Fate of antibiotic resistance genes during high-solid anaerobic co-digestion of pig manure with lignite

Unraveling the dual role in enhancing methane production and mitigating antibiotic resistance gene spread in anaerobic co-digestion of microalgae and waste activated sludge

Waste activated sludge (WAS) is a double-edged sword - a recognized repository for antibiotic resistance genes (ARGs) but also a renewable substrate for methane production. Developing effective WAS treatment strategies is therefore of both ecological and practical importance. In this study, we proposed an anaerobic co-digestion approach of WAS and microalgae Chlorella sp. at a 1:2 ratio (MAcoD-1:2). Results showed that MAcoD-1:2 notably increased cumulative methane production by 52.7 %. Co-digestion also demonstrated a significant increase in the abundance of hydrolyzing acidifying bacteria Candidatus_Promineofilum (12.25 %) and methanogenic archaea Methanothrix (61.2 %). This microbial shift suggested that cosubstrates availability fostered a stable bacterial community structure and synergistic metabolic interactions, thus enhancing methane production. Metagenomic analysis revealed a significant reduction in both ARGs and mobile genetic elements in MAcoD-1:2. Notably, substrate level regulation was found to drive restructuring of microbial communities and metabolic patterns. Investigation showed that the Embden-Meyerhof-Parnas pathways were significantly inhibited while the pentose phosphate pathway was promoted, which constrained the cellular energy budget available for ARG horizontal transfer. Partial least squares path modelling (PLS-PM) further substantiated these findings, revealing methane metabolism negatively affected ARGs (-4.52), whereas confirming its positive correlation with methane production (0.22). Our findings provided distinctive perspectives on WAS resource utilization and novel technologies to inhibit the spread of ARGs.

Biochar@MIL-88A(Fe) accelerates direct interspecies electron transfer and hydrogen transfer in waste activated sludge anaerobic digestion: Exploring electron transfer and biomolecular mechanisms

Adding additives exogenously is an effective strategy to enhance methanogenic activity and improve AD stability. Corn straw-based biochar@MIL-88A(Fe) (BM) was synthesized herewith and used as an exogenous additive to boost methane (CH4) production. After adding BM at 250 mg/g WAS VS, the accumulative CH4 production and maximum CH4 yield increased by 1.2 and 1.9 times, respectively, with CH₄ comprising 88% of the biogas. BM accelerated electron transfer through its unsaturated sites and surface functional groups, while also enhancing metabolic functions for facilitating enzymatic activities and converting organic substrates. The abundance of syntrophic bacteria and methanogen were higher after BM addition. BM-mediated DIET and IHT pathways effectively oxidized propionate and butyrate, promoting methane generation. Higher expression of key genes involved in methane production correlated with shifts in microbial structure and increased CH4 yield after BM dosage. The invention of BM may provide more solutions for addressing low energy recovery during AD.

Antibiotic resistance genes in anaerobic digestion: Unresolved challenges and potential solutions

Antimicrobial resistance (AMR) threatens public health, necessitating urgent efforts to mitigate the global impact of antibiotic resistance genes (ARGs). Anaerobic digestion (AD), known for volatile solid reduction and energy generation, also presents a feasible approach for the removal of ARGs. This review encapsulates the existing understanding of ARGs and antibiotic-resistant bacteria (ARB) during the AD process, highlighting unresolved challenges pertaining to their detection and quantification. The questions raised and discussed include: Do current ARGs detection methods meet qualitative and quantitative requirements? How can we conduct risk assessments of ARGs? What happens to ARGs when they come into co-exposure with other emerging pollutants? How can the application of internal standards bolster the reliability of the AD resistome study? What are the potential future research directions that could enhance ARG elimination? Investigating these subjects will assist in shaping more efficient management strategies that employ AD for effective ARG control.

A comprehensive review of antibiotic resistance gene contamination in agriculture: Challenges and AI-driven solutions

Since their discovery, the prolonged and widespread use of antibiotics in veterinary and agricultural production has led to numerous problems, particularly the emergence and spread of antibiotic-resistant bacteria (ARB). In addition, other anthropogenic factors accelerate the horizontal transfer of antibiotic resistance genes (ARGs) and amplify their impact. In agricultural environments, animals, manure, and wastewater are the vectors of ARGs that facilitate their spread to the environment and humans via animal products, water, and other environmental pathways. Therefore, this review comprehensively analyzed the current status, removal methods, and future directions of ARGs on farms. This article 1) investigates the origins of ARGs on farms, the pathways and mechanisms of their spread to surrounding environments, and various strategies to mitigate their spread; 2) determines the multiple factors influencing the abundance of ARGs on farms, the pathways through which ARGs spread from farms to the environment, and the effects and mechanisms of non-antibiotic factors on the spread of ARGs; 3) explores methods for controlling ARGs in farm wastes; and 4) provides a comprehensive summary and integration of research across various fields, proposing that in modern smart farms, emerging technologies can be integrated through artificial intelligence to control or even eliminate ARGs. Moreover, challenges and future research directions for controlling ARGs on farms are suggested.

Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm

Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.

Strong suppression of silver nanoparticles on antibiotic resistome in anammox process

This study comprehensively deciphered the effect of silver nanoparticles (AgNPs) on anammox flocculent sludge, including nitrogen removal performance, microbial community structure, functional enzyme abundance, antibiotic resistance gene (ARGs) dissemination, and horizontal gene transfer (HGT) mechanisms. After long-term exposure to 0-2.5 mg/L AgNPs for 200 cycles, anammox performance significantly decreased (P < 0.05), while the relative abundances of dominant Ca. Kuenenia and anammox-related enzymes (hzsA, nirK) increased compared to the control (P < 0.05). For antibiotic resistome, ARG abundance hardly changed with 0-0.5 mg/L AgNPs but decreased by approximately 90% with 1.5-2.5 mg/L AgNPs. More importantly, AgNPs effectively inhibited MGE-mediated HGT of ARGs. Additionally, structural equation model (SEM) disclosed the underlying relationship between AgNPs, the antibiotic resistome, and the microbial community. Overall, AgNPs suppressed the anammox-driven nitrogen cycle, regulated the microbial community, and prevented the spread of ARGs in anammox flocs. This study provides a theoretical baseline for an advanced understanding of the ecological roles of nanoparticles and resistance elements in engineered ecosystems.

Effect of reactor operation modes on mitigating antibiotic resistance genes (ARGs) and methane production from hydrothermally-pretreated pig manure

Numerous efforts have been made to enhance the performance of anaerobic digestion (AD) for accelerating renewable energy generation, however, it remains unclear whether the intensified measures could enhance the proliferation and transmissions of antibiotic resistance genes (ARGs) in the system. This study assessed the impact of an innovative pig manure AD process, which includes hydrothermal pretreatment (HTP) and a two-stage configuration with separated acidogenic and methanogenic phases, on biomethane (CH4) production and ARGs dynamics. Results showed that HTP significantly increase CH4 production from 0.65 to 0.75 L/L/d in conventional single-stage AD to 0.82 and 0.91 L/L/d in two-stage AD. This improvement correlated with a rise in the relative abundance of Methanosarcina, a key methanogenesis microorganism. In the two-stage AD, the methanogenic stage offered an ideal environment for methanogens growth, resulting in substantially faster and higher CH4 production by about 10% compared to single-stage AD. Overall, the combined use of HTP and the two-stage AD configuration enhanced CH4 production by 40% compared to traditional single-stage AD. The abundance and diversity of ARGs were significantly reduced in the acidogenic reactors after HTP. However, the ARGs levels increased by about two times in the following methanogenesis stage and reached similar or higher levels than in single stage AD. The erm(F), erm(G), ant(6)-Ia, tet(W), mef(A) and erm(B) were the six main ARGs with significant differences in relative abundances in various treatments. The two-stage AD mode could better remove sul2, but it also had a rebound which elevated the risk of ARGs to the environment and human health. Network analysis identified pH and TVFAs as critical factors driving microbial communities and ARG proliferation in the new AD process. With the results, this study offers valuable insights into the trade-offs between AD performance enhancement and ARG-related risks, pinpointing essential areas for future research and practical improvements.

Reduction of mobile genetic elements determines the removal of antibiotic resistance genes during pig manure composting after thermal pretreatment

Animal manure is a primary repository of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). This work explored the efficiency of ARGs and MGEs removal during pig manure composting after thermal pretreatment (TPC) and the underlying mechanisms. TPC resulted in a decrease of 94.7% and 92.3% in the relative abundance of ARGs and MGEs which was 48.9% and 76.6% lower than control, respectively. Network analysis indicated that reductions of ARGs and MGEs in TPC were relevant to decrease in the amount and abundance of bacterial hosts. Furthermore, total ARGs abundance in TPC was correlated with that of intI1 and Tn916/1545 (P < 0.001). Redundancy analysis supported a leading role of MGEs in ARGs dynamics in TPC. Reduction of MGEs rather than bacterial hosts contributed mainly to ARGs removal in TPC, as revealed by structural equation modeling. In conclusion, TPC was an effective method to treat animal manure containing ARGs.

Insights into the reduction of antibiotic-resistant bacteria and mobile antibiotic resistance genes by black soldier fly larvae in chicken manure

The increasing prevalence of antibiotic-resistant bacteria (ARB) from animal manure has raised concerns about the potential threats to public health. The bioconversion of animal manure with insect larvae, such as the black soldier fly larvae (BSFL, Hermetia illucens [L.]), is a promising technology for quickly attenuating ARB while also recycling waste. In this study, we investigated BSFL conversion systems for chicken manure. Using metagenomic analysis, we tracked ARB and evaluated the resistome dissemination risk by investigating the co-occurrence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial taxa in a genetic context. Our results indicated that BSFL treatment effectively mitigated the relative abundance of ARB, ARGs, and MGEs by 34.9%, 53.3%, and 37.9%, respectively, within 28 days. Notably, the transferable ARGs decreased by 30.9%, indicating that BSFL treatment could mitigate the likelihood of ARG horizontal transfer and thus reduce the risk of ARB occurrence. In addition, the significantly positive correlation links between antimicrobial concentration and relative abundance of ARB reduced by 44.4%. Moreover, using variance partition analysis (VPA), we identified other bacteria as the most important factor influencing ARB, explaining 20.6% of the ARB patterns. Further analysis suggested that antagonism of other bacteria on ARB increased by 1.4 times, while nutrient competition on both total nitrogen and crude fat increased by 2.8 times. Overall, these findings provide insight into the mechanistic understanding of ARB reduction during BSFL treatment of chicken manure and provide a strategy for rapidly mitigating ARB in animal manure.

Mitigation of antibiotic resistome in swine manure by black soldier fly larval conversion combined with composting

The increasing prevalence of antibiotic resistance genes (ARGs) in animal manure has attracted considerable attention because of their potential contribution to the development of multidrug resistance worldwide. Insect technology may be a promising alternative for the rapid attenuation of ARGs in manure; however, the underlying mechanism remains unclear. This study aimed to evaluate the effects of black soldier fly (BSF, Hermetia illucens [L.]) larvae conversion combined with composting on ARGs dynamics in swine manure and to uncover the mechanisms through metagenomic analysis. Compared to natural composting (i.e. without BSF), BSFL conversion combined with composting reduced the absolute abundance of ARGs by 93.2 % within 28 days. The rapid degradation of antibiotics and nutrient reformulation during BSFL conversion combined with composting indirectly altered manure bacterial communities, resulting in a lower abundance and richness of ARGs. The number of main antibiotic-resistant bacteria (e.g., Prevotella, Ruminococcus) decreased by 74.9 %, while their potential antagonistic bacteria (e.g., Bacillus, Pseudomonas) increased by 128.7 %. The number of antibiotic-resistant pathogenic bacteria (e.g., Selenomonas, Paenalcaligenes) decreased by 88.3 %, and the average number of ARGs carried by each human pathogenic bacterial genus declined by 55.8 %. BSF larvae gut microbiota (e.g., Clostridium butyricum, C. bornimense) could help reduce the risk of multidrug-resistant pathogens. These results provide insight into a novel approach to mitigate multidrug resistance from the animal industry in the environment by using insect technology combined with composting, in particular in light of the global "One Health" requirements.

Different rapid startups for high-solid anaerobic digestion treating pig manure: Metagenomic insights into antibiotic resistance genes fate and microbial metabolic pathway

High-solid anaerobic digestion (HSAD), as an emerging disposal technology for swine manure, was commonly hampered by the long lag phase and slow startup, resulting in poor performance. Rapid startups by different leachate reflux forms can solve the problem, but related study was scarcely reported. Therefore, metagenomic analysis was used to exploit the effects of different rapid startups on the biogas performance, antibiotic resistance genes (ARGs) removal and microbial metabolic pathway during HSAD. Compared anaerobic digestion with natural start (T1), three different rapid startups were set, including with autologous leachate reflux (T2), with water reflux (T3) and with exogenous leachate reflux (T4). The results showed that rapid startups (T2-T4) enhanced biogas yield and the cumulative methane yield was increased by 3.7-7.3 times compared with the control. Totally, 922 ARGs were found, most of which belonged to multidrug and MLS ARGs. About 56% of these ARGs could be reduced in T4, while just 32% of ARGs were reduced in T1. Antibiotic efflux pump is the main mechanism of microbial action, which could be decreased largely by these treatments. Moreover, all the rapid startups (T2-T4) made Methanosarcina content (9.59%-75.91%) higher than that in the natural startup of T1 (4.54%-40.27%). This is why these fast-startups helped methane production fast. Network analysis showed that microbial community and environmental factors (pH and VFAs) both contributed to the spread of ARGs. The reconstructed methane metabolic pathway by different identified genes showed that all methanogenesis pathways existed but acetate metabolic pathway was dominant. And the rapid startups made the abundance of acetate metabolic (M00357) higher than the natural startup.

Industrial-scale aerobic composting of livestock manures with the addition of biochar: Variation of bacterial community and antibiotic resistance genes caused by various composting stages

The presence of large amounts of antibiotic resistance genes (ARGs) in livestock manures poses an impending, tough safety risk to ecosystems. To investigate more comprehensively the mechanisms of ARGs removal from industrial-scale composting of livestock manure based on biochar addition, we tracked the dynamics of bacterial community and ARGs at various stages of aerobic composting of livestock manures with 10% biochar. There were no significant effects of biochar on the bacterial community and the profiles of ARGs. During aerobic composting, the relative abundance of ARGs and mobile genetic elements (MGEs) showed overall trends of decreasing and then increasing. The key factor driving the dynamics of ARGs was bacterial community composition, and the potential hosts of ARGs were Caldicoprobacter, Tepidimicrobium, Ignatzschineria, Pseudogracilibacillus, Actinomadura, Flavobacterium and Planifilum. The retention of the thermophilic bacteria and the repopulation of the initial bacteria were the dominant reasons for the increase in ARGs at maturation stage. Additionally, among the MGEs, the relative abundance of transposon gene was substantially removed, while the integron genes remained at high relative abundance. Our results highlighted that the suitability of biochar addition to industrial-scale aerobic composting needs to be further explored and that effective measures are needed to prevent the increase of ARGs content on maturation stage.

Investigating changes in the characteristics of antibiotic resistance genes at different reaction stages of high solid anaerobic digestion with pig manure

Contamination of antibiotic resistance genes (ARGs) from animals is a serious issue as they may spread to human pathogenic bacteria. The reduction of ARG contamination from livestock waste is thus essential. High solid anaerobic digestion (HSAD) is a new and effective technology although some aspects, such as change characteristics of ARGs at different reaction stages, have not been fully investigated. This study focused firstly on the variations in ARGs at different reaction stages in HSAD systems with five different starting methods: 1 natural start (the control) and 4 rapid starts by changing leachate reflux forms. The results showed that the rapid starting methods could accelerate start-up and increase biogas production by 312.5%. The starting and acidification stages showed higher microbial richness and diversity compared with the other stages. ARGs found to be reduced at acidification stage. Variation in ARGs at the starting and acidification stages was mainly driven by a combination of microbial community, mobile genetic elements (MGEs), and environmental factors; while the main contributory factors at the gas production stage were biomass and several unexplained factors. At the ending stage, the main driving factors were biomass and microbial communities. Most of the potential hosts (16/20) of the ARGs belonged to the Firmicutes phylum, which showed the lowest connections with the ARGs at the gas production stage.

Transmission of tetracycline resistance genes and microbiomes from manure-borne black soldier fly larvae frass to rhizosphere soil and pakchoi endophytes

Manure treatment with black soldier fly larvae (BSFL) and BSFL frass application in crop land is a sustainable strategy; however, whether residual antibiotic resistance genes (ARGs) and their transmission risk are related to the manure BSFL treatment process is still unknown. In this paper, the effect of BSFL addition density on residual tetracycline resistance genes (TRGs) and transmission from frass to pakchoi was determined. The results showed that BSFL frass can provide sufficient nutrients for growth, improve the economic value of pakchoi, and reduce the risk of transmission of TRGs in chicken manure regardless of BSFL density. The potential hosts of the TRGs we detected were found in BSFL frass (Oblitimonas and Tissierella), rhizosphere soil (Mortierella and Fermentimonas), and pakchoi endophytes (Roseomonas). The present study concluded that BSFL frass produced by adding 100 BSFL per 100 g of chicken manure has the advantages of high value and low risk. These findings will provide important strategic guidance for animal manure disposal and theoretical support for preventing the transmission of TRGs in BSFL applications.

Metagenomic insights into the influence of mobile genetic elements on ARGs along typical wastewater treatment system on pig farms in China

The wastewater treatment processes (WTP) on pig farms are heavily contaminated by antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) play an important role in shaping ARG profiles. Here we first employed metagenomic sequencing to follow the diversities and shifts of ARG associated mobile genetic elements (AAMGEs) including insertion sequences (ISs) and plasmids along the WTP for three pig farms in southeast China. The IS average relative abundance rose from the initial pig feces source to the wastewater storage lagoon (WSL) but decreased in the influent and rose in the effluent of the anaerobic digestor (AD). In contrast, plasmids were eliminated rapidly along this process. These results indicated that the AD reduced plasmid copies while IS abundance increased. We found a great diversity ISs, including IS91, ISNCY, IS630 and IS701, were large contributors to the transfer of multi-drug resistance. In addition, the tetracycline resistance genes co-occurred with a greater diversity of ISs than other ARG classes and this likely contributed to the high abundance of tetracycline resistance genes we found. The transfer of ARGs mediated by MGEs along the WTP of pig farms was a key contributor for the ARGs persistence in the environment of pig farms. Collectively, our findings demonstrated different fates for ISs and plasmids along the WTP for pig farms and suggested that AAMGE monitoring served as an important role in controlling ARGs in pig waste.

Exploration of machine learning algorithms for predicting the changes in abundance of antibiotic resistance genes in anaerobic digestion

The land application of digestate from anaerobic digestion (AD) is considered a significant route for transmitting antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) to ecosystems. To date, efforts towards understanding complex non-linear interactions between AD operating parameters with ARG/MGE abundances rely on experimental investigations due to a lack of mechanistic models. Herein, three different machine learning (ML) algorithms, Random Forest (RF), eXtreme Gradient Boosting (XGBoost), and Artificial Neural Network (ANN), were compared for their predictive capacities in simulating ARG/MGE abundance changes during AD. The models were trained and cross-validated using experimental data collected from 33 published literature. The comparison of model performance using coefficients of determination (R²) and root mean squared errors (RMSE) indicated that ANN was more reliable than RF and XGBoost. The mode of operation (batch/semi-continuous), co-digestion of food waste and sewage sludge, and residence time were identified as the three most critical features in predicting ARG/MGE abundance changes. Moreover, the trained ANN model could simulate non-linear interactions between operational parameters and ARG/MGE abundance changes that could be interpreted intuitively based on existing knowledge. Overall, this study demonstrates that machine learning can enable a reliable predictive model that can provide a holistic optimization tool for mitigating the ARG/MGE transmission potential of AD.

Semi-solid state promotes the methane production during anaerobic co-digestion of chicken manure with corn straw comparison to wet and high-solid state

Total solid content (TS) is an important factor for biogas production during anaerobic digestion. In this study, we explored the influence of different TS (5% wet, 15% semi-solid and 25% solid state) on the relative cumulative methane production (RCMP) during anaerobic co-digestion of chicken manure with corn straw. Results showed that total ammonium nitrogen and free ammonia nitrogen concentration increased with the increase of TS. Ammonium nitrogen in treatments at 15% TS was 2.25-2.76 times as high as that at 5% TS, which was below 3 times. The highest chemical oxygen demand removal and RCMP were obtained in the treatment of 15% TS with a ratio of 2:1 chicken manure: corn straw (based on TS). The RCMP in the treatments of 15% TS were 3.63-4.59 times higher than that of 5% TS based on the volume of substrates. The abundance of Caldicoprobacter improving the degradation of corn straw was significantly positively correlated with the RCMP, and the average abundance of Caldicoprobacter at 15% TS was 8.33 and 7.02 times higher than that at 5% and 25% TS, respectively. Structural equation models analysis suggested that TS significantly impacted the RCMP by indirectly impacting free ammonia nitrogen and microbial abundance. These findings indicated semi-solid state (15% TS) decreased ammonia nitrogen releasing and improved the abundance of Caldicoprobacter, and increased RCMP during anaerobic co-digestion of chicken manure with corn straw.

Impact of biochar on persistence and diffusion of antibiotic resistance genes in sediment from an aquaculture pond

Aquaculture sediments are a purported sizable pool of antibiotic resistance genes (ARGs). However, the pathways for transmission of ARGs from sediments to animals and humans remain unclear. We conducted an ARG survey in sediments from a bullfrog production facility located in Guangdong, China, and simulated zebrafish breeding systems were constructed, with or without biochar addition in sediments, to explore the effects of biochar on ARGs and their precursors of the sediment and zebrafish gut. After 60 days, 6 subtypes of ARGs and intI1 were detected, with sediments harboring more ARGs than zebrafish gut. The addition of biochar reduced the abundance of ARGs in the sediment and zebrafish gut, as well as suppressed the horizontal transmission of ARGs from sediment to zebrafish gut. Network analysis and partial least squares path modeling revealed that ARG enrichment was mainly affected by bacterial groups dominated by Nitrospirae, Gemmatimonades, Chloroflexi, and Cyanobacteria and intI1. Our findings provide insights into the transmission of ARGs from sediment to animals and highlight the efficacy of biochar amendments to aquaculture sediments to reduce the transmission of ARGs.

A meta-analysis reveals that operational parameters influence levels of antibiotic resistance genes during anaerobic digestion of animal manures

Anaerobic digestion (AD) has shown the potential to reduce the numbers and types of antibiotic-resistance genes (ARG) present in animal manures. However, the variability of the results has limited the ability to draw solid conclusions. To address this issue, we performed a series of meta-analyses to evaluate how AD of pig, cattle, and dairy manures affects ARG levels and how different parameters, such as temperature, pH, digestion times, and the addition of other substances (e.g., solids, antibiotics) influence ARG changes. Twenty studies with enough details on changes in ARG levels during the AD process were identified and used for the meta-analyses. The results suggested that AD could significantly reduce ARG levels regardless of the conditions of the process. Also, thermophilic AD was more effective than mesophilic AD at reducing ARGs, although this difference was only significant for pig manures. The results also suggested that long digestion times (>50 days) yielded better ARG reduction rates, and that the addition of solids from an external source (co-digestion) negatively affected the efficiency of ARG reduction. In general, the results suggested that ARG changes during AD could be linked to the abundance and activity of hydrolytic communities.

Evaluations of biochar amendment on anaerobic co-digestion of pig manure and sewage sludge: waste-to-methane conversion, microbial community, and antibiotic resistance genes

Effects of biochar on co-digestion of pig manure and dewatered sewage sludge under different total solids (TS) were investigated. Biochar could accelerate the start-up of methanogenesis and shorten the adaptation phase. At TS5%, the methane daily production in biochar group was 60.6% higher than the control; nevertheless, when TS increased, the gap between two groups gradually narrowed. Additionally, the change on antibiotics resistance genes (ARGs) was also affected by TS and the biochar addition. Moreover, biochar was beneficial to reduce ARGs in liquid phase. At TS14%, the total ARGs abundance in the liquid phase of biochar group was 41.4% lower than the control, among which the reduction rates of etB(P), sul1, rpoB2, macA, mupA and mupB were more prominent. These findings could provide useful guidance for developing ARGs elimination strategy before their release into the environment.

Responses of methane production, microbial community and antibiotic resistance genes to the mixing ratio of gentamicin mycelial residues and wheat straw in anaerobic co-digestion process

Anaerobic co-digestion (AcoD) of gentamicin mycelial residues (GMRs), a kind of nitrogen-rich biowaste, and wheat straw (WS) is an attractive technology for the recycling of GMRs. However, the effects of the co-substrate ratio on methane production, system stability and antimicrobial resistance during co-digestion remain unclear. Thus, this study aimed to fill in the blanks through AcoD of GMRs and WS with different mixing ratios (1:0, 2:1, 1:1, 1:2, 0:1, VS basis) via batch tests. Results showed that AcoD facilitated methane production than mono anaerobic digestion and reduced the accumulation of the toxic substances, such as ammonia nitrogen and humic-like substances. The maximum methane production was obtained at the reactors with the mixing ratio of 1:1 and 1:2 (R-1:1 and R-1:2), which matched with the relative abundance of key enzymes related to methanogenesis predicted by PICRUSt. Microbial community analysis indicated that Methanosaeta was the most dominant methanogen in the AcoD reactors. The highest relative abundance of Methanosaeta (45.1%) was obtained at R-1:1 due to the appropriate AcoD conditions, thus, providing greater possibilities for high stability of AcoD system. Additionally, AcoD of the GMRs and WS under the mixing ratio of 1:1 and 1:2 did not prompt the increase of antibiotic resistance genes (ARGs). Not only that, the likelihood of horizontal gene transfer declined in R-1:1 due to the weaker connection and transport between host and recipient bacteria. Findings of this study suggested that the suitable mixing ratio of GMRs and WS contributes to methane production and system stability, and reduces the dissemination risks of ARGs.

Chlortetracycline alters microbiota of gut or faeces in pigs and leads to accumulation and migration of antibiotic resistance genes

In this study, we investigated the effect of long-term use of chlortetracycline (CTC) on the gut microbiota composition and metabolism profiles in pigs, and the variation of antibiotic resistance genes (ARGs) and microbial communities in faeces and manure during aerobic composting (AC) and anaerobic digestion (AD). The pigs were fed the same basal diet supplemented with or without 75 mg/kg CTC, and fresh faeces of 30-, 60-, 90-, and 120-day-old pigs were collected from the CTC group. The results showed that CTC reduced the diversity of the gut microbiota significantly and changed its structure. Metabolomics analysis of intestinal contents revealed 23 differentially abundant metabolites, mainly organic acids, carbohydrates, and amino acids. Metabolic pathways, such as the TCA cycle, propionate metabolism, and pyruvate metabolism, were changed. From 30 to 120 days of age, the amount of CTC residues in faeces and the abundance of 3 tetracycline resistance genes increased significantly, and it was positively correlated with tetC, tetG, tetW, sul1 and intI2. CTC residue levels and ARGs abundance gradually decreased with fermentation time, and AC was better than AD at reducing ARGs abundance. The results suggest that in-feed CTC can reduce the diversity of the gut microbiota, change the structure, function and metabolism of the bacterial community, and increase the abundance of ARGs in faeces.

Additive 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.

Anaerobic co-digestion: Current status and perspectives

Anaerobic digestion is a long-established technology for the valorization of diverse organic wastes with concomitant generation of valuable resources. However, mono-digestion (i.e., anaerobic digestion using one feedstock) suffers from challenges associated with feedstock characteristics. Co-digestion using multiple feedstocks provides the potential to overcome these limitations. Significant research and development efforts have highlighted several inherent merits of co-digestion, including enhanced digestibility due to synergistic effects of co-substrates, better process stability, and higher nutrient value of the produced co-digestate. However, studies focused on the underlying effects of diverse co-feedstocks on digester performance and stability have not been synthesized so far. This review fills this gap by highlighting the limitations of mono-digestion and critically examining the benefits of co-digestion. Furthermore, this review discusses synergistic effect of co-substrates, characterization of microbial communities, the prediction of biogas production via different kinetic models, and highlights future research directions for the development of a sustainable biorefinery.

Improved reduction of antibiotic resistance genes and mobile genetic elements from biowastes in dry anaerobic co-digestion

This study investigated the performance of anaerobic co-digestion (AcoD) of pig manure and food waste on the reduction of antibiotic resistomes under wet and dry AcoD conditions. High-throughput quantitative PCR technology was utilized for a comprehensive assessment of the performances of the two processes. The results show that dry AcoD with a total solids (TS) content of 20% effectively reduced total antibiotic resistance genes (ARGs) by 1.24 log copies/g wet sample, while only 0.54 log copies/g wet sample was reduced in wet AcoD with a TS content of 5%. Dry AcoD was more efficient in reduction of aminoglycosides, multidrug and sulfonamide resistance genes compared with the reduction of other classes of ARGs. Dry AcoD caused a significant reduction of ARGs with resistance mechanisms of efflux pump and antibiotic deactivation. In contrast, there was no obvious difference in reductions of ARGs with different resistance mechanisms in wet AcoD. Network analysis showed that ARGs were significantly correlated with mobile genetic elements (MGEs) (Spearman's r > 0.8, P < 0.05), as well as microbial communities. Enrichment of ARGs and MGEs was found at the early period of AcoD processes, indicating some ARGs and MGEs increased during the hydrolysis and acidogenesis stages. But after a long retention time, their abundances were effectively reduced by dry AcoD in the subsequent stages.

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.

Impacts of pile temperature on antibiotic resistance, metal resistance and microbial community during swine manure composting

The impact of pile temperature on the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs) during aerobic composting was not fully explored. Here, three composting piles were tested with different maximum temperature control. A total of 211 ARGs, 9 MRGs and 44 MGEs were observed. After 42 days, the numbers and the total abundances of detected genes were generally decreased (3.8%-50.0% and 25.4%-66.0%, respectively) in three treatments, except for the total abundance of MRGs (increased by 82.2%-500.5%). Higher pile temperature substantially stimulated the attenuation of gene diversity, but had no significant impact on promoting the decline in total abundances. For certain gene subtypes, higher temperature remarkably promoted their removal or suppressed their rebounding during maturation phase. The erm(F), sul1 and floR were potential indicators of ARGs during composting. The MGEs IS26, int1, intl2, IncP_oriT and IncQ_oriT acted as crucial hubs for ARGs and MRGs. Genera Acinetobacter, Pseudomonas, Corynebacterium_1 and Proteiniphilum were major potential hosts for multiple genes. The ARG, MRG and MGE profiles were mainly driven by the joint effect of environmental factors and microbial community.

Lignite as additives accelerates the removal of antibiotic resistance genes during poultry litter composting

Antibiotic resistance genes (ARGs) in animal manure are a great threat to human health. This study investigated the effects of lignite addition at three levels (5%, 10%, 15% w/w) on the profiles of ARGs and the bacterial communities during poultry litter composting. Lignite addition effectively promoted the removal of manure-borne ARGs. After 65 days of composting, the relative abundances of ARGs decreased by 8.9% in control (no lignite), and by 15.8%, 27.7% and 41.5% in 5%, 10% and 15% lignite treatments, respectively. Although the total mobile genetic elements were enriched after composting, the enrichment of the intI-1 gene was significantly lower in the 10% and 15% lignite treatments compared with control. Network analysis indicated that Actinobacteria and Firmicutes were potential bacterial hosts for ARGs. Redundancy analysis showed that bacterial community succession played a key role in the shifts of ARGs. Taken together, this study provides evidence that lignite as additives promoted the removal efficacy of ARGs during composting of poultry litter.

Effect of mesophilic anaerobic digestion on the resistome profile of dairy manure

The effect of mesophilic anaerobic digestion (AD) on the resistome profile of manures from two different dairy farms was evaluated using a metagenomic approach. A total of 187 unique Antibiotic resistance genes (ARGs) for 17 different classes of antibiotics were detected in raw (undigested) manures. The results indicate that regardless of the origin of the dairy manure, mesophilic AD was capable of reducing or enriching the relative abundance of some ARGs. The main driver of these changes was strongly correlated with the evolution of the microbial community during the AD process. Putative ARG hosts were suggested by analyses of the co-occurrence of microbial groups and ARGs. Finally, network analyses revealed that mesophilic AD could also reduce the co-occurrence of different groups of ARGs potentially located in the same genetic elements. Our results provide valuable insights into the microbial mechanisms driving the diversity and abundance of ARGs during mesophilic AD.

Performance and Microbial Community of Different Biofilm Membrane Bioreactors Treating Antibiotic-Containing Synthetic Mariculture Wastewater

The performance of pollutant removals, tetracycline (TC) and norfloxacin (NOR) removals, membrane fouling mitigation and the microbial community of three Anoxic/Oxic membrane bioreactors (AO-MBRs), including a moving bed biofilm MBR (MBRa), a fixed biofilm MBR (MBRb) and an AO-MBR (MBRc) for control, were compared in treating antibiotic-containing synthetic mariculture wastewater. The results showed that MBRb had the best effect on antibiotic removal and membrane fouling mitigation compared to the other two bioreactors. The maximum removal rate of TC reached 91.65% and the maximum removal rate of NOR reached 45.46% in MBRb. The addition of antibiotics had little effect on the removal of chemical oxygen demand (COD) and ammonia nitrogen (NH₄⁺-N)—both maintained more than 90% removal rate during the entire operation. High-throughput sequencing demonstrated that TC and NOR resulted in a significant decrease in the microbial diversity and the microbial richness MBRs. Flavobacteriia, Firmicutes and Azoarcus, regarded as drug-resistant bacteria, might play a crucial part in the removal of antibiotics. In addition, the dynamics of microbial community had a great change, which included the accumulation of resistant microorganisms and the gradual reduction or disappearance of other microorganisms under antibiotic pressure. The research provides an insight into the antibiotic-containing mariculture wastewater treatment and has certain reference value.