Influence of zinc on biogas production and antibiotic resistance gene profiles during anaerobic digestion of swine manure

Environmental fate of antibiotic resistance genes in livestock farming

As emerging environmental pollutants, antibiotic resistance genes (ARGs) are prevalent in livestock farms and their surrounding environments. Although existing studies have focused on ARGs in specific environmental media, comprehensive research on ARGs within farming environments and their adjacent areas remains scarce. This review explores the sources, pollution status, and transmission pathways of ARGs from farms to the surrounding environment. Drawing on the "One Health" concept, it also discusses the potential risks of ARGs transmission from animals to human pathogens and the resulting impact on human health. Our findings suggest that the emergence of ARGs in livestock farming environments primarily results from intrinsic resistance and genetic mutations, while their spread is largely driven by horizontal gene transfer. The distribution of ARGs varies according to the type of resistance genes, seasonal changes, and the medium in which they are present. ARGs are disseminated into the surrounding environment via pathways such as manure application, wastewater discharge, and aerosol diffusion. They may be absorbed by humans, accumulating in the intestinal microbiota and subsequently affecting human health. The spread of ARGs is influenced by the interplay of microbial communities, antibiotics, heavy metals, emerging pollutants, and environmental factors. Additionally, we have outlined three control strategies: reducing the emergence of ARGs at the source, controlling their spread, and minimizing human exposure. This article provides a theoretical framework and scientific guidance for understanding the cross-media migration of microbial resistance in livestock farming environments.

Mechanisms and influencing factors of horizontal gene transfer in composting system: A review

Organic solid wastes such as livestock manure and sewage sludge are important sources and repositories of antibiotic resistance genes (ARGs). Composting, a solid waste treatment technology, has demonstrated efficacy in degrading various antibiotics and reducing ARGs. However, some recalcitrant ARGs (e.g., sul1, sul2) will enrich during the composting maturation period. These ARGs persist in compost products and spread through horizontal gene transfer (HGT). We analyzed the reasons behind the increase of ARGs during the maturation phase. It was found that the proliferation of ARG-host bacteria and HGT process play an important role. This article revealed that microbial physiological responses, environmental factors, pollutants, and quorum sensing (QS) can all influence the HGT process in composting systems. We examined the influence of these factors on HGT in the compost system and summarized potential mechanisms by analyzing the alterations in microbial communities. We comprehensively summarized the HGT hazards that these factors may present in composting systems. Finally, we summarized methods to inhibit HGT in compost, such as using additives, quorum sensing inhibitors (QSIs), microbial inoculation, and predicting HGT events. Overall, the HGT mechanism and driving force in complex composting systems are still insufficiently studied. In view of the current situation, using predictions to assess the risk of HGT in composting may be advisable.

Comparison of the short- and long-term effects of zinc ions on the anaerobic mesophilic co-digestion of food waste and waste activated sludge: Digester performance, antibiotic resistance gene reduction and the microbial community

Heavy metals contained in waste activated sludge (WAS), especially zinc ions, have an inhibitory effect on the anaerobic digestion. However, the effects of zinc ions on digester performance, antibiotic resistance genes (ARGs) reduction, and the microbial community involved in the anaerobic mesophilic co-digestion (AcoD) of WAS and food waste (FW) have not been fully characterized. Therefore, batch trials and continuous stirred tank reactors were used under different zinc-ion concentrations. Findings showed that the AcoD system can tolerate a maximum zinc ion of 540 mg/L in a short-term batch and 470 mg/L in a long-term AcoD system, promoting methane production of approximately 1.0-17.0 %. Metagenomic analysis revealed that syntrophic H2 transfer occurred between Syntrophomonas and Methanoculleus and the aceticlastic and hydrogenotrophic methanogenic pathways were both enhanced by 1.18- and 1.16 times, respectively. Moreover, the relative abundance of Methanosarcina increased from 58.4 % to 72.5 % at 470 mg/L to adapt to the high zinc ion concentration during long-term continuous operation. These results revealed that AcoD with a low zinc ion concentration can effectively increase the removal percentage of ARGs. The results provide guidance for biogas recovery and use of mesophilic AcoD with FW and WAS containing high zinc ion concentrations without pretreatment process.

Influential factors in anaerobic digestion of rice-derived food waste and animal manure: A comprehensive review

Utilization of organic community wastes towards deriving sustainable renewable energy and adequate disposal of the residual has been an important topic of investigation. Anaerobic digestion and co-digestion of rice-derived food waste and animal manure for sustainable biogas generation is crucial from the view-point of community consumption. This paper presents an extensive review of the important and recent contributions in the related areas. The critical physico-chemical parameters involved in such digestion process are analyzed, including temperature, carbon-nitrogen ratio, microorganisms, pH, substrate characteristics, organic loading rate, hydraulic retention time, volatile fatty acids, ammonia, and light/heavy metal ions. Studies implied that the optimum yield of biogas production could be achieved only when the values of the parameters exist in the specific ranges. Few recent studies highlighted the use of emerging techniques including micro-aerobic system, additives, laser radiation, bio-electrochemical field, among others for efficiency enhancement of the digestion process and optimum yield. The entire study provided a set of important conclusions and future research directives are as well proposed.

High-throughput profiling the effects of zinc on antibiotic resistance genes in the anaerobic digestion of swine manure

The problem of antibiotic resistance genes (ARGs) caused by heavy metals has attracted extensive attention of human beings. Zn, a widely used feed additive, has a very high residue in swine manure, but the distribution characteristics of ARGs imposed by Zn in anaerobic digestion (AD) products are not clear. In this study, the behaviour of mobile genetic elements (MGEs), bacterial community, and their association with ARGs were determined in the presence of 125 and 1250 mg L-1 Zn in AD system of swine manure. Zn-treated enriched the abundance of ARGs, and produced some new genotypes that were not detected in CK treatment. In addition, low concentration of Zn significantly increased the relative abundance of ARGs, as compared to higher Zn and CK group. Correspondingly, the abundances of most top30 genus were highest in ZnL (125 mg L-1 Zn), followed by CK and ZnH (1250 mg L-1 Zn). Notably, network analysis showed that the relationship between ARGs and MGEs is closer than that ARGs and bacteria, suggesting that ARGs increased in Zn-treated, especially low level Zn, may be due to the amplification transfer of ARGs among varied microorganisms by horizontal transfer with MGEs. Therefore, strengthen the management of in livestock manure is crucial to control the spread of ARGs in organic fertilizers.

An overview of the occurrence, impact of process parameters, and the fate of antibiotic resistance genes during anaerobic digestion processes

Antibiotic resistance genes (ARGs) have emerged as a significant global health threat, contributing to fatalities worldwide. Wastewater treatment plants (WWTPs) and livestock farms serve as primary reservoirs for these genes due to the limited efficacy of existing treatment methods and microbial adaptation to environmental stressors. Anaerobic digestion (AD) stands as a prevalent biological treatment for managing sewage sludge and manure in these settings. Given the agricultural utility of AD digestate as biofertilizers, understanding ARGs' fate within AD processes is essential to devise effective mitigation strategies. However, understanding the impact of various factors on ARGs occurrence, dissemination, and fate remains limited. This review article explores various AD treatment parameters and correlates to various resistance mechanisms and hotspots of ARGs in the environment. It further evaluates the dissemination and occurrence of ARGs in AD feedstocks and provides a comprehensive understanding of the fate of ARGs in AD systems. This review explores the influence of key AD parameters such as feedstock properties, pretreatments, additives, and operational strategies on ARGs. Results show that properties such as high solid content and optimum co-digestion ratios can enhance ARG removal, while the presence of heavy metals, microplastics, and antibiotics could elevate ARG abundance. Also, operational enhancements, such as employing two-stage digestion, have shown promise in improving ARG removal. However, certain pretreatment methods, like thermal hydrolysis, may exhibit a rebounding effect on ARG levels. Overall, this review systematically addresses current challenges and offers future perspectives associated with the fate of ARGs in AD systems.

Tracing the transfer characteristics of antibiotic resistance genes from swine manure to biogas residue and then to soil

Based on laboratory simulation experiments and metagenomic analysis, this study tracked the transmission of antibiotic resistance genes (ARGs) from swine manure (SM) to biogas residue and then to soil (biogas residue as organic fertilizer (OF) application). ARGs were abundant in SM and they were assigned to 11 categories of antibiotics. Among the 383 ARG subtypes in SM, 43 % ARG subtypes were absent after anaerobic digestion (AD), which avoided the transfer of these ARGs from SM to soil. Furthermore, 9 % of the ARG subtypes in SM were introduced into soil after amendment with OF. Moreover, 43 % of the ARG subtypes in SM were present in OF and soil, and their abundances increased slightly in the soil amended with OF. The bacterial community in the soil treated with OF was restored to its original state within 60 to 90 days, probably because the abundances of ARGs were elevated but not significantly in the soil. Network analysis identified 31 potential co-host bacteria of ARGs based on the relationships between the bacteria community members, where they mainly belonged to Firmicutes, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. This study provides a basis for objectively evaluating pollution by ARGs in livestock manure for agricultural use.

Abiotic and biotic roles of metals in the anaerobic digestion of sewage sludge: A review

Anaerobic digestion (AD) is a promising technique for sludge treatment and resource recovery. Metals are very important components of sludge and can have substantial effects on its complex nature and microbial activity. However, systematic reviews have not addressed how metals in sludge affect AD and how they can be regulated to improve AD. This paper comprehensively reviews the effects of metals on the AD of sludge from both abiotic and biotic perspectives. First, we introduce the contents and basic characteristics (e.g., chemical forms) of intrinsic metals in sewage sludge. Then, we summarise the main mechanism by which metals influence sludge properties and the methods for removing metals and thus improving AD. Next, we analyze the effects of both intrinsic and exogenous metals on the enzymes and microbial communities involved in anaerobic bioconversion, focusing on the types, critical concentrations and valence states of the metals. Finally, we propose ideas for future research on the roles of metals in the AD of sludge. In summary, this review systematically clarifies the roles of metals in the AD of sludge and provides a reference for improving AD by regulating these metals.

Mechanistic insights into synergistic facilitation of copper/zinc ions and dewatered swine manure-derived biochar on anaerobic digestion of swine wastewater

Biochar-assisted anaerobic digestion (AD) has been proposed an advanced system for swine wastewater (SW) management. However, the effects of metallic nutrients in SW, such as copper/zinc ions (Cu2+/Zn2+), on the biochar-assisted AD of SW are not well understood. This study investigated the influences of individual Cu2+/Zn2+ or dewatered swine manure-derived biochar, as well as their combined additions, on the AD of SW. The results showed that exposure to 50 mg/L Cu2+/Zn2+ temporary inhibited methane production, but the addition of 20 g/L biochar alleviated this inhibition by shortening the methanogenic lag time and increasing methane yield. Following a period of acclimation, both Cu2+/Zn2+ and biochar promoted methane production, although metagenomic analysis revealed distinct mechanisms underlying their promotion. Cu2+/Zn2+ enhanced ATP processing, including electron exchange between NADH/NAD+ and succinate/fumarate transformation, by 26.0-35.8%. Additionally, the gene encoding Coenzyme M methylation was upregulated by 36.2% along with enrichments of Methanocullus and Methanosarcina, contributing to accelerated hydrolysis and methanogenesis rates by 54.7% and 44.8%, respectively. On the other hand, biochar mainly stimulated bacterial F-type ATPase activities by 28.4%, likely facilitating direct interspecies electron transfer between Geobacter and Methanosarcina for syntrophic methanogenesis. The combined addition of Cu2+/Zn2+ and biochar resulted in "win-win" benefits, significantly increasing the maximum methane production rate from 40.3 mL CH4/d to 53.7 mL CH4/d. Moreover, the introduction of biochar into AD of SW facilitated the transformation of more Cu2+/Zn2+ from a reducible Fe-Mn oxides form to a residual form, which potentially reduced the metallic toxicity of the digestate for soil amendment. The findings of this study provide novel insights into understanding the synergistic impacts of heavy metals and biochar in regulating SW during AD, as well as the management of associated digestate.

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

Zinc/carbon nanomaterials inhibit antibiotic resistance genes by affecting quorum sensing and microbial community in cattle manure production

This study used metagenomic sequencing to examine the effects of carbon-based zinc oxide nanoparticles (CZnONPs) and graphene-based zinc oxide nanoparticles (GZnONPs) on quorum sensing (QS), antibiotic resistance genes (ARGs) and microbial community changes during cattle manure production. The manure zinc content was significantly reduced in GZnONPs group. In the QS pathway, the autoinducer gene increases significantly in Control group, while the transporter and repressor genes experience a substantial increase in CZnONPs group. These results contributed to the significantly decreased the abundance of ARGs in GZnONPs group. The co-occurrence network analysis revealed a correlation between core ARGs and QS-related KEGG Orthology or ARGs' hosts, indicating that the selective pressure of zinc influences microbial QS, forming a unique ARG pattern in in vivo anaerobic fermentation. These findings suggest that implementing nutritional regulation in farming practices can serve as a preventive measure to mitigate the potential transmission of ARGs resulting from livestock waste.

The Potential of Bioaugmentation-Assisted Phytoremediation Derived Maize Biomass for the Production of Biomethane via Anaerobic Digestion

Anthropogenic behaviors are causing the severe build-up of heavy metal (HM) pollutants in the environment, particularly in soils. Amongst a diversity of remediation technologies, phytoremediation is an environmentally friendly technology that, when coupling tolerant plants to selected rhizospheric microorganisms, can greatly stimulate HM decontamination of soils. Maize (Zea mays) is a plant with the reported capacity for HM exclusion from contaminated soil but also has energetic importance. In this study, Zea mays was coupled with Rhizophagus irregularis, an arbuscular mycorrhizal fungus (AMF), and Cupriavidus sp. strain 1C2, a plant growth-promoting rhizobacteria (PGPR), as a remediation approach to remove Cd and Zn from an industrial contaminated soil (1.2 mg Cd kg-1 and 599 mg Zn kg-1) and generate plant biomass, by contrast to the conservative development of the plant in an agricultural (with no metal pollution) soil. Biomass production and metal accumulation by Z. mays were monitored, and an increase in plant yield of ca. 9% was observed after development in the contaminated soil compared to the soil without metal contamination, while the plants removed ca. 0.77% and 0.13% of the Cd and Zn initially present in the soil. The resulting biomass (roots, stems, and cobs) was used for biogas generation in several biomethane (BMP) assays to evaluate the potential end purpose of the phytoremediation-resulting biomass. It was perceptible that the HMs existent in the industrial soil did not hinder the anaerobic biodegradation of the biomass, being registered biomethane production yields of ca. 183 and 178 mL of CH4 g-1 VS of the complete plant grown in non-contaminated and contaminated soils, respectively. The generation of biomethane from HM-polluted soils' phytoremediation-derived maize biomass represents thus a promising possibility to be a counterpart to biogas production in an increasingly challenging status of renewable energy necessities.

Effects of Metal and Metal Ion on Biomethane Productivity during Anaerobic Digestion of Dairy Manure

To overcome major limiting factors of microbial processes in anaerobic digestion (AD), metal and metal ions have been extensively studied. However, there is confusion about the effects of metals and metal ions on biomethane productivity in previous research. In this study, Zn and Zn2+ were selected as representatives of metals and metal ions, respectively, to investigate the effects on biomethane productivity. After the metals and metal ions at different concentrations were added to the batch AD experiments under the same mesophilic conditions, a Zn dose of 1 g/L and a Zn2+ dose of 4 mg/L were found to cause the highest biomethane production, respectively. The results indicate that metal (Zn) and metal ion (Zn2+) have different mechanisms to improve AD performance. There may be two possible explanations. To act as conductive materials in interspecies electron transfer (IET), relatively high doses of metals (e.g., 1 g/L of Zn, 10 g/L of Fe) are needed to bridge the electron transfer from syntrophic bacteria to methanogenic archaea in the AD process. As essential mineral nutrients, the AD system requires relatively low doses of metal ions (e.g., 4 mg/L of Zn2+, 5 mg/L of Fe2+) to supplement the component of various enzymes that catalyze anaerobic reactions and transformations. This research will provide clear insight for selecting appropriate amounts of metals or metal ions to enhance biomethane productivity for industrial AD processes.

Environmental drivers and interaction mechanisms of heavy metal and antibiotic resistome exposed to amoxicillin during aerobic composting

The environmental accumulation and spread of antibiotic resistance pose a major threat to global health. Aerobic composting has become an important hotspot of combined pollution [e.g., antibiotic resistance genes (ARGs) and heavy metals (HMs)] in the process of centralized treatment and resource utilization of manure. However, the interaction mechanisms and environmental drivers of HMs resistome (MRGs), antibiotic resistance (genotype and phenotype), and microbiome during aerobic composting under the widely used amoxicillin (AMX) selection pressure are still poorly understood. Here, we investigated the dynamics of HMs bioavailability and their MRGs, AMX-resistant bacteria (ARB) and antibiotic resistome (ARGs and intI1), and bacterial community to decipher the impact mechanism of AMX by conducting aerobic composting experiments. We detected higher exchangeable HMs and MRGs in the AMX group than the control group, especially for the czrC gene, indicating that AMX exposure may inhibit HMs passivation and promote some MRGs. The presence of AMX significantly altered bacterial community composition and AMX-resistant and -sensitive bacterial structures, elevating antibiotic resistome and its potential transmission risks, in which the proportions of ARB and intI1 were greatly increased to 148- and 11.6-fold compared to the control group. Proteobacteria and Actinobacteria were significant biomarkers of AMX exposure and may be critical in promoting bacterial resistance development. S0134_terrestrial_group was significantly negatively correlated with bla_TEM and czrC genes, which might play a role in the elimination of some ARGs and MRGs. Except for the basic physicochemical (MC, C/N, and pH) and nutritional indicators (NO₃ ^--N, NH₄ ⁺-N), Bio-Cu may be an important environmental driver regulating bacterial resistance during composting. These findings suggested the importance of the interaction mechanism of combined pollution and its synergistic treatment during aerobic composting need to be emphasized.

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.

A critical review of process parameters influencing the fate of antibiotic resistance genes in the anaerobic digestion of organic waste

The overuse and inappropriate disposal of antibiotics raised severe public health risks worldwide. Specifically, the incomplete antibiotics metabolism in human and animal bodies contributes to the significant release of antibiotics into the natural ecosystems and the proliferation of antibiotic-resistant bacteria carrying antibiotic-resistant genes. Moreover, the organic feedstocks used for anaerobic digestion are often highly-rich in residual antibiotics and antibiotic-resistant genes. Hence, understanding their fate during anaerobic digestion has become a significant research focus recently. Previous studies demonstrated that various process parameters could considerably influence the propagation of the antibiotic-resistant genes during anaerobic digestion and their transmission via land application of digestate. This review article scrutinizes the influences of process parameters on antibiotic-resistant genes propagation in anaerobic digestion and the inherent fundamentals behind their effects. Based on the literature review, critical research gaps and challenges are summarized to guide the prospects for future studies.

Quantitative assessment of exposure to fecal contamination in urban environment across nine cities in low-income and lower-middle-income countries and a city in the United States

BACKGROUND

During 2014 to 2019, the SaniPath Exposure Assessment Tool, a standardized set of methods to evaluate risk of exposure to fecal contamination in the urban environment through multiple exposure pathways, was deployed in 45 neighborhoods in ten cities, including Accra and Kumasi, Ghana; Vellore, India; Maputo, Mozambique; Siem Reap, Cambodia; Atlanta, United States; Dhaka, Bangladesh; Lusaka, Zambia; Kampala, Uganda; Dakar, Senegal.

OBJECTIVE

Assess and compare risk of exposure to fecal contamination via multiple pathways in ten cities.

METHODS

In total, 4053 environmental samples, 4586 household surveys, 128 community surveys, and 124 school surveys were collected. E. coli concentrations were measured in environmental samples as an indicator of fecal contamination magnitude. Bayesian methods were used to estimate the distributions of fecal contamination concentration and contact frequency. Exposure to fecal contamination was estimated by the Monte Carlo method. The contamination levels of ten environmental compartments, frequency of contact with those compartments for adults and children, and estimated exposure to fecal contamination through any of the surveyed environmental pathways were compared across cities and neighborhoods.

RESULTS

Distribution of fecal contamination in the environment and human contact behavior varied by city. Universally, food pathways were the most common dominant route of exposure to fecal contamination across cities in low-income and lower-middle-income countries. Risks of fecal exposure via water pathways, such as open drains, flood water, and municipal drinking water, were site-specific and often limited to smaller geographic areas (i.e., neighborhoods) instead of larger areas (i.e., cities).

CONCLUSIONS

Knowledge of the relative contribution to fecal exposure from multiple pathways, and the environmental contamination level and frequency of contact for those "dominant pathways" could provide guidance for Water, Sanitation, and Hygiene (WASH) programming and investments and enable local governments and municipalities to improve intervention strategies to reduce the risk of exposure to fecal contamination.

Quantification of antibiotic resistance genes and mobile genetic in dairy manure

Background

Antibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants of concern potentially posing risks to human and animal health, and this research studied the prevalence of antimicrobial resistance in dairy manure.

Methods

This study is focused on investigating prevalence of ARGs in California dairy farm manure under current common different manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: (1) flushed manure (FM), (2) fresh pile (FP), (3) compost pile (CP), (4) primary lagoon (PL), and (5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of eight ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLS_B) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1).

Results

Prevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current different manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of different manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment.

Degradation of antibiotic resistance genes and mobile gene elements in dairy manure anerobic digestion

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins–Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.

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.

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.

Fate of antibiotic resistance genes and metal resistance genes during the thermophilic fermentation of solid and liquid swine manures in an ectopic fermentation system

Environmental pollution due to resistance genes from livestock manure has become a serious issue that needs to be resolved. However, little studies focused on the removal of resistance genes in simultaneous processing of livestock feces and urine. This study investigated the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and class 1 integron-integrase gene (intI1) during thermophilic fermentation of swine manure in an ectopic fermentation system (EFS), which has been regarded as a novel system for efficiently treating both feces and urine. The abundances of MRGs and tetracycline resistance genes were 34.44-97.71% lower in the EFS. The supplementation of heavy metals significantly increased the abundance of intI1, with the enhancement effect of copper being more prominent than that of zinc. The highest abundances of resistance genes and intI1 were observed at high Cu levels (A2), indicating that Cu can increase the spreading of resistance genes through integrons. Network analysis revealed the co-occurrence of ARGs, MRGs, and intI1, and these genes potentially shared the same host bacteria. Redundancy analysis showed that the bacterial community explained most of the variations in ARGs, and environmental factors had influences on ARGs abundances by modulating the bacterial community composition. The decreased Sphingomonas, Comamonas, Acinetobacter, Lactobacillus, Bartonella, Rhizobium, and Bacteroides were mainly responsible for the reduced resistance genes. These results demonstrate that EFS can reduce resistance genes in simultaneous processing of livestock feces and urine.

Evaluation of biogas production potential of trace element-contaminated plants via anaerobic digestion

Within the domain of phytoremediation research, the proper disposal of harvestable plant parts, that remove pollutants from contaminated soil, has been attracted extensive attention. Here, the bioenergy generation capability of trace metals (Cu, Pb, Zn, Cd, Mn, and As) polluted plants was assessed. The biogas production potential of accumulators or hyperaccumulator plants, Elsholtzia haichowensis, Sedum alfredii, Solanum nigrum, Phytolacca americana and Pteris vittata were 259.2 ± 1.9, 238.7 ± 4.2, 135.9 ± 0.9, 129.5 ± 2.9 and 106.8 ± 2.1 mL/g, respectively. The presence of Cu (at approximately 1000 mg/kg) increased the cumulative biogas production, the daily methane production and the methane yield of E. haichowensis. For S. alfredii, the presence of Zn (≥500 mg/kg) showed a significant negative impact on the methane content in biogas, and the daily methane production, which decreased the biogas and methane yield. The biogas production potential increased when the content of Mn was at 5 000-10,000 mg/kg, subsequently, decreased when the value of Mn at 20,000 mg/kg. However, Cd (1-200 mg/kg), Pb (125-2000 mg/kg) and As (1250-10,000 mg/kg) showed no distinctive change in the cumulative biogas production of S. nigrum, S. alfredii and P. vittata, respectively. The methane yield showed a strong positive correlation (R² =0.9704) with cumulative biogas production, and the energy potential of the plant residues were at 415-985 kWh/ton. Thus, the anaerobic digestion has bright potential for the disposal of trace metal contaminated plants, and has promising prospects for the use in energy production.

The relationship between culturable doxycycline-resistant bacterial communities and antibiotic resistance gene hosts in pig farm wastewater treatment plants

Pig farm wastewater treatment plants (WWTPs) are an important repository for resistant bacterial communities (RBCs) and antibiotic resistance genes (ARGs). However, the relationship between RBCs and ARG hosts has not been well characterized. In this study, water samples from influent and effluent from five pig farm WWTPs were collected. Gradient concentrations of doxycycline (DOX) were used to screen the culturable RBCs. The abundance of 21 subtypes of ARGs and the bacterial community were investigated. This study detected a large number of culturable DOX-RBCs and ARGs in the influent and effluent of pig farm WWTPs. The abundances of ARGs and RBCs in all effluent samples was significantly lower than that in the influent samples (P < 0.05), which indicated that the WWTPs can effectively remove most ARGs and RBCs in pig farm wastewater. The main potential culturable RBCs in pig farm wastewater were the dominant bacteria Proteobacteria, Actinobacteria, Pseudomonas, and Rheinheimera. However, most of the ARGs were mainly present in Bacteroidetes, Actinobacteria, Corynebacteriaceae, Macellibacteroides, Acinetobacter, and Enterobacteriaceae, which are considered potential ARG hosts. The results presented here showed that there were obvious differences between the species of culturable DOX-RBCs and ARG hosts in the pig farm WWTPs, which may be due to various environmental factors. This highlights the urgent need for further research on the relationship between RBCs and ARG hosts.

Antibiotic resistance gene transfer during anaerobic digestion with added copper: Important roles of mobile genetic elements

The abuse of heavy metals as feed additives in livestock is widespread and it might aggravate the spread of antibiotic resistance genes (ARGs) in the environment. However, the mechanisms that allow heavy metals to increase the transmission of ARGs in the environment remain unclear. Cu is the heavy metal present at the highest concentration in livestock manure, and thus Cu was selected to investigate the responses of ARGs to heavy metals. The effects of the microbial communities, mobile genetic elements (MGEs), and heavy metal resistance genes (HMRGs) on ARGs were determined in the presence of 75 and 227 mg L^-1 Cu in a swine manure anaerobic digestion (AD) system. In the AD products, the presence of residual Cu (75 and 227 mg L^-1) increased the total ARGs, HMRGs, and some MGEs, and the higher Cu selected more ARGs than the lower Cu treatment. The results demonstrated that Cu could promote the co-selection of HMRGs, ARGs, and MGEs. The different levels of Cu did not change the bacterial community composition, but they influenced the abundances of bacteria during AD. Network analysis showed that the presence of Cu increased the co-occurrence of specific bacteria containing ARGs, HMRGs, and MGEs. Furthermore, the co-occurrence of MGEs and ARGs increased greatly compared with that of HMRGs and ARGs. Therefore, compared HMRGs, the increased MGEs had the main effect on increasing of ARGs.

Impacts of Cu and Zn on the performance, microbial community dynamics and resistance genes variations during mesophilic and thermophilic anaerobic digestion of swine manure

In this work, fate of antibiotic resistance genes (ARGs), heavy metal resistance genes (MRGs) and intI1 were investigated during mesophilic (mAD) and thermophilic anaerobic digestion (tAD) of swine manure with presence of Cu and Zn. Results showed that metal reduced the lag phase time. Cu showed stronger inhibition than Zn on archaea community and metals inhibited the growth of acetoclastic methanogens during mAD. Although total concentration of metals increased after AD, they were transformed into stable state. The abundance of qnrS, sul1, sul2 and drfA7 increased 1.2-5.7 times after mAD, while reduced after tAD, showed that tAD was effective in ARGs removal. Structural equation model analysis suggested that intI1 had the most standardized direct effects on ARGs variation in mAD (R = 0.85, p < 0.01), while the co-occurrence of MRGs with ARGs showed significantly positive influences on ARGs variation in tAD (R = 0.82, p < 0.01).

Effects of copper salts on performance, antibiotic resistance genes, and microbial community during thermophilic anaerobic digestion of swine manure

This study investigated methane production and ARGs reduction during thermophilic AD of swine manure with the addition of different Cu salts (cupric sulfate, cupric glycinate, and the 1:1 mixture of these two salts). Results showed methane production was increased by 28.78% through adding mixed Cu salts. The mixed Cu group effectively reduced total ARGs abundance by 26.94%, suggesting mixed Cu salts did not promote the potential ARGs risk. The positive effects of mixed Cu salts on AD performance and ARGs removal might be ascribed to the low bioavailability. Microbial community analysis indicated the highest abundances of Clostridia_MBA03 and Methanobacterium in the mixed Cu group might cause the increased methane production. Spearman's rank correlation analysis elucidated the succession in microbial community induced by environmental factors was the main driver for shaping ARGs profiles. Thus, mixed Cu salts could be an alternative to replace the inorganic Cu salt in animal feed additives.

Enhancing anaerobic digestion of dairy and swine wastewater by adding trace elements: evaluation in batch and continuous experiments

Trace elements play a critical role for microbial activity in anaerobic digestion (AD) but their effects were probably overestimated in batch tests and should be comparably evaluated in continuous systems. In this study, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺ and Zn²⁺ were added in different concentrations to manure wastewater, and the effects were compared in both batch and continuous systems. The results were used to demonstrate suitable trace element compositions for AD of dairy and swine wastewater, and to compare the outcomes from batch and continuous systems. Fe²⁺ and Zn²⁺ were identified as being the most efficient stimulant of dairy and swine wastewater respectively. The addition of 5 mg/L Fe²⁺ and 0.4 mg/L Zn²⁺ increased the batch specific methane yield by 62% and 126% for dairy and swine wastewater, respectively. Nevertheless, a lower increment of 2% and 21%, for dairy and swine wastewater was obtained in the 120-day continuously-fed experiments. The 16S rRNA gene sequencing results indicated a relationship between the methanogens population, specific methanogenic activities, propionate, and dissolved hydrogen. Conclusively, the addition of a low dosage of Fe²⁺ and Zn²⁺ is a feasible strategy to enhance the methanogenic metabolism of the AD of dairy and swine wastewater respectively.

Heavy metals interact with the microbial community and affect biogas production in anaerobic digestion: A review

Heavy metals (HMs), which accumulate in digestion substrates, such as plant residues and livestock manure, can affect biogas yields during anaerobic digestion (AD). Low concentration of Cu²⁺ (0-100 mg/L), Fe²⁺ (50-4000 mg/L), Ni²⁺ (0.8-50 mg/L), Cd²⁺ (0.1-0.3 mg/L), and Zn²⁺ (0-5 mg/kg) promote biogas production, while high concentrations inhibit AD. Trace amounts of HMs are necessary for the activity of some enzymes. For example, Cu²⁺ and Cd²⁺ serve as cofactors in the catalytic center of cellulase and stimulate enzyme activity. High contents of Cd²⁺ and Cu²⁺ inhibit enzyme activity by disrupting protein structures. Trace amounts of HMs stimulate the growth and activity of methanogens, while high levels have toxic effects on methanogens. HMs affect the hydrolysis, acidification, and other biochemical reactions of organics in AD by changing the enzyme structure and they also impact methanogen growth. A better understanding of the impact of HMs on AD can provide valuable insights for improving the digestion of poultry manure and plant residues contaminated with HMs, as well as help mitigate HMs pollution. Although several studies have been conducted in this field, few comprehensive reviews have examined the effect of many common HMs on AD. This review summarizes the effects of HMs on the biogas production efficiency of AD and also discusses the effects of HMs on the activities of enzymes and microbial communities.

Response of antibiotic resistance genes abundance by graphene oxide during the anaerobic digestion of swine manure with copper pollution

The pollution of various environments with antibiotic resistance genes (ARGs) is an urgent problem that needs to be addressed, especially in heavy metal-polluted environments. This study investigated the responses of ARGs and mobile genetic elements (MGEs) to the addition of graphene oxide (GO) to swine manure containing a high concentration copper during anaerobic digestion. The total copy numbers of ARGs and MGEs were significantly enhanced by the pressure due to Cu. GO significantly decreased the ARG and MGE copy numbers, where the low GO concentration performed better than the high GO concentration. Network analysis showed that most of the ARGs and MGEs co-occurred and they shared the same major potential host bacteria. The contributions of different factors to ARG abundances were assessed by redundancy analysis and MGEs had the most important effect on the fate of ARGs. Thus, GO may reduce the abundance of ARGs mainly by removing MGEs.

Performance evaluation of gaseous emissions and Zn speciation during Zn-rich antibiotic manufacturing wastes and pig manure composting

In this study, the co-composting performance of Zn-rich antibiotic manufacturing wastes (AMW) and pig manure (PM) was evaluated. Four treatments, representing 2.5%, 5%, 10% and 20% of AMW (of PM dry weight) and control without AMW, were established during composting. Results suggested that the temperature, pH, electrical conductivity, NH4+-N and germination index in end product met the maturity and sanitation requirement. More than 99% of residual antibiotic was removed. Compared with PM composting alone, the cumulative CH4 and N2O emissions in AMW composting increased by 13.46-79.00% and 10.78-65.12%, respectively. While the higher mixing ratios of AMW (10% and 20%) presented a negative impact on composing by inhibiting organic matter (OM) degradation and higher NH3 emissions. The AMW had highly bioavailable Zn, but the exchangeable faction of Zn significantly decreased with the composting progress.

Responses and successions of sulfonamides, tetracyclines and fluoroquinolones resistance genes and bacterial community during the short-term storage of biogas residue and organic manure under the incubator and natural conditions

Biogas residue and organic manure are frequently used for crop planting. However, the evaluation of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and bacterial community before their applications to fields is still lacking. This study monitored the variations of bacteria resistant to sulfadiazine, tetracycline and norfloxacin, 57 resistance genes for sulfonamides, tetracyclines and fluoroquinolones as well as the bacterial community during the 28-day aerobic storage of biogas residue and organic manure by using viable plate counts, high-throughput qPCR and Illumina MiSeq sequencing methods. Then two storage conditions, incubator (25 °C) and natural environment, were used to assess the responses of ARB and ARGs to the environmental factors. Results showed that a total of 35 and 21 ARGs were detected in biogas residue and organic manure, respectively. ARB and ARGs were enriched up to 8.01-fold in biogas residue after the 28-day storage, but varied in a narrow range during the storage of organic manure. Compared with the incubator condition, the proliferation of ARB and ARGs in biogas residue under the natural condition was relatively inhibited by the varied and complicated environmental factors. However, we found that there was no significant difference of ARB and ARGs in organic manure between the incubator and natural conditions. Bacterial community was also shifted during the storage of biogas residue, especially Bacteroidetes_VC2.1_Bac22, Aequorivita, Luteimonas and Arenimonas. Network analysis revealed that the relationship in biogas residue was much more complicated than that in organic manure, which ultimately resulted in large successions of ARB and ARGs during the short-term storage of biogas residue. Therefore, we suggest that further measures should be taken before the application of biogas residue to fields.

Contributions of the microbial community and environmental variables to antibiotic resistance genes during co-composting with swine manure and cotton stalks

Understanding the main drivers that affect the spread of antibiotic resistance genes (ARGs) during the composting process is important for the removal of ARGs. In this study, three levels of tylosin (25, 50, and 75 mg kg^-1 on a dry weight basis) were added to swine manure plus a control, which was composted with cotton stalks. Each treatment was repeated in triplicate and the ARG profiles were determined with different levels of tylosin. The top 35 genera and ARGs profiles were clustered together based on the composting time. Combined composting parameters (temperature, pH, NH₄⁺-N, NO₃-N, and moisture content) accounted for 78.4% of the total variation in the changes in the potential host bacteria. In addition, the selected five composting parameters and six phyla (including 25 potential host bacterial genera) explained 46.9% and 30.7% of the variation in the ARG profiles according to redundancy analysis, respectively. The variations in ARGs during the composting process were mainly affected by the dynamics of potential host bacteria rather than integrons and the selective pressure due to bio-Cu and bio-Zn.

Problematic effects of antibiotics on anaerobic treatment of swine wastewater

Swine wastewaters with high levels of organic pollutants and antibiotics have become serious environmental concerns. Anaerobic technology is a feasible option for swine wastewater treatment due to its advantage in low costs and bioenergy production. However, antibiotics in swine wastewater have problematic effects on micro-organisms, and the stability and performance of anaerobic processes. Thus, this paper critically reviews impacts of antibiotics on pH, COD removal efficiencies, biogas and methane productions as well as the accumulation of volatile fatty acids (VFAs) in the anaerobic processes. Meanwhile, impacts on the structure of bacteria and methanogens in anaerobic processes are also discussed comprehensively. Furthermore, to better understand the effect of antibiotics on anaerobic processes, detailed information about antimicrobial mechanisms of antibiotics and microbial functions in anaerobic processes is also summarized. Future research on deeper knowledge of the effect of antibiotics on anaerobic processes are suggested to reduce their adverse environmental impacts.