The profile of antibiotic resistance genes in pig manure composting shaped by composting stage: Mesophilic-thermophilic and cooling-maturation stages. - Related Documents




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802101.0000The profile of antibiotic resistance genes in pig manure composting shaped by composting stage: Mesophilic-thermophilic and cooling-maturation stages. The variation of antibiotic resistance genes (ARGs) and influential factors in pig manure composting were investigated by conducting simulated composting tests using four different supplement materials (wheat straw, corn straw, poplar sawdust and spent mushroom). The results show that the relative abundance of total ARGs increased by 0.19-1.61 logs after composting, and tetX, sulI, sulII, dfrA1 and aadA were the major contributors. The variations of ARG profiles and bacterial communities throughout the composting were clearly divided into mesophilic-thermophilic and cooling-maturation stages in all tests, while different supplement materials did not exert a noticeable influence. Network analysis demonstrated the diversity of bacterial hosts for ARGs, the existence of multiple antibiotic resistant bacteria, and the weak correlations between ARGs and physicochemical factors in the composting piles. Of note, integron intI1 and Mycobacterium (a potential pathogen) were positively correlated with eight and four ARGs, respectively, that displayed increased abundance after composting.202032109697
809010.9998Swine Manure Composting With Compound Microbial Inoculants: Removal of Antibiotic Resistance Genes and Their Associations With Microbial Community. In this study, compound microbial inoculants, including three Bacillus strains and one Yeast strain, were inoculated into swine manure composting to explore the effects on antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), microbial community structure, and pathogenic bacteria. The results indicated that the abundances of the detected ARGs ranged from 3.6 × 10(3) to 1.13 × 10(8) copies/g. The ARGs with the highest abundance was sul2, and the lowest was blaCTX. Composting removes most of the ARGs and MGEs by 22.8-99.7%. These ARGs were significantly reduced during the thermophilic phase of compost. The removal rate of ARGs at the different layers of compost pile was different as follows: middle layer > upper layer > lower layer. But some ARGs proliferated significantly in the maturation phase of compost, especially the sulfonamide resistance genes. Compound microbial inoculants increased the temperature of compost, accelerated water loss, nitrogen fixation, and increased the removal rate of β-lactamase resistance genes, the transposon gene tn916 and part of tetracycline resistance genes by 3.7-23.8% in compost. Compound microbial inoculants changed the community structure and increased the Bacillus abundance in the thermophilic phase of compost. And it was helpful for removing pathogens during composting. The addition of compound microbial inoculants causes the decrease of Firmicutes and the increase of Bacteroidetes, which may be related to the removal and proliferation of ARGs.202033250880
802520.9998Effect of temperature on sulfonamide antibiotics degradation, and on antibiotic resistance determinants and hosts in animal manures. Animal manure is a main reservoir of antibiotic residues and antibiotic resistance. Here, the effect of temperature on sulfonamide antibiotics (SAs), sulfonamide-resistant (SR) genes/bacteria was investigated by aerobically incubating swine and chicken manures at different temperatures. In swine manure, the SAs concentration declined with increasing temperature, with a minimum at 60°C. In chicken manure, the greatest degradation of SAs was noted at 30°C. The reduction of relative abundance of antibiotic resistance genes (ARGs) and sul-positive hosts in swine manure was more pronounced during thermophilic than mesospheric incubation; neither temperature conditions effectively reduced these parameters in chicken manure. The relationship between the residual levels/distribution profiles of SAs, ARGs (sul1, sul2 and intI1), cultivable SR bacteria and sul-positive hosts was further established. The antibiotic residual profile, rather than antibiotic concentration, acted as an important factor in the prevalence of ARGs and sul-positive hosts in manure. Corynebacterium and Leucobacter from the phylum Actinobacteria tend to be main carriers of sul1 and intI1; the relative abundance of sul2 was significantly correlated with the relative abundance of cultivable SR bacteria. Overall, differences in resistant bacterial communities also constitute a dominant factor affecting ARG variation. This study contributes to management options for reducing the pollution of antibiotics and antibiotic resistance within manure.201728711002
810030.9998Composting temperature directly affects the removal of antibiotic resistance genes and mobile genetic elements in livestock manure. The high antibiotic resistance gene (ARGs) contents in livestock manure pose a potential risk to environment and human health. The heap composting with an ambient temperature and thermophilic composting are two methods for converting livestock manure into fertilizer. This study investigated the variations in ARGs and mobile genetic elements (MGEs) and revealed potential mechanisms for ARGs removal using the two composting methods. The ARGs abundance were enriched by 44-fold in heap composting, among them, the macrolide-resistance genes increased significantly. On the contrary, the ARGs were removed by 92% in thermophilic composting, among them, tetracycline-resistance genes decreased by 97%. The bacterial hosts of ARGs were associated with the variations of ARGs and MGEs. The tetO was correlated with the most diverse bacteria in heap composting, and Bacteroidetes was the major host bacteria. While tetT was correlated with the most diverse bacteria in thermophilic composting, and Proteobacteria was the major host bacteria. Structural equation models showed that the enrichment of ARGs in heap composting was mainly correlated with bacterial communities, whereas, the removal of ARGs in thermophilic composting was directly affect by MGEs. Composting temperature directly affected the variations in ARGs. Higher and lower temperatures significantly decreased and increased, respectively, ARGs and MGEs abundance levels.202235306090
809140.9998Changes in antibiotic resistance genes and mobile genetic elements during cattle manure composting after inoculation with Bacillus subtilis. This study explored the effects of Bacillus subtilis at four levels (0, 0.5%, 1%, and 2% w/w compost) on the variations in ARGs, mobile genetic elements (MGEs), and the bacterial community during composting. The composting process had a greater impact on ARGs than Bacillus subtilis. The main ARG detected was sul1. The addition of Bacillus subtilis at 0.5% reduced the relative abundances of ARGs, MGEs, and human pathogenic bacteria (by 2-3 logs) in the mature products. Network and redundancy analyses suggested that intI1, Firmicutes, and pH were mainly responsible for the changes in ARGs, thus controlling these factors might help to inhibit the spread of ARGs.201931442833
802250.9998Enrichment of antibiotic resistance genes after sheep manure aerobic heap composting. In this study, physio-chemical properties, 45 antibiotics, 6 heavy metals, 42 antibiotic resistance genes (ARGs), 3 mobile genetic elements, and the bacterial community structure were investigated to analyze the fate of ARGs during sheep manure aerobic heap composting. Results showed that sheep manure heap composting could produce mature compost. The degradation processes reduced the total antibiotics content by 85%. The abundance of ARGs and mobile genetic elements (MGEs) were enriched 9-fold, with the major increases to sul and tet genes (sulI, sulII, tetQ, and tetX). Tetracycline and sulfonamide resistance genes were the most abundant ARGs after composting (more than 88% of all genes). The genes tetA, tetX and sulI were related to the most diverse bacteria that were most able to proliferate during heap composting. Therefore, sulI and tetX are the major ARGs to be controlled, and Actinobacteria and Bacteroidetes may be the major host bacteria.202133429314
809660.9998Effects of biochar on reducing the abundance of oxytetracycline, antibiotic resistance genes, and human pathogenic bacteria in soil and lettuce. Antibiotics and antibiotic resistance genes (ARGs) in soil can affect human health via the food chain. Biochar is a soil amendment but its impacts on ARGs and the microbial communities associated with soil and vegetables are unclear. Therefore, we established three lettuce pot culture experiments, i.e., O300: 300 mg/kg oxytetracycline (OTC), BO300: 300 mg/kg OTC + 2% biochar, and a control without OTC or biochar. We found that under BO300, the relative abundances of ARGs were reduced by 51.8%, 43.4%, and 44.1% in lettuce leaves, roots, and soil, respectively, compared with O300. intI1 was highly abundant in soil and lettuce, and it co-occurred with some ARGs (tetW, ermF, and sul1). Redundancy analysis and network analysis indicated that the bacterial community succession was the main mechanism that affected the variations in ARGs and intI1. The reduction of Firmicutes due to the biochar treatment of soil and lettuce was the main factor responsible for the removal of tetracycline resistance genes in leaves. Biochar application led to the disappearance of human pathogenic bacteria (HPB), which was significantly correlated with the abundances of ermF and ermX. In summary, biochar is an effective farmland amendment for reducing the abundances of antibiotics, ARGs, and HPB in order to ensure the safety of vegetables and protect human health.201728284554
809470.9998Additive quality influences the reservoir of antibiotic resistance genes during chicken manure composting. Aerobic composting is commonly used to dispose livestock manure and is an efficient way to reduce antibiotic resistance genes (ARGs). Here, the effects of different quality substrates on the fate of ARGs were assessed during manure composting. Results showed that the total relative abundances of ARGs and intI1 in additive treatments were lower than that in control, and high quality treatment with low C/N ratio and lignin significantly decreased the relative abundance of tetW, ermB, ermC, sul1 and sul2 at the end of composting. Additionally, higher quality treatment reduced the relative abundances of some pathogens such as Actinomadura and Pusillimonas, and some thermotolerant degrading-related bacteria comprising Pseudogracilibacillus and Sinibacillus on day 42, probably owing to the change of composting properties in piles. Structural equation models (SEMs) further verified that the physiochemical properties of composting were the dominant contributor to the variations in ARGs and they could also indirectly impact ARGs by influencing bacterial community and the abundance of intI1. Overall, these findings indicated that additives with high quality reduced the reservoir of antibiotic resistance genes of livestock manure compost.202134139628
802080.9998Influence of zeolite and superphosphate as additives on antibiotic resistance genes and bacterial communities during factory-scale chicken manure composting. Factory-scale chicken manure composting added with zeolite (F), superphosphate (G), or zeolite and ferrous sulfate (FL) simultaneously, were evaluate for their effects on the behaviors of antibiotic resistance genes (ARGs) and bacterial communities. After composting, ARGs in manure decreased by 67.3% in the control, whereas the reductions were 86.5%, 68.6% and 72.2% in F, G and FL, respectively. ARGs encoding ribosomal protection proteins (tetO, tetB(P), and tetM) were reduced to a greater extent than tetG, tetL, sul1 and sul2. Bacteria pathogens were also effectively removed by composting. Network analysis showed that Firmicutes were the important potential host bacteria for ARGs. The bacterial communities and environmental factors, as well as the intI gene, contributed significantly to the variation of ARGs. The ARGs and integrons were reduced more when zeolite was added than when superphosphate was added; thus, it may be useful for reducing the risks of ARGs in chicken manure.201829772500
801490.9998Contributions of the microbial community and environmental variables to antibiotic resistance genes during co-composting with swine manure and cotton stalks. Understanding the main drivers that affect the spread of antibiotic resistance genes (ARGs) during the composting process is important for the removal of ARGs. In this study, three levels of tylosin (25, 50, and 75 mg kg(-1) on a dry weight basis) were added to swine manure plus a control, which was composted with cotton stalks. Each treatment was repeated in triplicate and the ARG profiles were determined with different levels of tylosin. The top 35 genera and ARGs profiles were clustered together based on the composting time. Combined composting parameters (temperature, pH, NH(4)(+)-N, NO(3)-N, and moisture content) accounted for 78.4% of the total variation in the changes in the potential host bacteria. In addition, the selected five composting parameters and six phyla (including 25 potential host bacterial genera) explained 46.9% and 30.7% of the variation in the ARG profiles according to redundancy analysis, respectively. The variations in ARGs during the composting process were mainly affected by the dynamics of potential host bacteria rather than integrons and the selective pressure due to bio-Cu and bio-Zn.201829990821
8087100.9998Effect of different biochars on antibiotic resistance genes and bacterial community during chicken manure composting. Rice straw biochar (RSB) and mushroom biochar (MB) were added to lab-scale chicken manure composting to evaluate their effects on the behaviors of antibiotic resistance genes (ARGs) and on total and bio-available heavy metals (Cu, Zn and As). The associated bacterial community was characterized by 16SrRNA high-throughput sequencing. The abundance of pathogenic bacteria was also calculated. At the end of the control composting experiment, the average removal rate of ARGs was 0.86 log units and the removal rate of pathogenic bacteria was 57.1%. MB addition resulted in a higher removal rate than that in the control composting experiment. However, RSB addition yielded opposite results, which may be due to the higher abundance of Erysipelotrichaceae, Lactobacillaceae, Family_XI_Incertae_Sedis (belonging to Firmicutes carrying and disseminating ARGs) and pathogenic bacteria carrying ARGs. Furthermore, the correlations between bio-available heavy metals and ARGs were more obvious than those between total heavy metals and ARGs.201626720134
8023110.9998Effects of macroporous adsorption resin on antibiotic resistance genes and the bacterial community during composting. Swine manure is considered a reservoir for antibiotic resistance genes (ARGs), which may enter the soil and then the food chain to endanger human health. This study investigated the effects of adding 0%, 5%, and 15% (w/w) macroporous adsorption resin (MAR) on ARGs and the bacterial community during composting. The results showed that the addition of MAR reduced the abundances of ARGs (14.14-99.44%) and mobile genetic elements (MGEs) (47.83-99.48%) after swine manure composting. Significant positive correlations were detected between ARGs and MGEs, and thus the variations in MGEs may have led to the changes in ARGs. Redundancy analysis showed that MGEs had stronger effects on ARGs than environmental factors and the bacterial community. Network analysis suggested that ARGs and MGEs co-existed in common host bacteria. In conclusion, the results showed that adding 5% MAR can reduce the risk of ARG transmission.202031634802
8097120.9998Fate of antibiotic resistance genes in farmland soil applied with three different fertilizers during the growth cycle of pakchoi and after harvesting. The increasing prevalence of antibiotic resistance genes (ARGs) in the soil environment poses a serious threat to crop safety and even public health. In this study, the fate of ARGs in the soil was investigated during the growth period of pakchoi and after harvesting with the application of different kinds of fertilizers. The result showed that increasing rate of soil ARGs during the growth period of pakchoi followed the order of composted manure > commercial fertilizer > mineral fertilizer. After harvesting, soil ARGs abundance treated with mineral fertilizer, commercial fertilizer or composted manure significantly increased by 0.63, 3.19 and 8.65 times (p < 0.05), respectively, compared with the non-fertilized soil. The ARGs abundance in the pakchoi treated with composted manure was significantly higher than that of treatments with mineral fertilizer and commercial organic fertilizer. These findings indicated the application of composted pig manure would significantly increase the pollution load of ARGs in farmland soil and plant, and also promote the proliferation of farmland ARGs. Principal component analysis suggested that bacterial communities might have a significant influence on ARGs changes during the growth period of pakchoi. Network analysis further indicated ARGs changes may be mainly related to their host bacteria (including Gammaproteobacteria, Flavobacteriia and Bacilli). The results provided a proper method and useful information on reducing transmission risk of ARGs and control the propagation of ARGs in agricultural activities.202133865023
8099130.9998The fate of antibiotic resistance genes during co-composting of swine manure with cauliflower and corn straw. Composting is not completely effective in reducing antibiotic resistance genes (ARGs) in animal manure. This work studied the effects of different treatment conditions on the fate of ARGs in composting swine manure with cauliflower and corn straw as bulking agents. The results showed that the addition of microbial agents or the ratio of corn stalks to cauliflower (1:12) could significantly decrease the absolute abundances of most ARGs (an average of 480 times) compared with the control treatment. Principal component analysis indicated that bacterial communities were significantly correlated with ARG abundance, suggesting that microbial communities have an impact on ARG variation during co-composting. Redundancy and Network analysis confirmed the changing patterns of individual ARGs (qnrS, bla(AmpC), bla(TEM-1)) were influenced by the selectivity of host bacteria (Pseudomonas, Klebsiella, and Halocella) and environmental variables (TN, NH(3)-N, TOC, and pH). These findings helped to optimize composting conditions, thereby reducing the risk of ARGs spread.202031891854
7246140.9998Tetracycline resistance genes are more prevalent in wet soils than in dry soils. This study aimed to reveal the effects of water content on the spread of tetracycline resistance genes (TRGs) in the soil. Amendments of four samples with different soil water contents, namely 16% (dry soil) and 25% (wet soil), and with or without pig manures (PM) were conducted under laboratory conditions. Quantitative polymerase chain reaction (q-PCR) results showed that the relative abundance of TRGs (tetB, tetC, tetM, tetO, tetT, and tetZ) in the wet soils was significantly higher than that in the dry soils whether under fertilization or non-fertilization conditions. Moreover, PM application enhanced the relative abundance of TRGs. The absolute copies of TRGs did not decline with the decrease in 16S rRNA genes in wet soils, implying that most TRGs were probably located in facultative anaerobic bacteria. However, cultivable tetracycline-resistant bacteria (TRB) in the wet soils were not in line with the q-PCR results, further indicating that aerobes might not account for the increases in the relative abundance of TRGs. Diversities of aerobic TRB were significantly higher in the wet soils than in the dry soils, especially on days 14 and 28. The patterns of community structures of aerobic TRB in the wet soils or dry soils containing PM were different from those in the dry soils. Together, this study showed that the variations in bacterial communities between the wet and dry soils, especially reflected in the diversity of aerobic TRB and/or community structure of facultative anaerobic TRB, might be an important reason behind the changes in the abundance of TRGs.201829573724
8026150.9997A comparison of antibiotics, antibiotic resistance genes, and bacterial community in broiler and layer manure following composting. 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.202133219508
7242160.9997Exploring the persistence and spreading of antibiotic resistance from manure to biocompost, soils and vegetables. The main avenue in which antibiotic resistance enters soils is through the application of livestock manure. However, whether antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) persist and spread to vegetables with the application of manure and manure products is still unclear. This study assessed seven kinds of cultured ARB, 221 ARGs subtypes and three transposon genes in the vegetable production chain (from manure to biocompost, soils and vegetables). Results showed that at least 80% of ARB, ARGs and transposon genes were removed after aerobic composting. However, aerobic composting did not reduce the diversity of ARGs in pig and chicken manure. A total of 19 ARGs subtypes still persisted during aerobic composting. Compared to the temperature-thermophilic stage, the number of bacteria resistant to erythromycin, the relative abundance of ARGs and IS613 increased 1.7-4.9 times at the temperature-decreasing stage. Direct application of biocompost introduced 11 ARGs subtypes to pakchoi, but these ARGs did not present in biocompost-amended soil. A transposon gene tnpA was also detected in the biocompost-amended soil, but surprisingly was found in the control vegetable. This demonstrated that the transposon gene is intrinsic in pakchoi. Bacterial community analysis and network analysis revealed that a specific genus Terrisporobacter carrying tetO, tetW ermB and tnpA persisted in the vegetable production chain, which may generate a potential risk in the following production. Our study illuminates the persistence and spreading of antibiotic resistance in the vegetable production chain which could help manage the ecological risks arising from antibiotic resistance in manure sources.201931229823
8013170.9997New insight into fates of sulfonamide and tetracycline resistance genes and resistant bacteria during anaerobic digestion of manure at thermophilic and mesophilic temperatures. This study investigated the variations in antibiotic (sulfonamide and tetracycline) resistance genes (ARGs) and resistant bacteria (ARB) during manure anaerobic digestion (AD) at 35 ℃ and 55 ℃, and discussed the mechanisms of variations in ARGs. The AD lasted for 60 days, five ARGs and intI1 each decreased in abundance after AD at the thermophilic temperature, while only half decreased at the mesophilic temperature. On days 10, 30, and 60, sulfonamide and tetracycline ARB were screened on selective media. During thermophilic AD, ARB numbers reduced by 4-log CFUs per gram dry manure, but only by approximately 1-log CFU at the mesophilic temperature. However, ARB composition analysis showed that at either temperature, no significant reduction in identified ARB species was observed. Furthermore, 72 ARB clones were randomly selected to detect the ARGs they harbored, and the results showed that each ARG was harbored by various hosts, and no definitive link existed between ARGs and bacterial species. In addition, by comparison with the identified host by culture method, the host prediction results based on the correlation analysis between ARGs and the bacterial community was proven to be unreliable. Overall, these findings indicated that relationships between ARB and ARGs were intricate.202031685315
8095180.9997Heavy metals, antibiotics and nutrients affect the bacterial community and resistance genes in chicken manure composting and fertilized soil. Succession of bacterial communities involved in the composting process of chicken manure, including first composting (FC), second composting (SC) and fertilizer product (Pd) and fertilized soil (FS), and their associations with nutrients, heavy metals, antibiotics and antibiotic resistance genes (ARGs) were investigated. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla observed during composting. Overall, potential pathogenic bacteria decreased from 37.18% (FC) to 3.43% (Pd) and potential probiotic taxa increased from 5.77% (FC) to 7.12% (Pd). Concentrations of heavy metals increased after second composting (SC), however, no significant differences were observed between FS and CS groups. Alpha diversities of bacterial communities showed significant correlation with heavy metals and nutrients. All investigated antibiotics decreased significantly after the composting process. The certain antibiotics, heavy metals, or nutrients was significantly positive correlated with the abundance of ARGs, highlighting that they can directly or indirectly influence persistence of ARGs. Overall, results indicated that the composting process is effective for reducing potential pathogenic bacteria, antibiotics and ARGs. The application of compost lead to a decrease in pathogens and ARGs, as well as an increase in potentially beneficial taxa and nutrients in soil.202031868641
8098190.9997Elimination of antibiotic resistance genes and human pathogenic bacteria by earthworms during vermicomposting of dewatered sludge by metagenomic analysis. This study used a metagenomic approach to investigate the effects of earthworms on ARGs and HPB during the vermicomposting of dewatered sludge. Results showed that 139 types of ARGs were found in sludge vermicompost, affiliated to 30 classes. Compared with the control, the total abundance of ARGs in sludge vermicompost decreased by 41.5%. Moreover, the types and sequences of plasmids and integrons were also decreased by vermicomposting. Proteobacteria and Actinobacteria were the most dominant hosts of ARGs in sludge vermicompost. In addition, earthworms reduced the total HPB abundance and modified their diversity, thus leading to higher abundance of Enterobacteriaceae in sludge vermicompost. However, the sludge vermicompost was still ARG and HPB enriched, indicating a remaining environmental risk for agricultural purpose. The observed change of microbial community and the reduction of mobile genetic elements caused by earthworm activity are the main reasons for the alleviation of ARG pollution during vermicomposting.202031787516