Behavior of antibiotic resistance genes during co-composting of swine manure with Chinese medicinal herbal residues

Deciphering and predicting changes in antibiotic resistance genes during pig manure aerobic composting via machine learning model

Livestock manure is one of the most important pools of antibiotic resistance genes (ARGs) in the environment. Aerobic composting can effectively reduce the spread of antibiotic resistance risk in livestock manure. Understanding the effect of aerobic composting process parameters on manure-sourced ARGs is important to control their spreading risk. In this study, the effects of process parameters on ARGs during aerobic composting of pig manure were explored through data mining based on 191 valid data collected from literature. Machine learning (ML) models (XGBoost and Random Forest) were utilized to predict the rate of ARGs changes during pig manure composting. The model evaluation index of the XGBoost model (R2 = 0.651) was higher than that of the Random Forest (R2 = 0.490), indicating that XGBoost had better prediction performance. Feature importance was further calculated for the XGBoost model, and the XGBoost black box model was interpreted by Shapley additive explanations analysis. Results indicated that the influencing factors on the ARGs variation in pig manure were sequentially divided into thermophilic period, total composting period, composting real time, and thermophilic stage average temperature. The findings gave an insight into the application of ML models to predict and decipher the ARG changes during manure composting and provided suggestions for better composting manipulation and optimization of process parameters.

Typical antibiotic resistance genes and their association with driving factors in the coastal areas of Yangtze River Estuary

The massive use of antibiotics has led to the escalation of microbial resistance in aquatic environment, resulting in an increasing concern regarding antibiotic resistance genes (ARGs), posing a serious threat to ecological safety and human health. In this study, surface water samples were collected at eight sampling sites along the Yangtze River Estuary. The seasonal and spatial distribution patterns of 10 antibiotics and target genes in two major classes (sulfonamides and tetracyclines) were analyzed. The findings indicated a high prevalence of sulfonamide and tetracycline resistance genes along the Yangtze River Estuary. Kruskal-Wallis analysis revealed significant seasonal variations in the abundance of all target genes. The accumulation of antibiotic resistance genes in the coastal area of the Yangtze River Estuary can be attributed to the influence of urban instream runoff and the discharge of effluents from wastewater treatment plants. ANISOM analysis indicated significant seasonal differences in the microbial community structure. VPA showed that environmental factors contribute the most to ARG variation. PLS-PM demonstrate that environmental factors and microbial communities pose direct effect to ARG variation. Analysis of driving factors influencing ARGs in this study may shed new insights into the mechanism of the maintenance and propagation of ARGs.

Effect of biochar on the fate of antibiotic resistant genes and integrons in compost amended agricultural soil

The persistence and transmission of emerging pollutants such as antibiotic resistance genes (ARGs) via mobile genetic elements (MGEs) have caused concern to scientific community. Composting practises are often adapted for the reduction of organic waste or to enhance fertility in agriculture soil but its continuous usage has posed a potential risk of increased abundance of ARGs in soil. Thus, the present study scrutinises the emerging risk of ARGs and MGEs in agriculture soil and its potential mitigation using biochar owing to its proven environmental sustainability and performance. After 30 days incubation, ARG distribution of SulI, SulII, dfrA1, dfrA12, tetA, flor, and ErmA was 50, 37.5, 37.5, 62.5, 42.11, 62.5, and 52.63% in control samples whereas it was 5, 15.78, 21.05, 15.79, 10.53, 21.05, and 31.58%, respectively, for biochar amended samples. Similarly, IntI1 and IntI2 in control and biochar amended samples were 18.75 and 6.25% and 10.53 and 5.26%, respectively. Principal component analysis (PCA) factor suggests that biochar amendment samples showed enhanced value for pH, organic matter, and organic carbon over control samples. Furthermore, Pearson's correlation analysis performed between detected ARGs and MGEs demonstrated the positive and significant correlation at p < 0.05 for both control and biochar amended samples.

Resource-Efficient Use of Residues from Medicinal and Aromatic Plants for Production of Secondary Plant Metabolites

Although people's interest in green and healthy plant-based products and natural active ingredients in the cosmetic, pharmaceutical, and food industries is steadily increasing, medicinal and aromatic plants (MAPs) represent a niche crop type.It is possible to increase cultivation and sales of MAPs, by utilizing plant components that are usually discarded. This chapter provides an overview of studies concerning material flows and methods used for sustainable production of valuable metabolites from MAPs between 2018 and 2023. Additionally, it describes new developments and strategies for extraction and isolation, as well as innovative applications. In order to use these valuable resources almost completely, a systematic recycling of the plant material is recommended. This would be a profitable way to increase sustainability in the cultivation and usage of MAPs and provide new opportunities for extraction in plant science.

Biochar induces different responses of intracellular and extracellular antibiotic resistance genes and suppresses horizontal transfer during lincomycin fermentation dregs composting

This study aims to indicate the influence of biochar on extracellular and intracellular ARGs (e/iARGs) variation and proliferation during lincomycin fermentation dregs (LFDs) compost. Biochar addition made iARGs keep reducing but eARGs increase to the maximum at the middle thermophilic phase and reduce at the end of the compost. Compared to control 3.15-log and 5.42-log reduction of iARGs and eARGs were observed, respectively. Biochar addition, bacterial community, and MGEs were the major contributors to iARGs and eARGs removal, with the contribution percentages of 38.4%, 31.0%, 23.7%, and 27.2%, 29.1%, and 34.9%, respectively. Moreover, biochar significantly inhibited eARGs transformation and RP4 plasmid conjugative transfer among E. coli DH5α and Pseudomonas aeruginosa HLS-6. The underlying mechanism involved in broken cell membranes of bacteria, and altered expression of oxidative stress genes and save our souls (SOS) response-related genes. The results indicated that biochar addition in composting could limit the dissemination of ARGs.

Fates of extracellular and intracellular antibiotic resistance genes in activated sludge and plastisphere under sulfadiazine pressure

Microplastics, antibiotics, and antibiotic resistance genes (ARGs) represent prominent emerging contaminants that can potentially hinder the efficacy of biological wastewater treatment and pose health risks. Plastisphere as a distinct ecological niche for microorganisms, acts as a repository for ARGs and potential pathogenic bacteria. Nonetheless, the spread pattern of extracellular ARGs (eARGs) and intracellular ARGs (iARGs) in plastisphere under antibiotic exposure was not yet known. This study aimed to investigate disparities in extracellular polymeric substances (EPS) production, extracellular and intracellular microbial community structures, as well as the transmission of eARGs and iARGs between activated sludge and plastisphere in an anaerobic/anoxic/oxic system under sulfadiazine (SDZ) exposure. SDZ was found to enhance EPS production in activated sludge and plastisphere. Interestingly, as SDZ removal efficiency increased, EPS content decreased in activated sludge and plastisphere collected from oxic zone, and continued to increase in plastisphere samples collected from anaerobic and anoxic zones. There were significant differences in microbial community structure between activated sludge and plastisphere, and the DNA fragments of potential pathogenic bacteria were detected in extracellular samples. SDZ exhibited a promoting effect on the propagation of eARGs, which were more abundant in the plastisphere than in activated sludge, thus heightening the risk of ARGs dissemination. Extracellular mobile genetic elements played a pivotal role in driving the spread of eARGs, while the microbial community induced the changes of iARGs. Potential pathogenic bacteria emerged as potential hosts for ARGs and mobile genetic elements within activated sludge and plastisphere, leading to more serious environmental threats.

Insights into antibiotic resistance gene abundances and regulatory mechanisms induced by ionic liquids during composting

This study investigated the regulatory mechanism of the evolution of antibiotic resistance genes (ARGs) during the composting process with sawdust and cow manure as raw materials using ionic liquids (ILs) pretreatment. The results showed that genes of MLS, chloramphenicol, tetracycline, beta - lactam as composting gradually decreased. From day0 to day3, MLS in control group (CK) and experimental group (T) decreased by 25.62% and 26.66%, respectively. Tetracycline decreased by 7.21% in CK and by 7.86% in T. Chloramphenicol decreased by 2.85% in CK and 3.34% in T. Beta-lactam decreased by 1.95% in Ck and by 3.69% in T. Mechanism studies have shown that ILs can effectively decompose extracellular polymeric substances (EPS) and enhance lactose dehydrogenase (LDH) release, resulting in ARGs release and elimination. Meanwhile, ILs pretreatment can inhibit growth of some ARGs hosts, especially Firmicutes, resulting in decreased ARGs. Moreover, metabolic pathways and related genes take part in ARGs transmission were down regulated, leading to decreased ARGs.

Degradation of sulfamethoxazole and antibiotic resistance genes from surface water in the photocatalyst-loading bionic ecosystems

The behavior and removal of sulfamethoxazole (SMX) and 3 typical corresponding antibiotic resistance genes (ARGs) including sul1, sul2, sul3, and 16S rDNA in surface water were investigated in the photocatalyst-loading bionic ecosystems (PCBEs). Synthesized composite photocatalyst g-C3N4/TiO2 showing higher catalytic activity than Fe/g-C3N4/TiO2 was selected in the PCBEs. Five PCBEs, i.e., A-the control (without bionic grass or photocatalyst), B-bionic grass loaded with 4.12 g/m2 g-C3N4/TiO2, C-bionic grass loaded with 8.25 g/m2 g-C3N4/TiO2, D-bionic grass loaded with 12.37 g/m2 g-C3N4/TiO2, and E-bionic grass loaded with 16.5 g/m2 g-C3N4/TiO2 were constructed and operated in a medium-scale running cyclical flume. SMX could be photolyzed efficiently by g-C3N4/TiO2 with an optimal unit load on the bionic grass of 12.37 g/m2. 3-amino-5-methylisooxazole and p-aminobenzene sulfonamide were selected as main intermediates through the analyses of SMX degradation mechanisms and pathways, and detected in the aqueous phase and bionic grass. The intermediates were higher in the underwater part of the bionic grass than the above-water part. The overall removal of SMX ranged from 31.7 % to 82.3 % in 5 PCBEs, and the removal of sul1and sul2 were 0.2 %- 62.9 % in the aqueous phase and 8.4 %-63.2 % in the sediment. PCBE D might be the best construction when SMX and ARGs' removal was considered comprehensively. Moreover, the microbial structures showed Proteobacteria as the most dominant bacterial species had a relative abundance of 22.2 %-26.6 % and 33.4 %-68.2 % in the aquatic phase and sediment respectively, illustrating that the removal of the antibiotic and ARGs was bound up with the variations of dominant bacteria in the ecosystems. The findings illustrated that ecosystems with bionic grass and photocatalysts could be a promising technology for the removal of typical antibiotics and ARGs from surface water.

The fates of antibiotic resistance genes and their association with cell membrane permeability in response to peroxydisulfate during composting

The aims of this study were to use metagenomics to reveal the fates of antibiotic resistance genes (ARGs) during composting under the regulation of peroxydisulfate and clarify the relationship between ARGs and cell membrane permeability. Results showed that peroxydisulfate increased cell membrane permeability by effectively regulating the expression of outer membrane protein and lipopolysaccharide related genes. Besides, it reduced polysaccharides and proteins in extracellular polymer substances by 36% and 58%, respectively, making it easier for intracellular ARGs (i-ARGs) to reach the extracellular environment, among which the absolute intracellular abundance of mphK, Erm(31), and tet(44) decreased to 1.2, 1.0, and 0.89 fold of the control, respectively. Finally, variation partitioning analysis showed that i-ARGs dominated the removal of ARGs. These results revealed that the removal of i-ARGs by activated peroxydisulfate was the key to the removal of ARGs and increased cell membrane permeability played a key role for peroxydisulfate to remove i-ARGs during composting.

Effects of magnesium-modified biochar on antibiotic resistance genes and microbial communities in chicken manure composting

Abatement of antibiotic resistance genes (ARGs) in livestock manure by composting has attracted attention. This study investigated the effect of adding magnesium-modified biochar (MBC) on ARGs and microbial communities in chicken manure composting. Twelve genes for tetracyclines, sulfonamides, and macrolides, and mobile genetic elements were measured in the compost pile. The results showed that after 45 days of the composting, the treatment groups of MBC had longer high temperature periods, significantly higher germination indices (GI) and lower phytotoxicity. There were four major dominant phyla (Firmicutes, Actinobacteriota, Proteobacteria, and Bacteroidota) in the compost. The abundance of Firmicutes decreased significantly during the compost cooling period; tetracycline resistance genes demonstrated an extremely significant positive correlation with Firmicutes, showing a trend of the same increase and decrease with composting time; tetT, tetO, tetM, tetW, ermB, and intI2 were reduced in the MBC group; the total abundance of resistance genes in the 2% MBC addition group was 0.67 times that of the control; Proteobacteria and Chloroflexi were also significantly lower than the other treatment groups. Most ARGs were significantly associated with mobile genetic elements (MGEs); MBC can reduce the spread and diffusion of ARGs by reducing the abundance of MGEs and inhibiting horizontal gene transfer (HGT).

Pig manure treatment strategies for mitigating the spread of antibiotic resistance

Due to the risk of pathogenic antibiotic-resistant bacteria and their antibiotic-resistance genes transfer from livestock feces to the soil and cultivated crops, it is imperative to find effective on-farm manure treatments to minimize that hazardous potential. An introduced worldwide policy of sustainable development, focus on ecological agricultural production, and the circular economy aimed at reducing the use of artificial fertilizers; therefore, such treatment methods should also maximize the fertilization value of animal manure. The two strategies for processing pig manure are proposed in this study-storage and composting. The present study examines the changes in the physicochemical properties of treated manure, in the microbiome, and in the resistome, compared to raw manure. This is the first such comprehensive analysis performed on the same batch of manure. Our results suggest that while none of the processes eliminates the environmental risk, composting results in a faster and more pronounced reduction of mobile genetic elements harboring antibiotic resistance genes, including those responsible for multi-drug resistance. Overall, the composting process can be an efficient strategy for mitigating the spread of antibiotic resistance in the environment and reducing the risk of its transfer to crops and the food chain while providing essential fertilizer ingredients.

Metagenomic insights into dietary remodeling of gut microbiota and antibiotic resistome in meat rabbits

The gut microbiota is a repository of antibiotic resistance genes (ARGs), which may affect the health of humans and animals. The intestinal flora is affected by many factors but it is unclear how the intestinal microflora and antibiotic resistome in rabbits might change under dietary intervention. Feeding with lettuce led to the amplification and transfer of exogenous ARGs in the intestinal flora, but there were no significant differences when fed lettuces grown with different manure types. For example, the lsaC of lettuce fed with bovine, chicken and pig manure without adding organic fertilizer increased by 0.143, 0.151, 0.179 and 0.169 logs respectively after 4 weeks, and the efrB also increased by 0.074, 0.068, 0.079 and 0.106 logs respectively. Network analysis showed that Clostridium_ sensu_ stricto_ 18 was a potential host of type 6 virulence factor genes (VFGs). Mantel analysis showed that ARGs were directly influenced by mobile genetic elements (MGEs) and VFGs. Thus, feeding rabbits lettuce grown with different manure types contribute to the transmission of ARGs by remodeling the intestinal microenvironment. In addition, diet may affect exogenous ARGs to change the intestinal antibiotic resistome and possibly threaten health.

Succession of Bacteria Attached to Microplastics After Transferring from a Mariculture Area to a Seagrass Meadow

Microplastics have been recognized as a novel niche for bacteria. However, studies have characterized the plastisphere microbial community in situ without exploring the microbial changes after transferring to other ecosystems. Here we focus on bacterial succession on typical microplastics (polypropylene and expanded polystyrene) and natural substrates (wood) after transferring from mariculture area to seagrass meadows system. Using high-throughput sequencing of 16 S rRNA, we found that alpha diversity significantly reduced after transferring and microplastics especially PP had significant separations on PCoA plots at different succession stages. The abundance and metabolic pathways of potential pathogen-associated microorganisms are significantly decreased. The relative abundance of xenobiotics biodegradation pathways was significantly lower and of energy metabolism pathways was significantly higher by comparing before and after transferring. Main environmental factors affecting microbial communities changed from nutrient characteristics to basic physicochemical properties after transferring. The succession times of the microbial communities of the three materials were different.

Response characteristics of antibiotic resistance genes and bacterial communities during agricultural waste composting: Focusing on biogas residue combined with biochar amendments

This research investigated biogas residue and biochar addition on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and changes in bacterial community during agricultural waste composting. Sequencing technique investigated bacterial community structure and ARGs, MGEs changes. Correlations among physicochemical factors, ARGs, MGEs, and bacterial community structure were determined using redundancy analysis. Results confirmed that biochar and biogas residue amendments effectively lowered the contents of ARGs and MGEs. The main ARGs detected was sul1. Proteobacteria and Firmicutes were the main host bacteria strongly associated with the dissemination of ARGs. The dynamic characteristics of the bacterial community were strongly correlated with pile temperature and pH (P < 0.05). Redundancy and network analysis revealed that nitrate, intI1, and Firmicutes mainly affected the in ARGs changes. Therefore, regulating these key variables would effectively suppress the ARGs spread and risk of compost use.

Recycling utilization of Chinese medicine herbal residues resources: systematic evaluation on industrializable treatment modes

Traditional Chinese medicine (TCM) is an indispensable part of the world health and medical system and plays an important role in treatment, prevention, and health care. These TCM produce a large amount of Chinese medicine herbal residues (CHMRs) during the application process, most of which are the residues after the decoction or extraction of botanical medicines. These CMHRs contain a large number of unused components, which can be used in medical, breeding, planting, materials, and other industries. Considering the practical application requirements, this paper mainly introduces the low-cost treatment methods of CHMRs, including the extraction of active ingredients, cultivation of edible fungi, and manufacture of feed. These methods not only have low upfront investment, but also have some income in the future. Furthermore, other methods are briefly introduced. In conclusion, this paper can provide a reference for people who need to deal with CMHRs and contribute to the sustainable development of TCM.

Effect of homemade compound microbial inoculum on the reduction of terramycin and antibiotic resistance genes in terramycin mycelial dreg aerobic composting and its mechanism

In order to tackle the issue of terramycin mycelial dreg (TMD) diagnosis and removal of terramycin and antibiotic resistance genes (ARGs), this study adopted aerobic composting (AC) technology and added homemade compound microbial inoculum (HCMI) to promote the AC of TMD and enhance the removal of terramycin and ARGs. The findings demonstrated that terramycin residue could be basically harmless after AC. Moreover, HCMI not only reduced QacB and tetH but also increased the degradation rates of VanRA, VanT, and dfrA24 by 40.81%, 5.65%, and 54.18%, respectively. The HCMI improved the removal rate of ARG subtypes to a certain extent. According to redundancy analysis, during AC, the succession of the microbial community had a stronger influence on the variance of ARG subtype than the environmental conditions. Differences in the abundance of various bacteria due to changes in temperature may be an intrinsic mechanism for the variation of ARG subtypes.

Effect of Chinese medicinal herbal residues compost on tomato and Chinese cabbage plants: Assessment on phytopathogenic effect and nutrients uptake

Chinese medicinal herbal residues (CMHRs) are known for their antipathogenic properties due to the presence of bioactive compounds. Hence, CMHRs could be used as a potential resource to produce biofertilizer with antipathogenic properties for agricultural applications. In this study, a novel approach was used by utilizing the waste-derived biofertilizer, i.e., CMHRs compost (CMHRC) as a nutrient supplier as well as an organic bioagent against Alternaria solani (A. solani) and Fusarium oxysporum (F. oxysporum) on tomato (Lycopersicon esculentum) and Chinese cabbage (Brassica rapa subsp. Chinensis) plants. The experiments were conducted under greenhouse conditions using locally collected acidic soil wherein 2%, 5% and 10% CMHRC (dry weight) along with 5% food waste compost were used as treatments. In addition, only soil and soil with phytopathogens were used as control treatments. The results suggested that amending the compost into acidic soil significantly increased the pH to a neutral level along with enhanced uptake of nutrients. Among all the treatments, 5% CMHRs compost addition increased the tomato plant biomass production to 4.9 g/pot (dry weight) compared to 2.2 g/pot in control. A similar trend was observed in Chinese cabbage plants and the improved plant biomass production could be attributed to the combined effect of strong nutrient absorption ability by healthy roots and enhanced nutrient supply. At 5% CMHRC application rate, the nitrogen uptake by tomato and Chinese cabbage plants increased by 78% and 62%, respectively, whereas phosphorous uptake increased by 75% and 25%, respectively. The reduction in A. solani by 48% and F. oxysporum by 54% in the post-harvested soil of 5% CMHRC treatment against the control demonstrated the anti-phytopathogenic efficiency of CMHRC compost. Hence, the present study illustrates the beneficiary aspects of utilizing CMHRs to produce biofertilizer with anti-phytopathogenic properties which can be safely used for tomato and Chinese cabbage plant growth.

Influence of anthropogenic disturbances on antibiotic resistance gene distributions along the Minjiang River in Southeast China

River-reservoir systems have become ubiquitous among modern global aquatic environments due to the widespread construction of dams. However, little is known of antibiotic resistance gene (ARG) distributions in reservoir-river systems experiencing varying degrees of anthropogenic impacts. Here, the diversity, abundance, and spatial distribution of ARGs were comprehensively characterized along the main stem of the Minjiang River, a typical subtropic reservoir-river system in Southeast China using high-throughput quantitative PCR. A total of 252 ARG subtypes were detected from twelve sampling sites that were dominated by aac(3)-Via, followed by czcA, blaTEM, and sul1. Urban river waters (sites S9-S12) harbored more diverse ARGs than did the reservoir waters (sites S1-S7), indicating more serious antibiotic resistance pollution in areas with larger population densities. Dam construction could reduce the richness and absolute abundance of ARGs from upstream (site S7) to downstream (site S8). Urban river waters also harbored a higher proportion of mobile genetic elements (MGEs), suggesting that intensive human activities may promote ARG horizontal gene transfers. The mean relative abundance of Proteobacteria that could promote antibiotic resistance within microbial communities was also highest in urban river waters. Variance partitioning analysis indicated that MGEs and bacterial communities could explain 67.33%, 44.7%, and 90.29% of variation in selected ARGs for the entire watershed, aquaculture waters, and urban river waters, respectively. These results further suggest that urban rivers are ideal media for the acquisition and spread of ARGs. These findings provide new insights into the occurrence and potential mechanisms determining the distributions of ARGs in a reservoir-river system experiencing various anthropogenic disturbances at the watershed scale.

Effect of biochar on antibiotics and antibiotic resistance genes variations during co-composting of pig manure and corn straw

Pig manure is a reservoir of antibiotics and antibiotic resistance genes (ARGs). The effect of biochar on the variations in physicochemical properties, bacterial communities, antibiotics, ARGs, and mobile genetic elements (MGEs) of compost product during co-composting of pig manure and corn straw have been investigated in this study. Compared with the control treatment (CK), biochar addition accelerated the increase in pile temperature and prolonged the high temperature period (>55°C) for 2 days. Under biochar influence, organic matter degradation, NH₄⁺-N conversion and NO₃⁻-N production was accelerated, and dissolved total organic carbon (DOC) and dissolved total nitrogen (DTN) utilization by microorganisms were enhanced. Biochar addition altered the microbial community and promoted the vital activity of Actinobacteria in the later composting stage. The antibiotics removal efficiency (except danofloxacin and enrofloxacin) was accelerated in the early composting stage (1–14 days) by biochar addition, the pile temperature had a positive effect on antibiotics removal, and the total antibiotics removal efficiency in CK and CK+Biochar treatments was 69.58% and 78.67% at the end of the composting process, respectively. The absolute abundance of most of the ARGs in the CK+Biochar treatment was lower than that in the CK treatment during composting, and the ARGs removal mainly occurred in the early (1–14 days) and later (28–50 days) stages. Biochar addition reduced the absolute abundance of MGEs (intI1, intI2) in the compost product, and most of the ARGs had a significant positive correlation with MGEs. Network analysis and redundancy analysis showed that ARGs and MGEs occurred in various host bacteria (Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Halanaerobiaeota), and that DTN and NH₄⁺-N are the main factors regulating the changes in bacterial communities, antibiotics, ARGs, and MGEs during composting. Moreover, MGEs contributed the most to the variation in ARGs. In summary, biochar addition during composting accelerated antibiotics removal and inhibited accumulation and transmission of ARGs. The results of this study could provide theoretical and technical support for biochar application for antibiotics and ARGs removal during livestock and poultry manure composting.

Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion

Direct application of pig slurry to agricultural land, as a means of nutrient recycling, introduces pathogens, antibiotic resistant bacteria, or genes, to the environment. With global environmental sustainability policies mandating a reduction in synthetic fertilisation and a commitment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximises its fertilisation value and minimises risk to health and the environment. We assessed and compared the effect of storage, composting, and anaerobic digestion (AD) on pig slurry microbiome, resistome and nutrient content. Shotgun metagenomic sequencing and HT-qPCR arrays were implemented to understand the dynamics across the treatments. Our results identified that each treatment methods have advantages and disadvantages in removal pollutants or increasing nutrients. The data suggests that storage and composting are optimal for the removal of human pathogens and anaerobic digestion for the reduction in antibiotic resistance (AMR) genes and mobile genetic elements. The nitrogen content is increased in storage and AD, while reduced in composting. Thus, depending on the requirement for increased or reduced nitrogen the optimum treatment varies. Combining the results indicates that composting provides the greatest gain by reducing risk to human health and the environment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes will reduce the AMR content. KEGG analysis identified no significant change in the pathways across all treatments. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to minimise pathogen, AMR and excess or increasing nutrient transfer from slurry to environment.

Comparative analysis of antibiotic resistance genes on a pig farm and its neighboring fish ponds in a lakeside district

Antibiotics usage in animal production is considered a primary driver of the occurrence, supply and spread of antibiotic resistance genes (ARGs) in the environment. Pig farms and fish ponds are important breeding systems in food animal production. In this study, we compared and analyzed broad ARGs profiles, mobile genetic elements (MGEs) and bacterial communities in a representative pig farm and neighboring fish ponds around Poyang Lake, the largest freshwater lake in China. The factors influencing the distribution of ARGs were also explored. The results showed widespread detection of ARGs (from 57 to 110) among 283 targeted ARGs in the collected water samples. The differences in the number and relative abundance of ARGs observed from the pig farm and neighboring fish ponds revealed that ARG contamination was more serious on the pig farm than in the fish ponds and that the water treatment plant on the pig farm was not very effective. Based on the variance partition analysis (VPA), MGEs, bacterial communities and water quality indicators (WIs) codrive the relative abundance of ARGs. Based on network analysis, we found that total phosphorus and Tp614 were the most important WIs and MGEs affecting ARG abundance, respectively. Our findings provide fundamental data on farms in lakeside districts and provide insights into establishing standards for the discharge of aquaculture wastewater.

Diversity of microbial community structure and their association with phthalic acid esters and physicochemical parameters in informal landfills

Informal landfill is a common waste treatment method employed in rural areas of China, and phthalic acid esters (PAEs) are one of the typical pollutants in landfill leachate. However, there is no corresponding theoretical basis for whether microbial treatment technology can be used to reduce environmental risk of PAEs in informal landfills. Thus, a typical informal landfill site in northern China was selected and approximately 1,133,023 effective sequences were obtained from 21 samples collected from three layers (different deposit depths) of the landfill. This research explored the correlation between PAEs and the composition and distribution of microbial community in specific environments of informal landfill sites. Here we found that dis(2-ethylhexyl) phthalate (DEHP), di-n-octyl phthalate (DOP), and diethyl phthalate (DEP) were positively and significantly correlated with Bhargavaea, Planococcus, Virgibacillus, and Oceanobacillus, respectively. The redundancy analysis demonstrated that moisture content, pH, NO2--N, and SUVA254 among the seven physicochemical factors (pH, TN, NO3--N,NO2--N,NH4+-N, SUVA254, and moisture content) significantly affected bacterial communities. The research conclusion can provide theoretical basis for the degradation technology of PAEs by microorganism and research basis for the treatment of informal landfill sites.

Abundance and diversity of antibiotic resistance genes and bacterial communities in the western Pacific and Southern Oceans

This study investigated the abundance and diversity of antibiotic resistance genes (ARGs) and the composition of bacterial communities along a transect covering the western Pacific Ocean (36°N) to the Southern Ocean (74°S) using the Korean icebreaker R/V Araon (total cruise distance: 14,942 km). The relative abundances of ARGs and bacteria were assessed with quantitative PCR and next generation sequencing, respectively. The absolute abundance of ARGs was 3.0 × 10⁶ ± 1.6 × 10⁶ copies/mL in the western Pacific Ocean, with the highest value (7.8 × 10⁶ copies/mL) recorded at a station in the Tasman Sea (37°S). The absolute abundance of ARGs in the Southern Ocean was 1.8-fold lower than that in the western Pacific Ocean, and slightly increased (0.7-fold) toward Terra Nova Bay in Antarctica, possibly resulting from natural terrestrial sources or human activity. β-Lactam and tetracycline resistance genes were dominant in all samples (88-99%), indicating that they are likely the key ARGs in the ocean. Correlation and network analysis showed that Bdellovibrionota, Bacteroidetes, Cyanobacteria, Margulisbacteria, and Proteobacteria were positively correlated with ARGs, suggesting that these bacteria are the most likely ARG carriers. This study highlights the latitudinal profile of ARG distribution in the open ocean system and provides insights that will help in monitoring emerging pollutants on a global scale.

Risk of horizontal transfer of intracellular, extracellular, and bacteriophage antibiotic resistance genes during anaerobic digestion of cow manure

The fate of intracellular antibiotic resistance genes (iARGs), extracellular ARGs (eARGs) and bacteriophage ARGs (bARGs) during anaerobic digestion (AD) of cow manure is unclear. Thus, the characteristics of iARGs, eARGs and bARGs during mesophilic AD (MAD) and thermophilic AD (TAD) of cow manure were investigated. The absolute abundances of iARGs decreased by 69.82% after TAD. After MAD and TAD, the total absolute abundances of eARGs increased by 63.5 times and 67.6 times, respectively, whereas those of the bARGs increased by 47.60% and 59.22%. eARGs were mainly derived from the non-specific lysis of Firmicutes, Bacteroidetes, while bacteriophages had a wide range of hosts. The variations in iARGs, eARGs and bARGs were affected by the microbial hosts but also directly driven by physicochemical factors (e.g., pH). Overall, the findings of this study revealed that there may be a risk of eARGs and bARGs disseminating during the AD of cow manure.

The microbial mechanisms of enhanced humification by inoculation with Phanerochaete chrysosporium and Trichoderma longibrachiatum during biogas residues composting

This study investigated effects of composite microbes (CMs) (Phanerochaete chrysosporium and Trichoderma longibrachiatum) on humification during co-composting of biogas residue, spent mushroom substrate and rice straw. Results showed that CMs inoculation elevated degradation ratios of cellulose, hemicellulose and lignin by 7.86%, 8.87% and 6.45%, and contents of humus and humic acid were correspondingly promoted by 15.5% and 23.6%, respectively. Relative abundances of bacteria associated with refractory macromolecules degradation (Flavobacterium, Anseongella and Actinomadura) and cellulolytic fungi (Hypocreales_Incertae_sedis, Hypocreaceae and Psathyrellaceae) were raised by CMs addition. Redundancy analysis demonstrated a positive correlation between microbial communities and temperature, fulvic acid and lignocellulose contents. Moreover, CMs inoculation promoted pathways of xenobiotics biodegradation and metabolism, and biosynthesis of other secondary metabolites, which was closely associated with lignocellulose degradation and humus formation. These results suggested that biological inoculation could enhance composting efficiency and improve compost quality, benefiting biogas residues composting.

Microbial community competition rather than high-temperature predominates ARGs elimination in swine manure composting

Aerobic composting is commonly used in pig manure treatment, however, antibiotic resistance genes (ARGs) and their unclear transformation during composting process make the treated manure land using risky. The effects of enhanced thermophilic phase strategy (external heating (HTC) and thermophiles inoculation (MC)) on ARGs removal and the underlying mechanisms were investigated during swine manure composting. HTC increased the total relative abundance (RA) of ARGs by 32.38%, and MC decreased by 21.50% compared to CK by the end of the composting. Mantel test indicated that it was not temperature (P > 0.05), but environmental parameters (pH, Electric Conductivity (EC), etc.) and metabolic products (nitrogen forms) significantly affected the ARGs profile. Partial least-squares path modeling (PLS-PM) suggested that microbial community structure (bacterial abundance and diversities) was the main factor for ARGs evolution. Co-occurrence analysis revealed that HTC could promote the propagation of ARG hosts in later stage of the composting because the strong selection of thermophiles resulted in ecological niches vacancy, and MC enhanced the competition between hosts and nonhosts for ecological niches by increasing thermophiles diversities. These results suggested that competitive inhibition to potential ARGs hosts could be a helpful strategy in ARGs threaten elimination during composting.

Mechanism of a double-channel nitrogen-doped lignin-based carbon on the highly selective removal of tetracycline from water

A high-performance nitrogen-doped lignin-based carbon material (ILAC-N) was synthesized using industrial lignin and urea by hydrothermal and activation, as an absorbent of tetracycline hydrochloride (TC). The results showed that the ILAC-N comprises a double-channeled structure with micro and mesopores. It exhibits an excellent adsorption capacity of TC across a wide pH range (pH 2-11), with the highest adsorption capacity of 1396 mg g^-1 at 323 K. Tests in actual wastewater showed that the TC removal rate by ILAC-N exceeded 97.4%. Moreover, it maintained a removal rate of 84% after 10 regeneration cycles, revealing its high reusability. Mechanisms suggested that pore filling and π-π interaction played a critical role in this process. In conclusion, ILAC-N can be broadly applied to livestock manure and pharmaceutical wastewater treatment, owing to its high adsorption capacity, good adsorption properties across a wide pH range, excellent reusability. Furthermore, this research opens a new path for lignin utilization.

Bacterial and fungal community dynamics during different stages of agro-industrial waste composting and its relationship with compost suppressiveness

Composting is an advantageous and efficient process for recycling organic waste and producing organic fertilizers, and many kinds of microorganisms are involved in obtaining quality compost with suppressive activity against soil-borne pathogens. The aim of this work was to evaluate the main differences in the effects of three composting piles on the whole bacterial and fungal communities of baby-leaf lettuce crops and to determine the specific communities by high-throughput sequencing related to suppressiveness against the soil-borne plant pathogen Pythium irregulare- (P. irregulare). Compost pile A was composed of 47% vineyard pruning waste, 34% tomato waste and 19% leek waste; pile B was composed of 54% vineyard pruning waste and 46% tomato waste; and pile C was composed of 42% vineyard pruning waste, 25% tomato waste and 33% olive mill cake. The temperature and the chemical properties of the piles were monitored throughout the composting process. In addition, the potential suppressive capacity of the three composts (C_A, C_B and C_C) against P. irregulare in baby-leaf lettuce was assessed. We found that the bacterial community changed according to the composting phases and composting pile and was sensitive to chemical changes throughout the composting process. The fungal community, on the other hand, did not change between the composting piles and proved to be less influenced by chemical properties, but it did change, principally, according to the composting phases. All composts obtained were considered stable and mature, while compost C_C showed higher maturity than composts C_A and C_B. During composting, the three piles contained a greater relative abundance of Bacterioidetes, Proteobacterias and Actinobacterias related to the suppression of soil-borne pathogens such as Pythium irregulare. Composts C_A and C_B, however, showed higher suppressiveness against P. irregulare than compost C_C. Deeper study showed that this observed suppressiveness was favored by a higher abundance of genera that have been described as potential suppressive against P. irregulare, such as Aspergillus, Penicillium, Truepera and Luteimonas.

Dynamics and removal mechanisms of antibiotic and antibiotic resistance genes during the fermentation process of spectinomycin mycelial dregs: An integrated meta-omics study

Antibiotic mycelial dregs (AMDs) have been listed as industrial hazardous wastes. With the aim of reducing the environmental risk, the integrated-omics and qPCR approaches were used to reveal the dynamics and removal mechanisms of antibiotic and antibiotic resistance genes (ARGs) during the fermentation of different spectinomycin mycelial dregs (SMDs). The results showed that the removal efficiency of antibiotic in the fermentation of high moisture SMDs reached up to 98%. The high abundance of aadA1 gene encoded by Streptomyces, Lactobacillus, and Pseudomonas was associated with the efficient degradation of spectinomycin, and the inactivating enzymes secreted by degradative bacteria were identified. Furthermore, the dominant microbiota was impacted by moisture content significantly under high temperature environments. In the fermentation of low moisture SMDs, Saccharopolyspora was the dominant microbiota which secreted S8 endopeptidase, M14, M15, S10, S13 carboxypeptidases, M1, M28, S15 aminopeptidases, and antioxidant enzymes, while in the fermentation of high moisture SMDs, Bacillus and Cerasibacillus were dominant genera which mainly secreted S8 endopeptidase and antioxidant enzymes. The abundance of ARGs and mobile genetic elements decreased significantly at thermophilic phase, with maximum drops of 93.7% and 99.9%, respectively. Maintaining moisture content below 30% at the end phase could prevent the transmission of ARGs effectively.

Treatment and bioresources utilization of traditional Chinese medicinal herb residues: Recent technological advances and industrial prospect

Traditional Chinese medicine (TCM) has wide application and important functions in curing many diseases, but a great number of herb residues are usually generated after its manufacture and usage. Without proper and timely treatment, these traditional Chinese medicinal herb (TCMH) residues will cause some environmental pollution. In addition to treatment, bioresources utilization of TCMH residues is also important for its great potential as a suitable feedstock for the production of energy, materials, and chemicals. In this situation, advanced and well-designed solid waste management is important to make the TCM industry environmentally friendly and economically attractive. In this review article, the recent progress focusing on various methods for TCMH residues treatment and bioresources utilization are introduced in detail. In particular, the technologies for thermochemical conversion and biochemical conversion of TCMH residues are mainly focused on in order to show how to fulfill effective and efficient bioresources utilization. Besides, some other technologies which are suitable for the treatment and bioresources utilization of TCMH residues are presented as well. Finally, some industrial prospects are given from the economic, operational, and environmental aspects for the further development of treatment and bioresources utilization of TCMH residues. Overall, this work can provide some systematical and comprehensive information for the development of technologies that help sustainably manage the herb residues generated in the TCM industry.

Performance and microbial community dynamics during rice straw composting using urea or protein hydrolysate as a nitrogen source: A comparative study

Aerobic composting is a promising alternative for the recycling of rice straw (RS), and an applicable nitrogen source is necessary to improve the process. The aim of this study was to compare the performance and microbial community dynamics of RS composting using urea or protein hydrolysate from leather waste (PHL) as a nitrogen source. Results showed that PHL addition achieved a faster temperature increase rate at start-up (1.85 ℃·h^-1 vs 1.07 ℃·h^-1), higher volatile solid degradation efficiency (48.04% vs 46.98%), and greater germination indices (111.72% vs 89.87%) in the end products, as compared to urea. The major bacterial phyla included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria in both composting processes. Although the bacterial communities in both processes succeeded in a similar pattern according to different composting phases, PHL addition accelerated the succession rate of the microbial community. Co-occurrence network analysis revealed that bacterial community composition was strongly correlated with physicochemical properties such as dissolved organic carbon (DOC), NH₄⁺, pH, temperature, and total nitrogen (TN) content. These results proved the potential of using PHL as a nitrogen source to improve the RS composting process.

Chitosan as additive affects the bacterial community, accelerates the removals of antibiotics and related resistance genes during chicken manure composting

Manures, storages for antibiotic resistance genes (ARGs), pollute soil and water as well as endanger human health. Recently, we have been searching a better solution to remove antibiotics and ARGs during aerobic composting. Here, the dynamics of chitosan addition on the profiles of 71 ARGs, bacterial communities, chlortetracycline (CTC), ofloxacin (OFX) were investigated in chicken manure composting and compared with zeolite addition. Chitosan addition effectively reduces antibiotics contents (CTC under detection limit, OFX 90.96%), amounts (18) and abundance (56.7%, 11.1% higher than zeolite addition) of ARGs and mobile genetic elements (MGEs) after 42 days composting. Network analysis indicated that a total of 27 genera strains assigned into 4 phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) were the potential hosts of ARGs. Redundancy analysis (RDA) demonstrated that bacterial community succession is the main contributor in the variation of ARGs. Overall, chitosan addition may effect bacterial composition by influencing physic-chemical properties and the concentration of antibiotics, Cu²⁺, Zn²⁺ to reduce the risk of ARG transmission. This study gives a new strategy about antibiotics and ARGs removal from composting on the basis of previous studies.

Key factors driving the fate of antibiotic resistance genes and controlling strategies during aerobic composting of animal manure: A review

Occurrence of antibiotic resistance genes (ARGs) in animal manure impedes the reutilization of manure resources. Aerobic composting is potentially effective method for resource disposal of animal manure, but the fate of ARGs during composting is complicated due to the various material sources and different operating conditions. This review concentrates on the biotic and abiotic factors influencing the variation of ARGs in composting and their potential mechanisms. The dynamic variations of biotic factors, including bacterial community, mobile genetic elements (MGEs) and existence forms of ARGs, are the direct driving factors of the fate of ARGs during composting. However, most key abiotic indicators, including pH, moisture content, antibiotics and heavy metals, interfere with the richness of ARGs indirectly by influencing the succession of bacterial community and abundance of MGEs. The effect of temperature on ARGs depends on whether the ARGs are intracellular or extracellular, which should be paid more attention. The emergence of various controlling strategies renders the composting products safer. Four potential removal mechanisms of ARGs in different controlling strategies have been concluded, encompassing the attenuation of selective/co-selective pressure on ARGs, killing the potential host bacteria of ARGs, reshaping the structure of bacterial community and reducing the cell-to-cell contact of bacteria. With the effective control of ARGs, aerobic composting is suggested to be a sustainable and promising approach to treat animal manure.

Proliferation of antibiotic-resistant microorganisms and associated genes during composting: An overview of the potential impacts on public health, management and future

Antibiotic residues together with non-antibiotic drugs and heavy metals act as a selective pressure for the spread of antibiotic-resistant microorganisms (ARMs), antibiotic-resistant genes (ARGs), and mobile genetic elements (MGEs) during composting of livestock manure. ARMs, ARGs and MGEs have become emerging contaminants since they are regularly implicated in the majority of compost produced from livestock manure. The prevalence of these contaminants in agricultural soil receiving compost has drawn huge attention globally due to the risks they pose to the total environment. Although a large body of literature exists on the application of composting methods in minimizing the relative abundance of these contaminants, there is a paucity of information on the robustness, limitations and opportunities and threats of various composting protocols currently deployed. To address this knowledge gap, the current review compiled literature on the origin and mechanisms of the proliferation of ARMs, ARGs, and MGEs during composting of livestock manure. The effectiveness of current composting protocols in the reduction or removal of emerging contaminants was evaluated. Furthermore, the potential environmental impacts and human health risks of these contaminants following land application of compost were also presented. Finally, we propose some strategic approaches for the reduction of ARGs and MGEs during composting of livestock manure.

Behavior of antibiotic resistance genes in a wastewater treatment plant with different upgrading processes

Wastewater treatment plants (WWTPs) in China have been upgraded or renovated with a variety of emerging processes, but a comprehensive understanding of the behavior of antibiotic resistance genes (ARGs) in these WWTPs is still lacking. Here, the distribution of ARGs and bacterial community were investigated in a wastewater treatment plant with upgrading processes (WWTP-UP). 238 unique ARGs were detected in all samples. During the study period, the average ARGs concentration decreased by 98.4% along the entire treatment process. The removal efficiency of A²/O-membrane bioreactor (MBR) process was significantly higher than that of A²/O-high efficiency flocculent settling/cloth media filter (HEFS/CMF) process (p < 0.05), which corresponded to 3.5 and 2.1 log values on average, respectively. Notably, 35 ARGs and 14 mobile genetic elements (MGEs) were persistent in all samples. Based on the co-occurrence pattern revealed by network analysis, persistent ARGs possibly spread through the transfer of persistent MGEs among persistent bacteria. Using multiple linear regression analysis, we obtained 3 to 5 possible indicators for major ARG types, which might be served to evaluate the general distribution of ARGs or even predict the abundance of different ARG types. Our findings provide new insights into the impacts of upgrading process on ARGs and highlight the need for better strategies to improve ARGs elimination in WWTPs.

Effects of multi-phase inoculation on the fungal community related with the improvement of medicinal herbal residues composting

Composting has become the most important way to recycle medicinal herbal residues (MHRs). The traditional composting method, adding a microbial agent at one time, has been greatly limited due to its low composting efficiency, mutual influence of microbial agents, and unstable compost products. This study was conducted to assess the effect of multi-phase inoculation on the lignocellulose degradation, enzyme activities, and fungal community during MHRs composting. The results showed that multi-phase inoculation treatment had the highest thermophilic temperature (68.2 °C) and germination index (102.68%), significantly improved available phosphorus content, humic acid, and humic substances concentration, accelerated the degradation of cellulose and lignin, and increased the activities of cellulase in the mature phase, xylanase, manganese peroxidase, and utilization of phenolic compounds. Furthermore, the non-metric multi-dimensional scaling showed that the composting process and inoculation significantly influenced fungal community composition. In multi-phase inoculation treatment, Thermomyces in mesophilic, thermophilic, and mature phase, unclassified_Sordariales, and Coprinopsis in mature phase were the dominant genus that might be the main functional groups to degrade lignocellulose and improve the MHRs composting process.

Plastisphere enrich antibiotic resistance genes and potential pathogenic bacteria in sewage with pharmaceuticals

Microplastics (MPs) and pharmaceuticals are common emerging pollutants in sewage, and their coexistence may have more negative effects on the environments. This study chose tetracycline (TC), ampicillin (AMP) and triclosan (TCS) to investigate the responses of antibiotic resistance genes (ARGs) and microbial communities on different MPs (polyvinyl chloride (PVC), polyethylene (PE)) biofilms (plastisphere). The adsorption capacity of three pharmaceuticals on PVC and PE decreased in the order of AMP > TC > TCS. PE was more conducive to microbial attachment than PVC. MPs led to the increase of the total copies of ARGs and mobile genetic elements (MGEs) in the sewage. Importantly, multidrug ARGs and MGEs were enriched on plastisphere. Furthermore, the co-occurrence of TC and MPs led to higher risks of spreading ARGs and MGEs. In addition, potential pathogenic bacteria Legionella, Mycobacterium, Neisseria and Arcobacter were more abundant on plastisphere than those in sewage, and these bacteria might be the hosts for ARGs and MGEs. This study showed that plastisphere could be repositories of ARGs and MGEs in sewage and accumulated potential pathogenic bacteria.

Microplastics affect the ammonia oxidation performance of aerobic granular sludge and enrich the intracellular and extracellular antibiotic resistance genes

Microplastics (MPs) and antibiotic resistance genes (ARGs), as emerging pollutants, are frequently detected in wastewater treatment plants, and their threats to the environment have received extensive attentions. However, the effects of MPs on the nitrification of aerobic granular sludge (AGS) and the spread patterns of intracellular and extracellular ARGs (iARGs and eARGs) in AGS were still unknown. In this study, the responses of AGS to the exposure of 1, 10 and 100 mg/L of typical MPs (polyvinyl chloride (PVC), polyamide (PA), polystyrene (PS) and polyethylene (PE)) and tetracycline were focused on in 3 L nitrifying sequencing batch reactors. 10 mg/L MPs decreased the nitrification function, but nitrification could recover. Furthermore, MPs inhibited ammonia-oxidizing bacteria and enriched nitrite-oxidizing bacteria, leading partial nitrification to losing stability. PVC, PA and PS stimulated the secretion of extracellular polymeric substances and reactive oxygen species. PE had less negative effect on AGS than PVC, PA and PS. The abundances of iARGs and eARGs (tetW, tetE and intI1) increased significantly and the intracellular and extracellular microbial communities obviously shifted in AGS system under MPs stress. Potential pathogenic bacteria might be the common hosts of iARGs and eARGs in AGS system and were enriched in AGS and MPs biofilms.

Fate of antibiotic resistance genes during high solid anaerobic digestion with pig manure: Focused on different starting modes

As an emerging technology, high solid anaerobic digestion (HSAD) was usually hampered by the long lag phase of methane production. A reasonable starting mode enabled fast startup in HSAD, which was scarcely reported. This study established 5 starting modes for HSAD with pig manure. The results showed that system T4 (biogas slurry once and then autologous leachate reflux) had the shortest lag phase. Starting modes had a total effect of 36.6% on gas production, among which 17.1% affected gas production directly and 19.5% affected it through other factors. About 12/17 of antibiotic resistance genes (ARGs) and 3 mobile genetic elements (MGEs) were effectively reduced during HSAD. System T4 had the highest microbial diversity and the largest number of unique OTUs. MGEs explained most for ARGs variation (>50%), followed by microbial community. Most of the potential host genera for ARGs belonged to Firmicutes phyla, which could be decreased by starting modes.

Horizontal gene transfer is a key determinant of antibiotic resistance genes profiles during chicken manure composting with the addition of biochar and zeolite

Livestock manure is an important reservoir of antibiotic resistance genes (ARGs). Biochar and zeolite are commonly used to improve the quality of compost, however, little is known about the impacts of these additives on the fate of ARGs during composting and the underlying mechanisms involved. In this study, zeolite (ZL), biochar (BC), or zeolite and biochar (ZB) simultaneously were added to chicken manure compost to evaluate their effects on the ARGs patterns. After composting, the abundance of ARGs reduced by 92.6% in control, while the reductions were 95.9%, 98.7% and 98.2% for ZL, BC, ZB, respectively. Co-occurrence network analysis indicated that the potential hosts for most ARGs were predominantly affiliated to Firmicutes such as Lactobacillus and Fastidiosipila. Furthermore, shifts in ARGs were significantly correlated with class 1 integrase gene (intI1), and structural equation models further revealed that intI1 gene contributed most (standardized total effect 0.92) to the ARGs-removal, which was trigged by horizontal gene transfer. Together these results suggest that the addition of zeolite and biochar mitigate the accumulation and spread of ARGs during composting, and the crucial role of horizontal gene transfer (HGT) on the behaviors of ARGs should pay more attention to in the future.

The response of copper resistance genes, antibiotic resistance genes, and intl1/2 to copper addition during anaerobic digestion in laboratory

Heavy metal pollution can serve as a selective pressure for antibiotic resistance genes in polluted environments. Anaerobic fermentation, as a recommended wastewater treatment method, is an effective mitigation measure of antibiotic resistance diffusion. To explore the influence of copper on anaerobic fermentation, we exposed the fermentation substrate to copper in a laboratory setup. We found that the relative abundance of 8 genes (pcoD, tetT, tetA, tetB, tetO, qnrS, ermA and ermB) increased at the late stage of fermentation and their abundance was linked to copper content. Corynebacterium and Streptococcus were significantly positively correlated with ermA, ermB, tetA and tetB (P < 0.05). The relative abundance of tetT was significantly positively correlated with Terrisporobacter, Clostridium_sensu_stricto_1 and Turicibacter (P < 0.05). We screened 90 strains of copper resistant bacteria from blank, medium and high copper test groups on days 25, 31 and 37. The number of fragments carried by a single strain increased with time while intl1, ermA and ermB existed in almost all combinations of the multiple fragments we identified. The relative abundance of these three genes were linearly correlated with Corynebacterium and Streptococcus. The antibiotic resistance genes carried by class 1 integrons gradually increased with time in the fermentation system and integrons carrying ermA and ermB most likely contributed to host survival through the late stages of fermentation. The genera Corynebacterium and Streptococcus may be the primary carriers of such integrated mobile gene element and this was most likely the reason for their rebound in relative abundance during the late fermentation stages.

Effects of chlorotetracycline on antibiotic resistance genes and the bacterial community during cattle manure composting

Chlorotetracycline (CTC) is one of the most antibiotics present in cattle manure. In present study, three levels of CTC (0, 20 and 40 mg kg^-1) were added to cattle manure composting systems to investigate its effects on the distribution of antibiotic-resistant genes (ARGs) and succession of bacterial community. Adding CTC hindered the removal of ARGs during composting; the high level of CTC significantly increased the relative abundance (RA) of 9/11 ARGs and four MGEs. The bacterial community could be clustered according to the composting time under various treatments, with the high level of CTC having a more persistent effect on the bacterial community. Based on redundancy analysis, bacterial community explained the most variation in ARGs (50.1%), whereas based on network analysis, Firmicutes and Proteobacteria were the main hosts for ARGs. In conclusion, the presence of CTC increased the risks of spreading ARGs in compost products.

Horticulture and Orchards as New Markets for Manure Valorisation with Less Environmental Impacts

Animal manure management is a real challenge to minimize environmental impacts and ensure that this valuable material is efficiently used in a circular economy context. One of the main limitations for larger use of animal manure as fertilizer is the availability of land to receive it in an area close to the farm. Indeed, animal manure is traditionally used for cereals and animal feed growth, but the soil area occupied with these crops might not be enough to receive all the manure produced and/or part of this soil might have nutrient contents, namely phosphorous, that do not permit further application of manure. Hence, extra land used for other agricultural activities might be an option. The main objective of the present review was to analyse the constraints and solutions to increase the use of manure in horticulture and orchards. Emphasis was given to the legal framework for manure utilization in the EU that might stimulate or restrain such a solution. The main characteristics of manure that might limit or stimulate manure reuse were also described, and the potential of some treatments to valorise manure was analysed. Several examples of alternative uses of manure in horticulture and orchards were examined, and the society and farmers’ acceptance of the proposed solution was addressed.

In-feed antibiotic use changed the behaviors of oxytetracycline, sulfamerazine, and ciprofloxacin and related antibiotic resistance genes during swine manure composting

The dynamics of oxytetracycline (OTC), sulfamerazine (SM1), ciprofloxacin (CIP) and related antibiotic resistance genes (ARGs) during swine manure composting were compared between manure collected from swine fed a diet containing these three antibiotics (T_D) and manure directly spiked with these drugs (T_S). The composting removal efficiency of OTC (94.9 %) and CIP (87.8 %) in the T_D treatment was significantly higher than that of OTC (83.8 %, P <  0.01) and CIP (83.9 %, P <  0.05) in the T_S treatment, while SM1 exhibited no significant difference (P >  0.05) between the two treatments. Composting effectively reduced the majority of ARGs in both T_D and T_S types of manure, especially tetracycline resistance genes (TRGs). Compared with the T_S treatment, the abundance of some ARGs, such as tetG, qepA, sul1 and sul2, increased dramatically up to 309-fold in the T_D treatment. The microbial composition of the composting system changed significantly during composting due to antibiotic feeding. Redundancy analysis suggested that the abundance of ARGs had a considerable impact on alterations in the physicochemical parameters (C/N, pH and temperature) and bacterial communities (Actinobacteria, Proteobacteria and Firmicutes) during the composting of swine manure.

Comparative effects of different antibiotics on antibiotic resistance during swine manure composting

This study explored commonly-used antibiotics (lincomycin, chlorotetracycline, sulfamethoxazole, and ciprofloxacin) and their collective effects on antibiotic resistance during composting. In the first 7 days, ciprofloxacin showed the greatest influence on the physicochemical factors among the studied antibiotics; the removal of antibiotic resistance genes (ARGs) in the multiple-antibiotic treatment was significantly less than single-antibiotic treatments; especially, the largest removal of ribosomal protection genes (tetW and tetO) occurred in single ciprofloxacin treatment. In the end of composting, similar removal ratio (29.71-99.79%) of ARGs was achieved in different treatments (p greater than 0.05); Chloroflexi became the main phylum and it was closely associated with ARGs removal based on the network analysis. Potential host bacteria of ARGs varied with different antibiotics; in particular, the presence of multiple antibiotics increased potential host bacteria of ermA, sul1 and tetO. Above all, collective effects of different antibiotics led to the enrichment of antibiotic resistance in the composting.

Insight into the fate of antibiotic resistance genes and bacterial community in co-composting green tea residues with swine manure

Green tea residues (GTRs) are byproducts of tea production and processing, and this type of agricultural waste retains nutritious components. This study investigated the co-composting of GTRs with swine manure, as well as the effects of GTRs on antibiotic resistance genes (ARGs) and the bacterial community during co-composting. The temperature and C/N ratio indicate compost was mature after processing. The addition of GTRs effectively promoted the reduction in the abundances of most targeted ARGs (tet and sul genes), mobile genetic element (MGE; intI1), and metal resistance genes (MRGs; pcoA and tcrB). Redundancy analysis (RDA) showed that GTRs can reduce the abundance of MRGs and ARGs by reducing the bioavailability of heavy metals. Network analysis shows that Firmicutes and Actinobacteria were the main hosts of ARGs and ARGs, MGEs, and MRGs shared the same potential host bacteria. Adding GTRs during composting may reduce ARGs transmission through horizontal gene transfer (HGT). GTRs affected the bacterial community, thereby influencing the variations in the ARG profiles and reducing the potential risk associated with the compost product.

Assessing the effects of tylosin fermentation dregs as soil amendment on macrolide antibiotic resistance genes and microbial communities: Incubation study

Tylosin fermentation dregs (TFDs) are biosolid waste of antibiotics tylosin production process which contain nutritious components and may be recycled as soil amendments. However, the specific ecological safety of TFDs from the perspective of bacterial resistance in soil microenvironment is not fully explored. In the present study, a series of replicated lab-scale work were performed using the simulated fertilization to gain insight into the potential environmental effects and risks of macrolide antibiotic resistance genes (ARGs) and the soil microbial communities composition via quantitative PCR and 16S rRNA sequencing following the TFDs land application as the soil amendments. The results showed that bio-processes might play an important role in the decomposition of tylosin which degraded above 90% after 20 days in soil. The application of TFDs might induce the development of antibiotic-resistant bacteria, change soil environment and reduce the microbial diversity. Though the abundances of macrolide ARGs exhibited a decreasing trend following the tylosin degradation, other components in TFDs may have a lasting impact on both macrolide ARGs abundance and soil bacterial communities. Thus, this study pointed out the fate of TFDs on soil ecological environment when directly applying into soil, and provide valuable scientific basis for TFDs management.

Antidepressant-Like Effects of Coumaroylspermidine Extract From Safflower Injection Residues

In this study, a total coumaroylspermidine extract (CSE), which included four coumaroylspermidine compounds, was prepared from safflower injection (a traditional Chinese medicine) residues for the first time. The total content of the four coumaroylspermidine compounds was determined to be 64.86 ± 0.41% using high-performance liquid chromatography. We then evaluated the anti-depressant effect of CSE by using a chronic unpredictable mild stress (CUMS) model in rats. Results of sucrose preference tests, open field tests, and forced swimming tests suggest that CSE exhibits a significant anti-depressant effect. In studies to explore the mechanism, CSE was found to inhibit the increases in levels of corticosterone and decreases in levels of 5-hydroxytryptamine, dopamine, and noradrenaline induced by CUMS. Metabolic profiling showed that 10 endogenous metabolites and four metabolic pathways were altered after CSE treatment. Thus, this study not only found a spermidine extract with antidepressant effect from safflower injection residue for the first time but also provided a way for the efficient utilize of safflower injection residue.

The 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.