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

Evolution of the Black solider fly larvae gut antibiotic resistome during kitchen waste disposal

Kitchen waste (KW) is an important reservoir of antibiotic resistance genes (ARGs). Black solider fly larvae (BSFL) are extensively employed in KW disposal, closely linking to their robust gut microbes. However, antibiotic resistome in BSFL gut during the KW disposal processes and the mechanism remain unclear. In the present study, the antibiotic resistome in BSFL gut within the 12 days KW disposal processes were investigated. Results showed that, ARGs abundance initially increased and subsequently decreased, the five most prevalent core ARG classes were tetracycline, aminoglycoside, cephalosporin, lincosamide and multidrug. A total of 7 MGE types were observed and the horizontal gene transfer (HGT) of ARGs was predominantly mediated by plasmids. Host microbes were mainly categorized into Proteobacteria (98.12 %) and their assemblies were mainly classified into the deterministic processes. To elucidate the driving mechanisms, the mantel test and the structural equation model (SEM) were developed. Results indicated that microbial functions (0.912, p < 0.0001) and microbial community (1.014, p = 0.036), consistently showed very significant relationships with the patterns of ARGs, which presented higher direct effects than indirect effects. Overall, this study makes an initial contribution to a more deepgoing comprehension of the gut antibiotic resistome of BSFL during KW disposal.

Fate of intracellular and extracellular antibiotic resistance genes in sewage sludge by full-scale anaerobic digestion

Storage tank (ST) is a promising strategy for solid-liquid separation following anaerobic digestion (AD). However, little is known regarding the effects of ST on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial communities. Therefore, this study first investigated eight typical ARGs (sul1, sul2, tetW, tetA, tetO, tetX, ermF, and ermB) and three MGEs (int1, int2, and tnpA) during full-scale AD of sludge and the liquid and biosolids phases of ST. Following that, intracellular ARGs (iARGs), extracellular polymeric substances (EPS)-associated ARGs, and cell-free ARGs removal were quantified in AD process, which is largely unknown for full-scale AD of sludge. The qPCR results showed that both AD and ST significantly removed ARGs, with ST biosolids showing the highest removal efficiency for the total measured relative (82.27 ± 2.09 %) and absolute (92.38 ± 0.89 %) abundance of ARGs compared to the raw sludge. Proteobacteria, Bacteroidota, Firmicutes and Campilobacterota were the main potential ARGs hosts in the sludge. Moreover, the results of different ARGs fractions showed that the total relative and absolute abundance of iARGs decreased by 90.12 ± 0.83 % and 79.89 ± 1.41 %, respectively, following AD. The same trend was observed for the abundance of EPS-associated ARGs, while those of cell-free ARGs increased after AD. These results underscore the risk of extracellular ARGs and provided new insights on extracellular ARGs dissemination evaluation.

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.

Role of suspended solids on the co-precipitation of pathogenic indicators and antibiotic resistance genes with struvite from digested swine wastewater

Struvite recovered from wastewater contains high concentration of fecal indicator bacteria (FIB), porcine adenoviruses (PAdV) and antibiotic resistance genes (ARGs), becoming potential resources of these microbial hazards. Understanding the precipitation behavior of pathogenic indicators and ARGs with suspended solids (SS) will provide the possible strategy for the control of co-precipitation. In this study, SS was divided into high-density SS (separated by centrifugation) and low-density SS (further separated by filtration), and the role of SS on the co-precipitation of FIB, PAdV and ARGs was investigated. The distribution analysis showed that 35.5-73.0% FIB, 79.6% PAdV and 64.5-94.8% ARGs existed in high-density SS, while the corresponding values were 26.9-64.4%, 11.7% and 3.5-24.3% in low-density SS. During struvite generation, 82.7-96.9% FIB, 75.5% PAdV and 56.3-86.5% ARGs were co-precipitated into struvite. High-density SS contributed 20.7-68.5% FIB, 63.9% PAdV and 38.7-87.2% ARGs co-precipitation, and the corresponding contribution of low-density SS was 31.4-79.2%, 3.9% and 6.2-54.7%. Moreover, the precipitated SS in struvite obviously decreased inactivation efficiency of FIB and ARGs in drying process. These results provide a potential way to control the co-precipitation and inactivation of FIB, PAdV and ARGs in struvite through removing high-density SS prior to struvite recovery.

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

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

Magnetic biochar promotes the risk of mobile genetic elements propagation in sludge anaerobic digestion

Mobile genetic elements (MGEs) mediated horizontal gene transfer is the primary reason for the propagation of antibiotic resistance genes in environment. The behavior of MGEs under magnetic biochar pressure in sludge anaerobic digestion (AD) is still unknown. This study evaluated the effects of different dosage magnetic biochar on the MGEs in AD reactors. The results showed that the biogas yield was highest (106.68 ± 1.16 mL g^-1 VS_added) with adding optimal dosage of magnetic biochar (25 mg g^-1 TS_added), due to it increased the microorganism's abundance involved in hydrolysis and methanogenesis. While, the total absolute abundance of MGEs in the reactors with magnetic biochar addition increased by 11.58%-77.37% compared with the blank reactor. When the dosage of magnetic biochar was 12.5 mg g^-1 TS_added, the relative abundance of most MGEs was the highest. The enrichment effect on ISCR1 was the most significant, and the enrichment rate reached 158.90-214.16%. Only the intI1 abundance was reduced and the removal rates yield 14.38-40.00%, which was inversely proportional to the dosage of magnetic biochar. Co-occurrence network explored that Proteobacteria (35.64%), Firmicutes (19.80%) and Actinobacteriota (15.84%) were the main potential host of MGEs. Magnetic biochar changed MGEs abundance by affecting the potential MGEs-host community structure and abundance. Redundancy analysis and variation partitioning analysis showed that the combined effect of polysaccharides, protein and sCOD exhibited the greatest contribution (accounted for 34.08%) on MGEs variation. These findings demonstrated that magnetic biochar increases the risk of MGEs proliferation in AD system.

The Antibiotics Degradation and Its Mechanisms during the Livestock Manure Anaerobic Digestion

Antibiotics are administered to livestock at subtherapeutic levels to promote growth, and their degradation in manure is slow. High antibiotic concentrations can inhibit bacterial activity. Livestock excretes antibiotics via feces and urine, leading to their accumulation in manure. This can result in the propagation of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Anaerobic digestion (AD) manure treatment technologies are gaining popularity due to their ability to mitigate organic matter pollution and pathogens, and produce methane-rich biogas as renewable energy. AD is influenced by multiple factors, including temperature, pH, total solids (TS), substrate type, organic loading rate (OLR), hydraulic retention time (HRT), intermediate substrates, and pre-treatments. Temperature plays a critical role, and thermophilic AD has been found to be more effective in reducing ARGs in manure compared to mesophilic AD, as evidenced by numerous studies. This review paper investigates the fundamental principles of process parameters affecting the degradation of ARGs in anaerobic digestion. The management of waste to mitigate antibiotic resistance in microorganisms presents a significant challenge, highlighting the need for effective waste management technologies. As the prevalence of antibiotic resistance continues to rise, urgent implementation of effective treatment strategies is necessary.

Microbial cooperation promotes humification to reduce antibiotic resistance genes abundance in food waste composting

Antibiotic resistance genes (ARGs) fate in a full-scale Food waste (FW) facility was investigated. Results showed that with the changes in ARGs, microbial networks could be naturally divided into two clusters, named as the ARGs increasing group (AI group) and the ARGs decreasing group (AD group). The significant difference between two groups (i.e. stronger microbial competition in the AI group and stronger microbial cooperation in the AD group) implied that the variation in ARGs over time were caused by a switch between competition and cooperation. These results indicated that microbial competition might increase ARGs abundance, while cooperation might reduce it. Meanwhile, structural-equation-model (SEM model) showed that humification indexes (e.g. GI value) was an indicator for characterizing microbial interactions and ARGs. The results of the linear model further confirmed that mature compost (GI values > 92.6 %) could reduce the risk of ARGs.

Recent advances in conductive materials amended anaerobic co-digestion of food waste and municipal organic solid waste: Roles, mechanisms, and potential application

Recently, conductive materials (i.e., carbon-based and iron-based materials) as a feasible and attractive approach have been introduced to anaerobic co-digestion (ACoD) system for promoting its performance and stability through direct interspecies electron transfer. Owing to the key roles of conductive materials in ACoD process, it is imperative to gain a profound understanding of their specific functions and mechanisms. Here, this review critically examined the state of the art of conductive materials assisted ACoD of food waste and common municipal organic solid waste. Then, the fundamental roles of conductive materials on ACoD enhancement and the relevant mechanisms were discussed. Last, the perspectives for co-digestate treatment, reutilization, and disposal were summarized. Moreover, the main challenges to conductive materials amended ACoD in on-site application were proposed and the future remarks were put forward. Collectively, this review poses a scientific basis for the potential application of conductive materials in ACoD process in the future.

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

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

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.

The role of iron-based nanoparticles (Fe-NPs) on methanogenesis in anaerobic digestion (AD) performance

Several strategies have been proposed to improve the performance of the anaerobic digestion (AD) process. Among them, the use of various nanoparticles (NPs) (e.g. Fe, Ag, Cu, Mn, and metal oxides) is considered one of the most effective approaches to enhance the methanogenesis stage and biogas yield. Iron-based NPs (zero-valent iron with paramagnetic properties (Fe⁰) and iron oxides with ferromagnetic properties (Fe₃O₄/Fe₂O₃) enhance microbial activity and minimise the inhibition effect in methanogenesis. However, comprehensive and up-to-date knowledge on the function and impact of Fe-NPs on methanogens and methanogenesis stages in AD is frequently required. This review focuses on the applicative role of iron-based NPs (Fe-NPs) in the AD methanogenesis step to provide a comprehensive understanding application of Fe-NPs. In addition, insight into the interactions between methanogens and Fe-NPs (e.g. role of methanogens, microbe interaction and gene transfer with Fe-NPs) beneficial for CH₄ production rate is provided. Microbial activity, inhibition effects and direct interspecies electron transfer through Fe-NPs have been extensively discussed. Finally, further studies towards detecting effective and optimised NPs based methods in the methanogenesis stage are reported.

Stimulatory effects of biochar addition on dry anaerobic co-digestion of pig manure and food waste under mesophilic conditions

The stimulatory effect of biochar addition on dry anaerobic digestion (AD) has been rarely investigated. In this study, the effects of commonly used biochars (bamboo, rice husk, and pecan shell) on dry co-AD were investigated using mesophilic batch digesters fed with pig manure and food waste as substrates. The results show that the specific methane yield was mildly elevated with the addition of biochars by 7.9%, 9.4%, and 12.0% for bamboo, rice husk, and pecan shell-derived biochar additions, respectively. Biochar did facilitate the degradation of poorly biodegradable organics. In comparison, there was no significant effect on the peak methane production rate by the supplementation of the selected biochars. Among the three mechanisms of enhancing methanogenesis by biochar (buffering, providing supporting surface, and enhancing electron transfer), the first two mechanisms did not function significantly in dry co-AD, while the third mechanism (i.e., enhancing electron transfer) might play an important part in dry AD process. It is recommended that the utilization of biochar for the enhancement of biomethanation in dry AD should be more focused on mono digestion in future studies.

Dynamics of antibiotics and antibiotic resistance genes in four types of kitchen waste composting processes

Kitchen waste might be a potential source of antibiotics and antibiotic resistance genes. Composting is recognized as an effective way for kitchen waste disposal. However, the effects of different kitchen waste composting types on the removal of antibiotics and antibiotic resistance genes haven't been systematically studied. In this study, the dynamics of antibiotics and antibiotic resistance genes from kitchen waste of four composting processes were compared. Results showed that although kitchen waste was composted, it remained an underestimated source of antibiotics (25.9-207.3 μg/kg dry weight) and antibiotic resistance genes (10¹²-10¹⁷ copies/kg dry weight). Dynamic composting processes (i.e., dynamic pile composting and mechanical composting) decreased the antibiotic removal efficiency and increased the abundance of some antibiotic resistance genes (5.35-8534.7% enrichment). Partial least-squares path model analysis showed that mobile genetic elements played a dominant role in driving antibiotic resistance genes dynamics. Furthermore, redundancy analysis revealed that temperature, pH, and water content considerably affected the removal of antibiotics and mobile genetic elements. This study provides further insights into exploring the effective strategies in minimizing the risk of antibiotic resistance from kitchen waste via composting process.