contaminated soil were obviously different from those in the control soil. The relative abundance of sul1 (sulfonamide resistance gene) remarkably increased in the SMX-contaminated soil, while that of other ARGs, such as sul2 and tetracycline and quinolone resistance genes, showed no significant change. [ABSTRACT FROM AUTHOR]

The amendment of organic fertilizer derived from livestock manure or biosolids is a significant driver of increasing antibiotic resistance in agricultural soils; however, it remains unclear whether increasing organic fertilizer application rates consistently enhances soil antibiotic resistance levels. Herein, we collected soils with long-term amendment with three types of organic fertilizers at four application rates (15, 30, 45, and 60 t/ha/y) and found that the higher the fertilization rate, the higher the antibiotic resistance gene (ARG) abundance. However, when the fertilization rate exceeded 45 t/ha/y, the ARG abundance ceased to significantly increase. Moreover, the soil ARG abundance was positively correlated with total nitrogen (TN) content and bacterial abundance, especially Firmicutes, and negatively affected by pH and bacterial diversity. Soil TN/bacterial abundance and pH/bacterial diversity reached maximum and minimum values at the 45 t/ha/y fertilization rate, respectively. Meanwhile, at this fertilization rate, Firmicutes enrichment peaked. Therefore, an organic fertilization rate of 45 t/ha/y appeared to represent the threshold for soil antibiotic resistance in this study. The underlying mechanism for this threshold was closely related to soil TN, pH, bacterial abundance, and diversity. Taken together, the findings of this study advance the current understanding regarding the soil resistome under different fertilization rates, while also providing novel insights into organic fertilizer management in agricultural practices. [Display omitted] • Organic fertilization rate of 45 t/ha/y is soil antibiotic resistance threshold. • Resistance threshold is related to soil TN, pH, bacterial abundance/diversity. • Soil ARG abundance positively correlates with TN and bacterial abundance. • Soil ARG abundance negatively correlates with pH and bacterial diversity. • Firmicutes abundance peaks at a 45 t/ha/y fertilization rate. [ABSTRACT FROM AUTHOR]

Animal manure is an important raw material for Agaricus bisporus production; however, it is also a reservoir for antibiotic residues, antibiotic resistance genes (ARGs), and antibiotic-resistant bacteria. Little is known about the influence of the commercial cultivation of A. bisporus on the dynamics of ARGs and the underlying mechanisms that cause their variations. In this study, we investigated the fate of 285 ARGs, 10 mobile genetic elements, and seven major categories of antibiotic residues in substrate and mushroom samples at different production phases. The results showed that commercial substrate preparation, particularly the pasteurization phase, was highly efficient in removing ARGs from the substrate. We further found that mycelium proliferation of A. bisporus contributed significantly to the removal of ARGs from the substrate and casing soil. The bacterial community is the key driver of changes in ARGs during the commercial cultivation of A. bisporus , which explained 46.67% of the variation in ARGs. Our results indicate that, despite the addition of animal manure, the risk of ARG dissemination to fruiting bodies and the environment is low. We propose that bioremediation by specific edible fungi might be a novel and promising method for scavenging antimicrobial resistance contamination from soil environment. [Display omitted] • Effects of A. bisporus production on ARGs and bacterial communities were clarified. • Pasteurization was highly efficient in removing ARGs from the substrate. • Proliferation of A. bisporus mycelia effectively eliminated ARGs and MGEs. • Kurthia , Pseudoxanthomonas, and Psychrobacter may be main potential hosts for ARGs. • Edible fungi may help scavenge antimicrobial resistance contamination from soil. [ABSTRACT FROM AUTHOR]

Antibiotic fermentation residue is a key issue for the sustainable operation of pharmaceutical companies, and its improper disposal may cause antibiotic resistance transfer in the environment. However, little is known about the resource recycling strategy of this pharmaceutical waste. Herein, we used hydrothermal spray-dried (HT+SD) and multi-plate dryer (MD) methods to produce bio-organic fertilizers and applied them to an internal recycling model of a field trial. The concentrations of antibiotics (penicillin, cephalosporin, and erythromycin) in the bio-fertilizer, wastewater, and exhaust gas were in the range of 0.002–0.68 mg/kg, ≤ 0.35 ng/mL, and 0.03–0.89 ng/mL, respectively. The organic matter and total nitrogen, phosphorus, and potassium contents were approximately 80% and 10%, respectively. The soil bacterial community was similar among the fertilizer treatments in the same crop cultivation. A total of 233 antibiotic resistance genes (ARGs) and 43 mobile genetic elements (MGEs) were detected, including seven Rank I ARGs and five Rank II ARGs. Random forest analysis showed that gene acc(3)-Via and plasmid trb-C were biomarkers, for which the resistance and the transfer mechanisms were antibiotic inactivation and conjugation, respectively. The results imply that AFR recycling disposal mode is a promising prospect for pharmaceutical waste management. [Display omitted] • Hydrothermal spray-dried and multi-plate dryer can effectively reduce antibiotics. • The concentrations of antibiotics in the bio-fertilizer were 0.002 – 0.68 mg/kg. • Crop species affect the soil microbial community structure. • 233 antibiotic resistance genes and 43 mobile genetic elements were detected. • ARG acc(3)-Via and the MGE trb-C were biomarkers. [ABSTRACT FROM AUTHOR]

Antibiotic resistance genes (ARGs) in the endophytes of vegetables represent a potential route of human exposure to the soil resistome. However, the effect of vegetable species on the endophytic ARG profiles is unclear, hampering our understanding of how ARGs migrate into the soil-vegetable system and their potential health risks. Here, we planted four leafy vegetables (cilantro, endive, lettuce, and pak choi), which are commonly eaten raw, and analyzed the resistomes and microbiomes in three sample types (rhizosphere soil, root, and leaf endophytes). A total of 150 ARG subtypes were detected using high-throughput quantitative PCR. Vegetable species had a significant effect on ARG diversity and abundance, and pak choi accumulated more ARGs in its associated microbiome than the other three vegetables. The bacterial community was the primary factor shaping ARG profiles and was significantly correlated with ARG subtypes. We identified aadE , tet(34) , and vanSB as shared ARGs among leaves of the four vegetables; the bacterial families correlated with tet(34) and vanSB were also shared across the vegetables and belonged to Proteobacteria. This study deepens our understanding of how endophytic ARG profiles vary among different vegetables and highlights the potential health risk associated with consuming these vegetables raw. [Display omitted] • Antibiotic resistance genes (ARGs) are examined in four vegetable microbiomes. • Vegetable species significantly affect ARG diversity and abundance. • Lettuce and pak choi leaves harbor more abundant ARGs than cilantro or endive. • The ARGs, aadE , tet(34) , and vanSB , are shared across all four vegetable leaves. • Burkholderiaceae is markedly correlated with ARGs, tet(34) and vanSB. [ABSTRACT FROM AUTHOR]

Antibiotic accumulation in soil and plants is an escalating problem in agriculture and is receiving increasing attention. However, the effect of plant species on the fate of different types of antibiotics in a soil-vegetable system and soil resistome has not been adequately explored. To this end, greenhouse pot experiments were conducted to simulate contamination by ciprofloxacin (CIP), oxytetracycline (OTC), sulfamethoxazole (SMZ), and tylosin (TY) at 1 mg kg−1 in the soils in which cabbage, endive, and spinach were grown. We investigated antibiotic persistence in soils and accumulation in vegetables (i.e., spinach, endive, and cabbage), microbial community profiles, and the abundance of 17 antibiotic resistance genes (ARGs) in contaminated soils. After 40 days, the residues of CIP and OTC in soil and their accumulation in vegetables were significantly higher than those of SMZ and TY. Of all vegetables, spinach had the highest antibiotic accumulation. Further, antibiotic contamination had no significant effect on soil microbial abundance; however, soil microbial diversity significantly decreased in soils amended with TY. The antibiotic type more significantly affected microbial composition than the kind of vegetable species. The relative abundances of some ARGs significantly increased in contaminated soils. Particularly, in endive soil, quinolone-associated cmlA, cmlA2, and qnrS1 increased with CIP contamination, OTC contamination increased tetG2 and otrA , SMZ increased sul1 , and TY increased macrolide - related carB and msrc-01 relative abundance. However, some individual ARGs declined upon antibiotic contamination. Our results indicated that antibiotic type and vegetable species jointly shape the profiles of soil microorganisms and ARGs. Image 1 • CIP and OTC more significantly contaminated soil and vegetables than SMZ and TY. • CIP, OTC, SMZ, and TY did not significantly influence soil microbial abundance. • Antibiotic type influenced microbial community more than vegetable species. • There was no obvious correlation between ARGs and corresponding antibiotics. • Vegetable species significantly affected soil ARGs abundance. [ABSTRACT FROM AUTHOR]