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

Meta-analysis addressing the potential of antibiotic resistance gene elimination through aerobic composting

The significant increase in antibiotic resistance genes (ARGs) in organic solid wastes (OSWs) has emerged as a major threat to the food chain. Aerobic composting is a widely used technology for OSW management, with the potential to influence the fate of AGRs. However, the variability of the ARG elimination effects reported in different studies has highlighted the uncertainty regarding the effects of composting on ARGs. To identify the potential of composting in reducing ARG and the factors (e.g., composting technologies and physiochemical properties) influence ARG changes, a meta-analysis was conducted with a database including 4,232 observations. The abundances of ARGs and mobile genetic elements (MGEs) can be substantially reduced by 74.3% and 78.8%, respectively, via aerobic composting. During composting, the ARG levels in chicken and swine manure tended to be reduced more significantly (81.7% and 78.0%) compared to those in cattle manure (52.3%) and sewage sludge (32.6%). The reduction rate of sulfonamide resistant genes was only 35.3%, which was much lower than those of other types. MGEs and composting duration (CD) were identified as the most important factors driving ARG changes during composting. These findings provide a comprehensive insight into the effects of composting on ARG reduction, which may help prevent the transmission in food systems.

Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland

Manure from food-producing animals, rich in antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), poses significant environmental and healthcare risks. Despite global efforts, most manure is not adequately processed before use on fields, escalating the spread of antimicrobial resistance. This study examined how different cattle manure treatments, including composting and storage, affect its microbiome and resistome. The changes occurring in the microbiome and resistome of the treated manure samples were compared with those of raw samples by high-throughput qPCR for ARGs tracking and sequencing of the V3-V4 variable region of the 16S rRNA gene to indicate bacterial community composition. We identified 203 ARGs and mobile genetic elements (MGEs) in raw manure. Post-treatment reduced these to 76 in composted and 51 in stored samples. Notably, beta-lactam, cross-resistance to macrolides, lincosamides and streptogramin B (MLSB), and vancomycin resistance genes decreased, while genes linked to MGEs, integrons, and sulfonamide resistance increased after composting. Overall, total resistance gene abundance significantly dropped with both treatments. During composting, the relative abundance of genes was lower midway than at the end. Moreover, higher biodiversity was observed in samples after composting than storage. Our current research shows that both composting and storage effectively reduce ARGs in cattle manure. However, it is challenging to determine which method is superior, as different groups of resistance genes react differently to each treatment, even though a notable overall reduction in ARGs is observed.

Potential of combined reactor and static composting applications for the removal of heavy metals and antibiotic resistance genes from chicken manure

Chicken manure (CM) can pose a serious threat to environmental and human health, and need to be managed properly. The compost can effectively treat CM. However, there is limited research on the heavy metals and antibiotic resistance genes (ARGs) during compost CM. In this study, the combined application of reactor and static composting (RSC) was used to produce organic fertilizer of CM (OCM), and heavy metals, ARGs and bacterial community structure was investigated. The results show that RSC could be used to produce OCM, and OCM meet the National organic fertilizer standard (NY/T525-2021). Compared to the initial CM, DTPA-Cu, DTPA-Zn, DTPA-Pb, DTPA-Cr, DTPA-Ni and DTPA-As in OCM decreased by 40.83%, 23.73%, 34.27%, 38.62%, 16.26%, and 43.35%, respectively. RSC decreased the relative abundance of ARGs in CM by 84.06%, while the relative abundance of sul1 and ermC increased. In addition, the relative abundance and diversity of ARGs were mainly influenced by the bacterial community, with Actinobacteria, Firmicutes, and Proteobacteria becoming the dominant phyla during composting, and probably being the main carriers and dispersers of most of the ARGs. Network analyses confirmed that Gracilibacillus, Lactobacillus, Nocardiopsis, Mesorhizobium and Salinicoccus were the main potential hosts of ARGs, with the main potential hosts of sul1 and ermC being Mesorhizobium and Salinicoccus. The passivation and physicochemical properties of heavy metals contribute to the removal of ARGs, with sul1 and ermC being affected by the toal heavy metals. Application of RSC allows CM to produce mature, safe organic fertilizer after 32 d and reduces the risk of rebound from ARGs, but the issues of sul1 and ermC gene removal cannot be ignored.

Semi-permeable membrane-covered high-temperature aerobic composting: A review

Semi-permeable membrane-covered high-temperature aerobic composting (SMHC) is a suitable technology for the safe treatment and disposal of organic solid waste as well as for improving the quality of the final compost. This paper presents a comprehensive summary of the impact of semi-permeable membranes centered on expanded polytetrafluoroethylene (e-PTFE) on compost physicochemical properties, carbon and nitrogen transformations, greenhouse gas emission reduction, microbial community succession, antibiotic removal, and antibiotic resistance genes migration. It is worth noting that the semi-permeable membrane can form a micro-positive pressure environment under the membrane, promote the uniform distribution of air in the heap, reduce the proportion of anaerobic area in the heap, improve the decomposition rate of organic matter, accelerate the decomposition of compost and improve the quality of compost. In addition, this paper presents several recommendations for future research areas in the SMHC. This investigation aims to guide for implementation of semi-permeable membranes in high-temperature aerobic fermentation processes by systematically compiling the latest research progress on SMHC.

Enterobacteria in anaerobic digestion of dairy cattle wastewater: Assessing virulence and resistance for one health security

Samples from a dairy cattle waste-fed anaerobic digester were collected across seasons to assess sanitary safety for biofertilizer use. Isolated enterobacteria (suggestive of Escherichia coli) were tested for susceptibility to biocides, antimicrobials, and biofilm-forming capability. Results revealed a decrease in total bacteria, coliforms, and enterobacteria in biofertilizer compared to the effluent. Among 488 isolates, 98.12 % exhibited high biofilm formation. Biofertilizer isolates exhibited a similar biofilm formation capability as effluent isolates in summer, but greater propensity in winter. Resistance to biocides and antimicrobials varied, with tetracycline resistance reaching 19 %. Of the isolates, 25 were multidrug-resistant (MDR), with 64 % resistant to three drugs. Positive correlations were observed between MDR and increased biofilm formation capacity in both samples, while there was negative correlation between MDR and increased biocide resistance. A higher number of MDR bacteria were found in biofertilizer compared to the effluent, revealing the persistence of E. coli resistance, posing challenges to food safety and public health.

The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum

The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.

Size matters: Powder biochar promotes the elimination of antibiotics resistance genes and potential hosts during swine manure composting

Livestock manure faced acute environmental pollution and ecology risky caused by antibiotic resistance genes (ARGs). This study investigated the effects of biochar particle size including powder biochar (75 μm, PB), and granular biochar (2 mm, GB) on ARGs variation during the aerobic composting. The results showed that the total relative abundance (RA) of the ARGs decreased significantly in all the treatments after composting. While compared to the removal efficiency of total RA in the control (CK), PB decreased by 90.99 % and GB increased by 93.25 %, and both PB and GB removed MGEs completely. Sulfonamide antibiotic resistance genes were the main contributor of the ARGs rebounding. PB addition could hinder the rebounding of sulfonamide antibiotic resistance genes during the later stage of the composting. Co-occurrence network analysis showed that the addition of biochar (both types) increased the complexity of the microbial community the competition of inter-phylum, which was indicated by the higher number of edge and density and lower positive connection. The different ARGs removal efficiency in these two treatments might be that PB promoted the competition both inter-phylum and potential hosts-other microbes, resulted in fewer kinds and abundance of ARGs hosts, while GB increased the stability of ARGs hosts making it more resistant to environment changes. Totally, compared with the global adjustment strategy of microbial communities, more exclusive methods focusing on the controlling of ARGs hosts should be explored to decrease the ecological risk of composting products during composting process.

Distribution characteristics and potential risks of bioaerosols during scattered farming

In most economically underdeveloped areas, scattered farming and human‒livestock cohabitation are common. However, production of bioaerosols and their potential harm in these areas have not been previously researched. In this study, bioaerosol characteristics were analyzed in scattered farming areas in rural Northwest China. The highest bacteria, fungi, and Enterobacteria concentrations were 125609 ± 467 CFU/m³, 25175 ± 10305 CFU/m³, and 4167 ± 592 CFU/m³, respectively. Most bioaerosols had particle sizes >3.3 μm. A total of 71 bacterial genera and 16 fungal genera of potential pathogens were identified, including zoonotic potential pathogenic genera. Moreover, our findings showed that the scattered farming pattern of human‒animal cohabitation can affect the indoor air environment in the surrounding area, leading to chronic respiratory diseases in the occupants. Therefore, relevant government departments and farmers should enhance their awareness of bioaerosol risks and consider measures that may be taken to reduce them.

A Critical Review of AMR Risks Arising as a Consequence of Using Biocides and Certain Metals in Food Animal Production

The focus of this review was to assess what evidence exists on whether, and to what extent, the use of biocides (disinfectants and sanitizers) and certain metals (used in feed and other uses) in animal production (both land and aquatic) leads to the development and spread of AMR within the food chain. A comprehensive literature search identified 3434 publications, which after screening were reduced to 154 relevant publications from which some data were extracted to address the focus of the review. The review has shown that there is some evidence that biocides and metals used in food animal production may have an impact on the development of AMR. There is clear evidence that metals used in food animal production will persist, accumulate, and may impact on the development of AMR in primary animal and food production environments for many years. There is less evidence on the persistence and impact of biocides. There is also particularly little, if any, data on the impact of biocides/metal use in aquaculture on AMR. Although it is recognized that AMR from food animal production is a risk to human health there is not sufficient evidence to undertake an assessment of the impact of biocide or metal use on this risk and further focused in-field studies are needed provide the evidence required.

Antibiotic resistome and associated bacterial communities in agricultural soil following the amendments of swine manure-derived fermentation bed waste

The practice of utilizing animal manures on land is widespread in agriculture, but it has raised concerns about the possible spread of antibiotic resistance genes (ARGs) and the potential risk it poses to public health through food production. Fermentation bed culture is an effective circular agricultural practice commonly utilized in pig farming that minimizes the environmental impact of livestock farming. However, this method generates a significant amount of fermentation bed waste (FBW), which can be turned into organic fertilizer for land application. The objective of this research was to examine the impacts of amending agricultural soil samples with swine manure-derived FBW on microbial communities, mobile genetic elements (MGEs), and ARG profiles over different periods. The study findings indicated that the amendment of swine manure-derived FBW significantly increased the diversity and abundance of ARGs and MGEs during the early stages of amendment, but this effect diminished over time, and after 12 months of FBW amendments, the levels returned to those comparable to control samples. The shift in the bacterial communities played a significant role in shaping the patterns of ARGs. Actinobacteriota, Proteobacteria, and Bacteroidetes were identified as the primary potential hosts of ARGs through metagenomic binning analysis. Furthermore, the pH of soil samples was identified as the most important property in driving the composition of the bacterial community and soil resistome. These findings provided valuable insights into the temporal patterns and dissemination risks of ARGs in FBW-amended agriculture soil, which could contribute to the development of effective strategies to manage the dissemination risks of FBW-derived ARGs.

Impact of environment on transmission of antibiotic-resistant superbugs in humans and strategies to lower dissemination of antibiotic resistance

Antibiotics are the most efficient type of therapy developed in the twentieth century. From the early 1960s to the present, the rate of discovery of new and therapeutically useful classes of antibiotics has significantly decreased. As a result of antibiotic use, novel strains emerge that limit the efficiency of therapies in patients, resulting in serious consequences such as morbidity or mortality, as well as clinical difficulties. Antibiotic resistance has created major concern and has a greater impact on global health. Horizontal and vertical gene transfers are two mechanisms involved in the spread of antibiotic resistance genes (ARGs) through environmental sources such as wastewater treatment plants, agriculture, soil, manure, and hospital-associated area discharges. Mobile genetic elements have an important part in microbe selection pressure and in spreading their genes into new microbial communities; additionally, it establishes a loop between the environment, animals, and humans. This review contains antibiotics and their resistance mechanisms, diffusion of ARGs, prevention of ARG transmission, tactics involved in microbiome identification, and therapies that aid to minimize infection, which are explored further below. The emergence of ARGs and antibiotic-resistant bacteria (ARB) is an unavoidable threat to global health. The discovery of novel antimicrobial agents derived from natural products shifts the focus from chemical modification of existing antibiotic chemical composition. In the future, metagenomic research could aid in the identification of antimicrobial resistance genes in the environment. Novel therapeutics may reduce infection and the transmission of ARGs.

Whole-Genome Sequencing and Biotechnological Potential Assessment of Two Bacterial Strains Isolated from Poultry Farms in Belgorod, Russia

Bacteria, designated as A1.1 and A1.2, were isolated from poultry waste based on the ability to form ammonia on LB nutrient medium. Whole genome sequencing identified the studied strains as Peribacillus frigoritolerans VKM B-3700D (A1.1) and Bacillus subtilis VKM B-3701D (A1.2) with genome sizes of 5462638 and 4158287 bp, respectively. In the genome of B. subtilis VKM B-3701D, gene clusters of secondary metabolites of bacillin, subtilisin, bacilisin, surfactin, bacilliacin, fengycin, sactipeptide, and ratipeptide (spore killing factor) with potential antimicrobial activity were identified. Clusters of coronimine and peninodin production genes were found in P. frigoritolerans VKM B-3700D. Information on coronimine in bacteria is extremely limited. The study of the individual properties of the strains showed that the cultures are capable of biosynthesis of a number of enzymes, including amylases. The B. subtilis VKM V-3701D inhibited the growth of bacterial test cultures and reduced the growth rate of the mold fungus Aspergillus unguis VKM F-1754 by 70% relative to the control. The antimicrobial activity of P. frigoritolerans VKM V-3700D was insignificant. At the same time, a mixture of cultures P. frigoritolerans VKM B-3700D/B. subtilis VKM B-3701D reduced the growth rate of A. unguis VKM F-1754 by 24.5%. It has been shown that strain A1.1 is able to use nitrogen compounds for assimilation processes. It can be assumed that P. frigoritolerans VKM V-3700D belongs to the group of nitrifying or denitrifying microorganisms, which may be important in developing methods for reducing nitrogen load and eutrophication.

Risk assessment and dissemination mechanism of antibiotic resistance genes in compost

In recent years, the excessive of antibiotics in livestock and poultry husbandry, stemming from extensive industry experience, has resulted in the accumulation of residual antibiotics and antibiotic resistance genes (ARGs) in livestock manure. Composting, as a crucial approach for the utilization of manure resources, has the potential to reduce the levels of antibiotics and ARGs in manure, although complete elimination is challenging. Previous studies have primarily focused on the diversity and abundance of ARGs in compost or have solely examined the correlation between ARGs and their carriers, potentially leading to a misjudgment of the actual risk associated with ARGs in compost. To address this gap, this study investigated the transfer potential of ARGs in compost and their co-occurrence with opportunistic pathogenic bacteria by extensively analyzing metagenomic sequencing data of compost worldwide. The results demonstrated that the potential risk of ARGs in compost was significantly lower than in manure, suggesting that composting effectively reduces the risk of ARGs. Further analysis showed that the microbes shifted their life history strategy in manure and compost due to antibiotic pressure and formed metabolic interactions dominated by antibiotic-resistant microbes, increasing ARG dissemination frequency. Therefore, husbandry practice without antibiotic addition was recommended to control ARG evolution, dissemination, and abatement both at the source and throughout processing.

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.

Neglected Drivers of Antibiotic Resistance: Survival of Extended-Spectrum β-Lactamase-Producing Pathogenic Escherichia coli from Livestock Waste through Dormancy and Release of Transformable Extracellular Antibiotic Resistance Genes under Heat Treatment

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae has caused a global pandemic with high prevalence in livestock and poultry, which could disseminate into the environment and humans. To curb this risk, heat-based harmless treatment of livestock waste was carried out. However, some risks of the bacterial persistence have not been thoroughly assessed. This study demonstrated that antibiotic-resistant bacteria (ARB) could survive at 55 °C through dormancy, and simultaneously transformable extracellular antibiotic resistance genes (eARGs) would be released. The ESBL-producing pathogenic Escherichia coli CM1 from chicken manure could enter a dormant state at 55 °C and reactivate at 37 °C. Dormant CM1 had stronger β-lactam resistance, which was associated with high expression of β-lactamase genes and low expression of outer membrane porin genes. Resuscitated CM1 maintained its virulence expression and multidrug resistance and even had stronger cephalosporin resistance, which might be due to the ultra-low expression of the porin genes. Besides, heat at 55 °C promoted the release of eARGs, some of which possessed a certain nuclease stability and heat persistence, and even maintained their transformability to an Acinetobacter baylyi strain. Therefore, dormant multidrug-resistant pathogens from livestock waste will still pose a direct health risk to humans, while the resuscitation of dormant ARB and the transformation of released eARGs will jointly promote the proliferation of ARGs and the spread of antibiotic resistance.

Risk control of antibiotics, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) during sewage sludge treatment and disposal: A review

Sewage sludge is an important reservoir of antibiotics, antibiotic resistance genes (ARGs), and antibiotic resistant bacteria (ARB) in wastewater treatment plants (WWTPs), and the reclamation of sewage sludge potentially threats human health and environmental safety. Sludge treatment and disposal are expected to control these risks, and this review summarizes the fate and controlling efficiency of antibiotics, ARGs, and ARB in sludge involved in different processes, i.e., disintegration, anaerobic digestion, aerobic composting, drying, pyrolysis, constructed wetland, and land application. Additionally, the analysis and characterization methods of antibiotics, ARGs, and ARB in complicate sludge are reviewed, and the quantitative risk assessment approaches involved in land application are comprehensively discussed. This review benefits process optimization of sludge treatment and disposal, with regard to environmental risks control of antibiotics, ARGs, and ARB in sludge. Furthermore, current research limitations and gaps, e.g., the antibiotic resistance risk assessment in sludge-amended soil, are proposed to advance the future studies.

Surfactant aggravated the antibiotic's stress on antibiotic resistance genes proliferation by altering antibiotic solubilization and microbial traits in sludge anaerobic fermentation

The excessive application of antibiotics and surfactants resulted in their massive accumulation in waste activated sludge (WAS), but the co-occurrent impacts of antibiotics and surfactants on the antibiotic resistant genes (ARGs) fates have seldom reported. This work mainly revealed the roles and critical mechanisms of sodium dodecyl benzene sulfonate (SDBS) on the sulfadiazine (SDZ) stressing for ARGs distribution during WAS anaerobic fermentation. High-throughput qPCR and metagenomic analysis revealed that SDBS aggravated the SDZ selective pressure, and accelerated the proliferation of ARGs. The total abundance of ARGs was increased from 8.81 × 10¹⁰ in SDZ to 1.17 × 10¹¹ copies/g TSS in the SDBS/SDZ co-occurrence system. Specifically, the absolute abundances of ermF (MLSB), mefA (MLSB), tetM-01 (tetracycline), tetX (tetracycline), sul2 (sulfonamide) and strB (aminoglycoside) were risen from 4.60 × 10⁸-7.44 × 10⁹ copies/g TSS in the SDZ reactor to 1.02 × 10⁹-4.63 × 10¹⁰ copies/g TSS in SDBS/SDZ reactor. SDBS was contributed to the SDZ solubilization and simultaneously effective in disintegrating extracellular polymeric substances and improving cell membrane permeability, which would facilitate the SDZ transport and its interactions with ARGs hosts. Consequently, the microbial community structure was evidently altered, and the typical ARGs hosts (i.e., Saccharimonadales and Ahniella) were greatly enriched. Also, the cell signal transduction systems (i.e., glnL, glrK and pilG), oxidative stress response (i.e., frmA and recA) and bacterial secretion systems (i.e., VirB4), which were related with ARGs propagation, were all provoked in the co-occurred SDBS/SDZ reactor compared with that of sole SDZ. PLS-PM analysis suggested that the bacterial community was the predominant factor that determined the ARGs fates, followed by mobile genetic elements and metabolic pathway. This work demonstrated the interactive effects of surfactants and antibiotics on the ARGs fates in WAS fermentation systems and gave insightful implications on the ecological risks of different exogenous pollutants.

Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks

As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.

Enterobacteria Survival, Percolation, and Leaching on Soil Fertilized with Swine Manure

Swine manure has a high load of pathogens, which can pose a risk to human and environmental health. In Brazil, studies evaluating the survival of pathogens in soil are scarce. Therefore, this study aimed to evaluate the survival, percolation, and leaching of enterobacteria in clayey soil after fertilization with swine manure. For this purpose, soil columns were fertilized with manure spiked with enterobacteria. The microorganisms' behavior was monitored in terms of survival, percolation, and leaching with and without rain. Soil samples were collected, and Escherichia coli and Salmonella enterica serovar Senftemberg were quantified. The results indicated that E. coli survived for a longer period (43 days) than S. senftemberg (14 days). E. coli percolated quickly through the soil, leaching 60 cm in less than 5 min during rainy events and remaining viable for up to 24 h after the rain. The results show the importance of treating manure effectively before being added to the soil. An efficient treatment could be anaerobic digestion, followed by a pond system. Considering the characteristics of swine-producing regions, the load of effluents applied to the soil may percolate, leach, or run off and consequently contaminate water bodies with pathogens.

Emerging soil contamination of antibiotics resistance bacteria (ARB) carrying genes (ARGs): New challenges for soil remediation and conservation

Soil plays a vital role as a nutrient source for microflora and plants in ecosystems. The accumulation and proliferation of antibiotics resistance bacteria (ARB) and antibiotics resistance genes (ARGs) causes emerging soil contamination and pollution, posing new challenges for soil remediation, recovery, and conservation. Fertilizer application in agriculture is one of the most important sources of ARB and ARGs contamination in soils. The recent existing techniques for the remediation of soil polluted with ARB and ARGs are very limited in terms of ARB and ARGs removal in soil. Bioelectrochemical remediation using bioelectrochemical systems such as microbial fuel cells and microbial electrolysis cells are promising technologies for the removal of ARB and ARGs in soil. Herein, diverse sources of ARB and ARGs in soil have been reviewed, their effects on soil microbial diversity have been analyzed, and the causes of ARB and ARGs rapid proliferation in soil are explained. Bioelectrochemical systems used for the remediation of soil contaminated with ARB and ARGs is still in its infancy stage and presents serious disadvantage and limits, therefore it needs to be well understood and implemented. In general, merging soil contamination of ARB and ARGs is an increasing concern threatening the soil ecosystem while the remediation technologies are still challenging. Efforts need to be made to develop new, effective, and efficient technologies for soil remediation and conservation to tackle the spread of ARB and ARGs and overcome the new challenges posed by ARB and ARGs contamination in soil.

Sensitive response mechanism of ARGs and MGEs to initial designed temperature during swine manure and food waste co-composting

The rapid aerobic composting process has been used to reduce organic wastes, but the associated risks of antibiotic resistance genes (ARGs) need to evaluate in an efficient way. The primary objective of this work was to explore the underlying mechanism of initial adjustment in composting temperature on the variation of ARGs, mobile genetic elements (MGEs), and microbial composition during co-composting. The co-composting was initially externally heated (T2) for 5 days. The results showed that ARGs abundance in conventional composting (T1) was reduced by 49.36%, while multidrug was enriched by 86.16% after a period of 30 days. While in T2 ARGs were removed by 79.46% particularly the fraction of sulfonamide, multidrug, and vancomycin resistance genes were >90% without rebounding of any ARGs. Whereas, MGEs were reduced by 68.12% and 93.62% in T1 and T2, while the half-lives of ARGs and MGEs were lower in T2 compared to T1 (86.3%,86.7%). T2 also affected the metabolism function by regulating carbohydrate metabolism (9.62-10.39%) and amino acid metabolism (9.92-10.93%). Apart from this, the potential human pathogenic bacteria Pseudomonas was reduced by 90.6% in T2 and only 32.9% in T1 respectively. Network analysis showed that Ureibacillus, Weissella, Corynebacterium, Escherichia-Shigella, Acinetobacter were the main host of multiple genes. Structural equation models exhibited that bacterial communities were mainly responsible for the enrichment of ARGs in T1, whereas, it was directly affected by MGEs in T2. Similarly, ARGs variation was directly related to composting temperature. With this simple strategy, ARGs associated risk can be significantly reduced in composting.

Removal of antibiotic resistance genes and mobile genetic elements in a three-stage pig manure management system: The implications of microbial community structure

In this work, the removal of antibiotic resistance genes (ARGs) in the industrial-scale pig manure management system has been investigated. Additionally, the implications of mobile genetic elements (MGEs) and microbial community structure have been discussed. During the whole period of manure management, 19 ARGs and 7 MGEs were obtained from the system. The results identified that the 9 ARGs and 2 MGEs were removed from the pig manure-based materials after composting, while 5 ARGs and 2 MGEs were still remained, indicating that the ARGs/MGEs could not be removed completely as contaminants by composting. The pig farm without additional antibiotics in-feed was still faced with the risk of ARGs/MGEs from outside. Microbial community analysis illuminated that a greater decrease in the abundance of norank_f__JG30-KF-CM45, Corynebacterium, Terrisporobacter, Truepera, Salinispora and Clostridium, was responsible for the removal of ARGs/MGEs. The genes, including tnpA-01, tnpA-02, tnpA-05, Tp614, tetQ, tetM-01, tetR-02, tetX, cfxA, floR, dfrA1 and ermF exhibited significantly positive correlation with fungal communities. Fungal community analysis verified that a remarkable decrease in the abundance of Aspergillus and Thermomyces after composting was responsible for the ARGs/MGEs removal. The results elucidated the crucial roles of the related bacterial and fungal communities in the removal of ARGs/MGEs. The compound microbial agent assisted the temperature rise of composting, thereby changing the related microbial community structure and resulting in ARGs/MGEs removal.

Simultaneous reductions in antibiotic, antibiotic resistance genes and nitrogen loss during bioaugmentation tylosin fermentation dregs co-composting

Considering the main problems presented in the typical solid wastes antibiotic fermentation dregs (AFDs) composting that the residual antibiotics could result in the propagation of antibiotic resistance genes (ARGs), and the reduced value of agronomic production caused by the ammonia gas (NH₃) emissions. This study established a bio-augmented tylosin fermentation dregs (TFDs) aerobic co-composting system to investigate the effects of a novel isolated high-efficiency strain Klebsiella sp. TN-1 inoculation on tylosin degradation, reduction in ammonia emissions, and ARG abundances during this process. Results showed that the application of strain Klebsiella sp. TN-1 extended the thermophilic stage and promoted compost maturity. Moreover, bio-enhanced co-composting with strain Klebsiella sp. TN-1 led to a totally degradation of tylosin, and removed most of ARGs, metal resistance genes (MRGs) and mobile genetic elements (MGEs), and also effectively reduce ammonia emission by 49.76 %.via increasing ammoxidation rates. Principal co-ordinates analysis further suggested that the strain Klebsiella sp. TN-1 had little influence on the bacterial community composition, while the changes of other physical and chemical properties during this process were the main reasons for the evolution of bacterial community and propagation of ARGs in the TFDs co-composting. This study suggests the potential of the bio-enhanced strain Klebsiella sp. TN-1 for antibiotic biodegradation and its application for nitrogen conservation in the AFDs co-composting process, which could decrease the risk of ARGs spreading and make compost products more secure.

Membrane-covered composting significantly decreases methane emissions and microbial pathogens: Insight into the succession of bacterial and fungal communities

In this study, the effects of semipermeable membrane-covered on methane emissions and potential pathogens during industrial-scale composting of the solid fraction of dairy manure were investigated. The results showed that the oxygen concentration in the membrane-covered group (CT) was maintained above 10 %, and the cumulative methane emission in CT was >99 % lower than that in the control group (CK). Microbial analysis showed that the bacterial genus Thermus and the fungal genus Mycothermus were dominant in CT, and the richness and diversity of the bacterial community were greater than those of the fungal community. At the end of the composting, the relative abundance of potential bacterial pathogens in CT was 32.59 % lower than that in CK, and the relative abundance of potential fungal pathogens in each group was <2 %. Structural equation models revealed that oxygen concentration was a major factor influencing the bacterial diversity in CT, and the increase of oxygen concentration could limit methane emissions by inhibiting the growth of anaerobic bacteria. Therefore, membrane-covered composting could effectively improve compost safety and reduce methane emissions by regulating microbial community structure.

A Review of the Current State and Future Prospects in Resource Recovery of Chinese Cereal Vinegar Residue

Vinegar residue (VR) is a typical organic solid waste in Chinese cereal vinegar production. It is characterized by high yield, high moisture and low pH and is rich in lignocellulose and other organic matter. To avoid the environmental pollution caused by VR, it should be properly treated. The industry’s existing treatment processes, landfills and incineration, cause secondary pollution and waste of resources. Therefore, there is an urgent demand for environmentally friendly and cost-effective resource recovery technologies for VR. To date, a considerable amount of research has been performed in the area of resource recovery technologies for VR. This review summarizes the reported resource recovery technologies, mainly anaerobic digestion, feed production, fertilizer production, high-value product production and soil/water remediation. The principles, advantages and challenges of these technologies are highlighted. Finally, as a future perspective, a cascade and full utilization model for VR is proposed by considering the inherent drawbacks and economic-environmental feasibility of these technologies.

Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost

BACKGROUND

Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts.

RESULTS

In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86-99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting.

CONCLUSIONS

Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs.

Enhanced removal of antibiotics and antibiotic resistance genes in a soil microbial fuel cell via in situ remediation of agricultural soils with multiple antibiotics

Soil microbial fuel cells (MFCs) have been applied for the in situ remediation of soils polluted by single antibiotics. However, the investigation of only single antibiotic pollution has hindered MFC application in real-world soil remediation, where the effects of multiple antibiotics with similar chemical structures on the fate of antibiotics and their corresponding antibiotic resistance genes (ARGs) remain unknown. In this study, antibiotic removal rates, microbial community compositions, metabolite compositions, and ARG abundances were investigated in soil MFCs by adding two commonly used antibiotics (sulfadiazine, SDZ, and sulfamethoxazole, SMX), and comparing them with the addition of only a single antibiotic (SDZ). The antibiotic removal rate was higher in the soil MFC with addition of mixed antibiotics compared to the single antibiotic due to enhanced biodegradation efficiency in both the upper (57.24% of the initial antibiotic concentration) and lower layers (57.07% of the initial concentration) of the antibiotic-polluted soils. Bacterial community diversity in the mixed antibiotic conditions increased, and this likely resulted from the decreased toxicity of intermediates produced during antibiotic biodegradation. Moreover, the addition of mixed antibiotics led to lower risks of ARG release into soil environments, as reflected by higher abundances of host bacteria in the single antibiotic treatment. These results encourage the further development of soil MFC technology for in situ remediation of antibiotic-polluted soils.

Polyethylene terephthalate microplastic fibers increase the release of extracellular antibiotic resistance genes during sewage sludge anaerobic digestion

Microplastic fibers (MFs), as the most frequently detected microplastic shape in sewage sludge, have posed emerging concern for sludge treatment and disposal. However, the effect of MFs on antibiotic resistance genes (ARGs), especially extracellular ARGs (eARGs) during sludge treatment remains far from explicit. Therefore, this study investigated the potential impact of MFs on eARGs during sludge anaerobic digestion (AD), a commonly used sludge treatment method, through long-term operation. The qPCR results showed that both absolute and relative abundances of eARGs increased with the MFs exposure during sludge AD. The average absolute and relative abundances of eight tested eARGs in the AD reactor with the highest MFs dosage (170 items/gTS) were 1.70 and 2.15 times higher than those in the control AD reactor. The metagenomics results further comfirmed the increase of eARGs abundance during sludge anaerobic digestion after MFs exposure and the enhancement did not show significant selectivity. The identification of the potential hosts of eARGs suggested the host numbers of eARGs also increased with MFs exposure, which may suggest enhanced horizonal transformation as a result of increased eARGs. Further exploring the mechansims showed that the genes involved in type IV secretion system was upregulated after MFs exposure, suggesting the active release of eARGs was enhanced with MFs exposure. In contrast, the MFs may not affect the passive release of eARGs as its impact on cell membrance damage was insignificant. The enhanced eARGs in sludge AD process may further accelerate the transport of ARGs in environment, which should be considered during sludge treatment and disposal.

Elucidating the beneficial effects of diatomite for reducing abundances of antibiotic resistance genes during swine manure composting

Diatomite (DE) has been used for nitrogen conservation during the composting of feces but its effects on antibiotic resistance genes (ARGs) and the associated mechanisms are still unclear. In this study, DE was added at three different proportions (0%, 4%, and 8%) to swine manure during composting. The results showed that adding DE helped to reduce the abundances of ARGs and the maximum decrease (88.99%) occurred with the highest dose. DE amendment promoted the transformation of reducible copper into a more stable form, i.e., the residual fraction, which reduced the selective pressure imposed by copper and further decreased the abundances of ARGs. Tn916/1545 and intI1 were critical genetic components related to ARGs, and thus the reductions in the abundances of ARGs may be attributed to the suppression of horizontal transfer due to the decreased abundances of mobile genetic elements (MGEs). The microbial community structure (bacterial abundance and diversity) played key role in the evolution of ARGs. DE could enhance the competition between hosts and non-hosts of ARGs by increasing the bacterial community diversity. Compared with CK, DE amendment optimized the bacterial community by reducing the abundances of the potential hosts of ARGs and pathogens such as Corynebacterium, thereby improving the safety of the compost product. In addition, KEGG function predictions revealed that adding DE inhibited the metabolic pathway and genes related to ARGs. Thus, composting with 8% DE can reduce the risk of ARG transmission and improve the practical value for agronomic applications.

Safety Level of Microorganism-Bearing Products Applied in Soil-Plant Systems

The indiscriminate use of chemical fertilizers adversely affects ecological health and soil microbiota provoking loss of soil fertility and greater pathogen and pest presence in soil-plant systems, which further reduce the quality of food and human health. Therefore, the sustainability, circular economy, environmental safety of agricultural production, and health concerns made possible the practical realization of eco-friendly biotechnological approaches like organic matter amendments, biofertilizers, biopesticides, and reuse of agro-industrial wastes by applying novel and traditional methods and processes. However, the advancement in the field of Biotechnology/Agriculture is related to the safety of these microorganism-bearing products. While the existing regulations in this field are well-known and are applied in the preparation and application of waste organic matter and microbial inoculants, more attention should be paid to gene transfer, antibiotic resistance, contamination of the workers and environment in farms and biotech-plants, and microbiome changes. These risks should be carefully assessed, and new analytical tools and regulations should be applied to ensure safe and high-quality food and a healthy environment for people working in the field of bio-based soil amendments.

Effect of biochar addition on the dynamics of antibiotic resistant bacteria during the pig manure composting

In present study, the taxonomic variation of antibiotic resistant bacteria (ARB) in pig manure (PM) composting with coconut shell biochar (CSB) and bamboo biochar (BB) addition was investigated. The experiment was divided into three treatments: T1 (as control or without biochar amendment), T2 was added 10% coconut shell biochar and T3 supplemented with 10% bamboo biochar. The initial feed stock were properly homogenized using a mechanical crusher. PM and wheat straw (WS) were mixed in a 5: 1 dry weight ratio to adjust the initial carbon/nitrogen ratio 25:1, bulk density to ~0.5 (kg/L) and ~60% moisture content, respectively. This experiment was lasted for 42 days. The results indicated the bacterial communities in the three treatments were more different in terms of relative abundance and diversity of dominant bacteria. The control group had the highest abundance of Kingdome bacteria. The changes in ARB was noticed by variation in the relative abundances of Actinobacteria, Proteobacteria, Firmicutes and Bacteroidota. At the end of composting (on day 42), the total RAs of ARB at the class, order, and family levels were considerably reduced in T2 and T3 by ~35.78-38.75%, 36.42-40.63% and 45.82-47.70%, respectively. But in T1 was decreased by 6.16-8.62%, 7.93-8.72% and 8.70-10.15%, as compared with the day 0 sample. However, the CSB was much more effective to reduce 55 to 60% of ARB than T3 or BB applied treatment has 40 to 42% ARB reduction, while control has certainly very less RAa of ARB reduction. Finally, the biochar amendment was significant approach to mitigate the total ARB abundance in compost and it's further used for organic farming purposes.

Thermophilic Composting of Human Feces: Development of Bacterial Community Composition and Antimicrobial Resistance Gene Pool

In times of climate change, practicing sustainable, climate-resilient, and productive agriculture is of primordial importance. Compost from different resources, now treated as wastes, could be one form of sustainable fertilizer creating a resilience of agriculture to the adverse effects of climate change. However, the safety of the produced compost regarding human pathogens, pharmaceuticals, and related resistance genes must be considered. We have assessed the effect of thermophilic composting of dry toilet contents, green cuttings, and straw, with and without biochar, on fecal indicators, the bacterial community, and antibiotic resistance genes (ARGs). Mature compost samples were analyzed regarding fecal indicator organisms, revealing low levels of Escherichia coli that are in line with German regulations for fertilizers. However, one finding of Salmonella spp. exceeded the threshold value. Cultivation of bacteria from the mature compost resulted in 200 isolates with 36.5% of biosafety level 2 (BSL-2) species. The majority is known as opportunistic pathogens that likewise occur in different environments. A quarter of the isolated BSL-2 strains exhibited multiresistance to different classes of antibiotics. Molecular analysis of total DNA before and after composting revealed changes in bacterial community composition and ARGs. 16S rRNA gene amplicon sequencing showed a decline of the two most abundant phyla Proteobacteria (start: 36-48%, end: 27-30%) and Firmicutes (start: 13-33%, end: 12-16%), whereas the abundance of Chloroflexi, Gemmatimonadetes, and Planctomycetes rose. Groups containing many human pathogens decreased during composting, like Pseudomonadales, Bacilli with Bacillus spp., or Staphylococcaceae and Enterococcaceae. Gene-specific PCR showed a decline in the number of detectable ARGs from 15 before to 8 after composting. The results reveal the importance of sufficiently high temperatures lasting for a sufficiently long period during the thermophilic phase of composting for reducing Salmonella to levels matching the criteria for fertilizers. However, most severe human pathogens that were targeted by isolation conditions were not detected. Cultivation-independent analyses also indicated a decline in bacterial orders comprising many pathogenic bacteria, as well as a decrease in ARGs. In summary, thermophilic composting could be a promising approach for producing hygienically safe organic fertilizer from ecological sanitation.

Antibiotic resistome in a large urban-lake drinking water source in middle China: Dissemination mechanisms and risk assessment

The increasing pollution of urban drinking water sources by antibiotic resistance genes (ARGs) threatens human health worldwide. However, the distribution and influencing factors of ARGs, especially how to reveal the risks of ARGs in this environment remains unclear. Hence, Chaohu Lake was selected as an example to investigate the characteristics of ARGs and explore the interactions among physicochemical factors, microorganisms, and ARGs by metagenomic approach. In this work, 75 ARG subtypes with an average of 30.4 × /Gb (ranging from 15.2 ×/Gb to 57.9 ×/Gb) were identified, and multidrug and bacA were most frequent in Chaohu Lake. Non-random co-occurrence patterns and potential host bacteria of ARGs were revealed through co-occurrence networks. Microbial community and mobile genetic elements (MGEs) were the major direct factors in ARG profiles. The dissemination of ARGs was mainly driven by plasmids. Considering the interactions among MGEs, human bacterial pathogens, and ARGs, antibiotic resistome risk index (ARRI) was proposed to manifest the risks of ARGs. Overall, our work systemically investigated the composition and associated factors of ARGs and built ARRI to estimate the potential risks of ARGs in a typical urban drinking water source, providing an intuitive indicator for managing similar lakes.

Influence of microbial inoculants on co-composting of lignocellulosic crop residues with farm animal manure: A review

The rapidly developing agro-industry generates huge amounts of lignocellulosic crop residues and animal manure worldwide. Although co-composting represents a promising and cost-effective method to treat various agricultural wastes simultaneously, poor composting efficiency prolongs total completion time and deteriorates the quality of the final product. However, supplementation of the feedstock with beneficial microorganisms can mitigate these negative effects by facilitating the decomposition of recalcitrant materials, enhancing microbial enzyme activity, and promoting maturation and humus formation during the composting process. Nevertheless, the influence of microbial inoculation may vary greatly depending on certain factors, such as start-up parameters, structure of the feedstock, time of inoculation, and composition of the microbial cultures used. The purpose of this contribution is to review recent developments in co-composting procedures involving different lignocellulosic crop residues and farm animal manure combined with microbial inoculation strategies. To evaluate the effectiveness of microbial additives, the results reported in a large number of peer-reviewed articles were compared in terms of composting process parameters (i.e., temperature, microbial activity, total organic carbon and nitrogen contents, decomposition rate of lignocellulose fractions, etc.) and compost characteristics (humification, C/N ratio, macronutrient content, and germination index). Most studies confirmed that the use of microbial amendments in the co-composting process is an efficient way to facilitate biodegradation and improve the sustainable management of agricultural wastes. Overall, this review paper provides insights into various inoculation techniques, identifies the limitations and current challenges of co-composting, especially with microbial inoculation, and recommends areas for further research in this field.