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

Antibiotic resistance gene pollution in poultry farming environments and approaches for mitigation: A system review

Antibiotic resistance genes (ARG) pollution in poultry farming environments has become increasingly critical, primarily driven by the widespread use of antibiotics in animal husbandry. Prolonged antibiotic use has led to the emergence of ARGs and antibiotic-resistant bacteria, spreading via horizontal and vertical gene transfer. The complexity of ARG pollution in poultry farming arises from the unique farming practices, physiological characteristics of poultry, and manure management methods, with manure, wastewater, and air serving as significant vectors for ARG dissemination. Current research indicates that the spread of ARGs poses a significant threat to ecosystems and public health. In response to this growing concern, this review outlines the sources, distribution characteristics, and transmission mechanisms of ARGs in poultry farming environments. It also evaluates the efficacy of existing waste treatment technologies in mitigating ARG contamination. The review proposes several strategies to control ARG dissemination effectively, including reducing antibiotic usage, improving farming practices, optimizing waste management, and strengthening regulatory oversight. It also highlights the need for further research to address existing knowledge gaps and explore more efficient pollution control technologies and management measures. This review aims to provide theoretical support for protecting the environment and public health in the context of poultry farming.

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.

Effect of on-farm poultry litter composting processes on physicochemical, biological, and toxicological parameters and reduction of antibiotics and antibiotic-resistant Escherichia coli

Poultry litter is a valuable source of nutrients for crop production, but its use in agriculture can lead to environmental and public health concerns due to the presence of pollutants, antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs). We compared the effect of different on-farm poultry litter composting processes on physicochemical, biological, and toxicological parameters, as well as on the occurrence of antibiotics and resistant Escherichia coli. The composting treatments consisted of passively-aerated piles C:N = 19 (PAC19), mechanically-aerated piles C:N = 19 (MAC19), and mechanically-aerated piles C:N = 30 (MAC30). Poultry litter composting led to a significant reduction of antibiotic residues, enteroparasites and antibiotic resistant E. coli. The conditions of the process, such as extra C source and mechanical aeration influence the quality of the final product. MAC19 is a low-cost effective method to reduce the potential risks associated with poultry litter use in agriculture and produce good quality compost.

The addition of nano zero-valent iron during compost maturation effectively removes intracellular and extracellular antibiotic resistance genes by reducing the abundance of potential host bacteria

Applying compost to soil may lead to the spread of antibiotic resistance genes (ARGs) in the environment. Therefore, removing ARGs from compost is critical. In this study, for the first time, nano zero-valent iron (nZVI) was added to compost during the maturation stage to remove ARGs. After adding 1 g/kg of nZVI, the abundance of total intracellular and total extracellular ARGs was decreased by 97.62% and 99.60%, and that of total intracellular and total extracellular mobile genetic elements (MGEs) was decreased by 92.39% and 99.31%, respectively. A Mantel test and network analysis indicated that the reduction in potential host bacteria and intI1 after nZVI treatment promoted the removal of intracellular and extracellular ARGs. The addition of nZVI during composting reduced the horizontal transfer of ARGs and improve the total nitrogen and germination index of compost, allowing it to meet the requirements for organic fertilizers.

Antibiotic resistome associated with influencing factors in industrial-scale organic waste aerobic composting plants

This study investigated the fate of antibiotic resistance genes (ARGs) and bacterial evolution in six industrial-scale organic wastes aerobic composting plants and identified key factors driving ARGs dynamics. A total of 226 ARGs and 46 mobile genetic elements (MGEs), mainly resistant to aminoglycoside and MLSB, were detected by high-throughput qPCR. Briefly, aerobic composting showed good performance in reducing the diversity and abundance of ARGs, where the total absolute abundance was reduced by 88.34%-97.08% except for cattle manures. Rapid composting may lead to a rebound of ARGs due to long-term storage compared to traditional composting. Hub ARGs and bacterial genera were screened out by co-occurrence patterns. As the dominant phyla in composting, the main potential hosts of ARGs were Firmicutes, Bacteroidota and Proteobacteria. Structural equation model indicated that MGEs and heavy metals were key factors affecting ARGs dynamics. In addition, nutrients and bacterial α-diversity can indirectly influence ARGs by affecting MGEs.

Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements

Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO₂ nanoparticles (SiO₂NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO₂NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO₂NPs to reduce the propagation of ARGs.

Mitigating gas emissions from poultry litter composting with waste vinegar residue

The composting process is important in the recycling of organic wastes produced in agriculture, food, and municipal waste management. This study explored the suitability of using waste vinegar residue (WVR) as an amendment in poultry litter (PL) composting. Four treatments, including poultry litter (CK), poultry litter+vinegar residue (VR), poultry litter+vinegar residue+lime (VR_Ca) and poultry litter+vinegar residue+biochar (VR_B), were conducted. During a 42-day composting period, the dynamics of carbon dioxide (CO₂), ammonia (NH₃), nitrous oxide (N₂O) and methane (CH₄) emissions, as well as the physicochemical properties and abundances of the bacteria and fungi of the feedstock were tracked to examine the potential barriers in the co-composting of WVR and PL. Compared to those of the CK, using a WVR amendment lowered the pH, increased the electrical conductivity significantly at the early stage, resulted in a strong inhibition of bacterial and fungal growth and delayed the thermophilic period of poultry litter composting while significantly reducing NH₃ and N₂O and GHG (CO₂-e) emissions. A preadjustment of the WVR with alkaline biochar or lime lengthened the thermophilic period and increased the germination index (GI) by alleviating the inhibitory effect of the WVR on bacterial and fungal growth during composting. However, such preadjustment might reduce the mitigation effect on NH₃. In conclusion, WVR can be recycled through co-composting with poultry litter, and the additional mitigation of N losses and N conservation can be achieved without halting compost quality.

Liming mitigates the spread of antibiotic resistance genes in an acid black soil

The threat of antibiotic resistance genes (ARGs) caused by animal manure application to human health has been the focus of attention in agriculture. Applying lime to acid soil for the amelioration of soil acidity is a prevailing agricultural practice. However, the role of lime on the spread of antibiotic resistome from soil to plant is unknown. In this study, a pot experiment of lettuce was established in the acid black soil with lime addition at the rate (w/w) of 0%, 0.08%, 0.16%, and 0.32% of the total soil mass to explore the transmission of ARGs introduced by the fresh poultry manure in the soil-plant system. The bulk and rhizosphere soils as well as the leaf samples were collected after lettuce was cultivated for 60 days, the bacterial community and antibiotic resistome in these samples were determined by using Illumina sequencing and high-throughput quantitative PCR (HT-qPCR) methods, respectively. Results showed that lime application decreased the number and abundance of ARGs and slowed down the spread of manure-derived ARGs in the soil-plant system. The ARGs and bacterial community composition were significantly varied among bulk soils, rhizosphere soils and leaf endophyte, and also influenced by lime within the same sampling types. The structural equation model further demonstrated that the lime addition had a negative effect on ARG diversity, which was also indirectly regulated by bacterial community diversity. These findings suggest that lime addition can alleviate the level and dissemination of ARGs in soils and provide a potential measure to control the spread of ARGs derived from animal manure.

A sustainable and economic strategy to reduce risk antibiotic resistance genes during poultry manure bioconversion by black soldier fly Hermetia illucens larvae: Larval density adjustment

Black soldier fly (Hermetia illucens) larvae (BSFL) are common insects that are known for bioconversion of organic waste into a sustainable utilization resource. However, a strategy to increase antibiotic resistance gene (ARG) elimination in sustainable and economic ways through BSFL is lacking. In the present study, different larval densities were employed to assess the mcr-1 and tetX elimination abilities, and potential mechanisms were investigated. The application and economic value of each larval density were also analyzed. The results showed that the 100 larvae cultured in 100 g of manure group had the best density because the comprehensive disadvantage evaluation ratio was the lowest (14.97%, good bioconversion manure quality, low ARG deposition risk and reasonable larvae input cost). Further investigation showed that mcr-1 could be significantly decreased by BSFL bioconversion (4.42 ×10⁷ copies/g reduced to 4.79 ×10⁶-2.14 ×10⁵ copies/g)(P＜0.05); however, mcr-1 was increasingly deposited in the larval gut with increasing larval density. The tetX abundance was stabilized by BSFL bioconversion, except that the abundance at the lowest larval density increased (1.22 ×10¹⁰ copies/g increase, 34-fold). Escherichia was the host of mcr-1 and tetX in all samples, especially in fresh manure; Alcaligenes was the host of tetX in bioconversion manure; and the abundance of Alcaligenes was highly correlated with the pH of bioconversion manure. The pH of bioconversion manure was extremely correlated with the density of larvae. Klebsiella and Providencia were both hosts of tetX in the BSF larval gut, and Providencia was also the host of mcr-1 in the BSF larval gut. The density of larvae influenced the bioconversion manure quality and caused the ARG host abundance to change to control the abundance of ARGs, suggesting that larval density adjustment was a useful strategy to manage the ARG risk during BSFL manure bioconversion.

Response of bacterial community to iron oxide nanoparticles during agricultural waste composting and driving factors analysis

The succession of bacterial communities and their function, and the core microorganisms for water soluble organic carbon (WSC) and organic matter (OM) changes during agricultural waste composting with addition of iron oxide nanomaterials (FeONPs, Fe₂O₃ NPs and Fe₃O₄ NPs) were investigated. Moreover, driving factors for bacterial composition and metabolism were analyzed. Results showed that FeONPs treatments increased the relative abundance of thermophilic microorganisms for OM degradation. Most of the core genera were responsible for decomposition of OM and synthesis of WSC. Additionally, FeONPs promoted the metabolism of amino acids. The most significant factors for dominant genera in control, Fe₂O₃ NPs and Fe₃O₄ NPs group were moisture (62.1%), moisture (62.0%) and OM (58.2%), respectively. For metabolism, the most significant factors in control, Fe₂O₃ NPs and Fe₃O₄ NPs group were temperature (57.2%), NO₃^--N (60.5%), NO₃^--N (62.6%), respectively. The relationships between compost properties, bacterial community and metabolism were changed by FeONPs.

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

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

Effects of emerging pollutants on the occurrence and transfer of antibiotic resistance genes: A review

The emergence and spread of antibiotic resistance genes (ARGs) have become major concerns for both public health and environmental ecosystems. Emerging pollutants (EPs) that accumulate in environmental compartments also pose a potential risk for the enrichment of ARGs in indigenous microorganisms. This paper presents a comprehensive review of the effects and intrinsic mechanisms of EPs, including microplastics, engineered nanomaterials, disinfection byproducts, pharmaceuticals, and personal care products, on the occurrence and dissemination of ARGs. State-of-the-art methods for identifying culture-independent ARG-host interactions and monitoring horizontal gene transfer (HGT) processes in real-time are first reviewed. The contributions of EPs to the abundance and diversity of ARGs are then summarized. Finally, we discussed the underlying mechanisms related to the regulation of HGT, increased mutagenesis, and the evolution of microbial communities. Further details of three HGT (i.e., conjugation, transformation, and transduction) frequency patterns in response to various EPs are also examined. This review contemplates and reassesses the risks of ARG evolution posed by the manufacture and application of EPs.

New developments in biological phosphorus accessibility and recovery approaches from soil and waste streams

Phosphorus (P) is a non-renewable resource and is on the European Union's list of critical raw materials. It is predicted that the P consumption peak will occur in the next 10 to 20 years. Therefore, there is an urgent need to find accessible sources in the immediate environment, such as soil, and to use alternative resources of P such as waste streams. While enormous progress has been made in chemical P recovery technologies, most biological technologies for P recovery are still in the developmental stage and are not reaching industrial application. Nevertheless, biological P recovery could offer good solutions as these technologies can return P to the human P cycle in an environmentally friendly way. This mini-review provides an overview of the latest approaches to make P available in soil and to recover P from plant residues, animal and human waste streams by exploiting the universal trait of P accumulation and P turnover in microorganisms and plants.

Lignite Improved the Quality of Composted Manure and Mitigated Emissions of Ammonia and Greenhouse Gases during Forced Aeration Composting

Lignite amendment of livestock manure is considered a viable ammonia (NH3) emission mitigation technique. However, its impact on the subsequent composting of the manure has not been well studied. This work compared changes in biochemical parameters (e.g., organic matter loss and nitrogen (N) transformation) and also the emissions of NH3 and greenhouse gases (GHGs) between lignite-amended and unamended cattle manure during forced aeration composting. Amending manure with lignite did not alter the time to compost stability despite delaying the onset of the thermophilic temperatures. Lignite treatments retained N in the manure by suppressing NH3 loss by 35–54%, resulting in lignite-amended manure composts having 10–19% more total N than the unamended compost. Relative to manure only, lignites reduced GHG emissions over the composting period: nitrous oxide (N2O) (58–72%), carbon dioxide (CO2) (12–23%) and methane (CH4) (52–59%). Low levels of CH4 and N2O emissions were observed and this was attributed to the continuous forced aeration system used in the composting. Lignite addition also improved the germination index of the final compost: 90–113% compared to 71% for manure only. These findings suggest that lignite amendment of manure has the potential to improve the quality of the final compost whilst mitigating the environmental release of NH3 and GHGs.

High-throughput characterization of the expressed antibiotic resistance genes in sewage sludge with transcriptional analysis

Antibiotic resistance genes (ARGs) are emerging micro-pollutants that pose potential threats to environments and humans. Sewage sludge from wastewater is an important source for ARGs and current studies mainly focus on their existence in microbial genomes. However, little is known about which ARGs are expressed even though ARGs expression remains a better proxy for functional activity. In this study, the expressed ARGs in sewage sludge were characterized by high-throughput quantitative PCR (296 primer sets) combined with transcriptional analysis. A total of 202 ARG transcripts were detected and their abundances ranged from 3.1 × 10⁹ to 1.2 × 10¹⁰ copies/g dry weight. The sum abundance of five most abundant ARG transcripts (qacEdelta1-02, sul2, qacEdelta1-01, aadA2-03, tetX) exhibited a linear correlation with the total abundance of ARG transcripts (R² = 0.88, p < 10^-4), suggesting that these genes could be regarded as indicators to quantitatively predict the total abundance of expressed ARGs. Dynamics of expressed ARGs were observed with lower abundances in summer and winter than those in other seasons (p < 0.05, Kruskal-Wallis test). Variation partitioning analysis indicated that the shift in bacterial community structures induced by changes in environmental attributes might be the main driver for the dynamics of expressed ARGs. Results of this study provided new insights into the ARGs in sewage sludge.

Impact on degradation of antibiotics from poultry litter using Autothermal Thermophilic Aerobic Digestion (ATAD)

Tetracycline (TC) is one of the common antibiotics which is widely used in livestock growth promotion. The prevalent application TC may pave way to progression of antibiotic resistant bacteria. The main objective of this study is to determine the effect of Autothermal Thermophilic Aerobic Digestion (ATAD) on the fate of TC residues found in digested poultry litter. For the determination of TC in poultry litter, thin layer chromatography (TLC) and high performance liquid chromatography (HPLC) were done. TLC result revealed that the R_f value of standard TC on TLC plate was 0.97 which correlates with the R_f value of TC at 0, 12, 24 and 36 h of digested poultry litter sample and not at 48, 60 and 72 h. HPLC chromatogram revealed that the limits of detection and the recovery were 5 µg/kg and 96% for standard TC. Linear correlation curves were obtained over the series of 100–500 µg/mL with correlation coefficient of 0.996 and the calibration curve was Y = 0.001X + 0.066. These results confirmed the degradation of TC in ATAD digestion of poultry litter by abiotic processes.