The behavior of antibiotic resistance genes and arsenic influenced by biochar during different manure composting

The fates of antibiotic resistance genes and their association with cell membrane permeability in response to peroxydisulfate during composting

The aims of this study were to use metagenomics to reveal the fates of antibiotic resistance genes (ARGs) during composting under the regulation of peroxydisulfate and clarify the relationship between ARGs and cell membrane permeability. Results showed that peroxydisulfate increased cell membrane permeability by effectively regulating the expression of outer membrane protein and lipopolysaccharide related genes. Besides, it reduced polysaccharides and proteins in extracellular polymer substances by 36% and 58%, respectively, making it easier for intracellular ARGs (i-ARGs) to reach the extracellular environment, among which the absolute intracellular abundance of mphK, Erm(31), and tet(44) decreased to 1.2, 1.0, and 0.89 fold of the control, respectively. Finally, variation partitioning analysis showed that i-ARGs dominated the removal of ARGs. These results revealed that the removal of i-ARGs by activated peroxydisulfate was the key to the removal of ARGs and increased cell membrane permeability played a key role for peroxydisulfate to remove i-ARGs during composting.

Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves

Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.

Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain

Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.

The effects of biochar on antibiotic resistance genes (ARGs) removal during different environmental governance processes: A review

Antibiotic resistance genes (ARGs) pollution has been considered as one of the most significant emerging environmental and health challenges in the 21st century, many efforts have been paid to control the proliferation and dissemination of ARGs in the environment. Among them, the biochar performs a positive effect in reducing the abundance of ARGs during different environmental governance processes and has shown great application prospects in controlling the ARGs. Although there are increasing studies on employing biochar to control ARGs, there is still a lack of review paper on this hotspot. In this review, firstly, the applications of biochar to control ARGs in different environmental governance processes were summarized. Secondly, the processes and mechanisms of ARGs removal promoted by biochar were proposed and discussed. Then, the effects of biochar properties on ARGs removal were highlighted. Finally, the future prospects and challenges of using biochar to control ARGs were proposed. It is hoped that this review could provide some new guidance for the further research of this field.

Review on fate and bioavailability of heavy metals during anaerobic digestion and composting of animal manure

Anaerobic digestion and composting are attracting increasing attention due to the increased production of animal manure. It is essential to know about the fate and bioavailability of heavy metals (HMs) for further utilisation of animal manure. This review has systematically summarised the migration of HMs and the transformation of several typical HMs (Cu, Zn, Cd, As, and Pb) during anaerobic digestion and composting. The results showed that organic matter degradation increased the HMs content in biogas residue and compost (with the exception of As in compost). HMs migrated into biogas residue during anaerobic digestion through various mechanisms. Most of HMs in biogas residue and compost exceeded relevant standards. Then, anaerobic digestion increased the bioavailable fractions proportion in Zn and Cd, decreased the F4 proportion, and raised them more than moderate environmental risks. As (III) was the main species in the digester, which extremely increased As toxicity. The increase of F3 proportion in Cu and Pb was due to sulphide formation in biogas residue. Whereas, the high humus content in compost greatly increased the F3 proportion in Cu. The F1 proportion in Zn decreased, but the plant availability of Zn in compost did not reduce significantly. Cd and As mainly converted the bioavailable fractions into stable fractions during composting, but As (V) toxicity needs to be concerned. Moreover, additives are only suitable for animal manure treated with slightly HM contaminated. Therefore, it is necessary to combine more comprehensive methods to improve the manure treatment and make product utilisation safer.

Effects of composting on the fate of doxycycline, microbial community, and antibiotic resistance genes in swine manure and broiler manure

Aerobic composting is an economical and effective technology that is widely used to treat animal manure. To study the fate of doxycycline (DOX), the microbial community, and antibiotic resistance genes (ARGs) during composting, aerobic composting of broiler manure and swine manure was carried out under natural environmental conditions. Aerobic composting effectively removed DOX (with a removal rate > 97%) and most ARGs from animal manure. The microbial diversity and the numbers of ARGs were higher in composted swine manure compared with composted broiler manure. The microbial community structure changed during composting, and the dominant phyla of broiler manure and swine manure changed from Firmicutes to Bacteroidetes and Proteobacteria, respectively. DOX changed the structure and relative abundance of the microbial community during composting, and the relative abundance of multidrug resistance genes and mobile genetic elements (MGEs) increased, which might lead to the risk of transmission of resistance in the environment. The C / N ratio, DOX concentration, Firmicutes, intl1, and intl2 were the key factors driving the change in ARGs during composting. These results help to reveal the effects of DOX on microbial communities, ARGs, and MGEs during composting and clarify the possible ways to reduce the risk of resistance gene transmission in the environment.

Biochar and Manure Applications Differentially Altered the Class 1 Integrons, Antimicrobial Resistance, and Gene Cassettes Diversity in Paddy Soils

Integrons are genetic components that are critically involved in bacterial evolution and antimicrobial resistance by assisting in the propagation and expression of gene cassettes. In recent decades, biochar has been introduced as a fertilizer to enhance physiochemical properties and crop yield of soil, while manure has been used as a fertilizer for centuries. The current study aimed to investigate the impact of biochar, manure, and a combination of biochar and manure on integrons, their gene cassettes, and relative antimicrobial resistance in paddy soil. Field experiments revealed class 1 (CL1) integrons were prevalent in all samples, with higher concentration and abundance in manure-treated plots than in biochar-treated ones. The gene cassette arrays in the paddy featured a broad pool of cassettes with a total of 35% novel gene cassettes. A majority of gene cassettes encoded resistance to aminoglycosides, heat shock protein, heavy metals, pilus secretory proteins, and twin-arginine translocases (Tat), TatA, TatB, and TatC. Both in combination and solo treatments, the diversity of gene cassettes was increased in the manure-enriched soil, however, biochar reduced the gene cassettes’ diversity and their cassettes array. Manure considerably enhanced CL1 integrons abundance and antimicrobial resistance, whereas biochar amendments significantly reduced integrons and antimicrobial resistance. The results highlighted the differential effects of biochar and manure on integrons and its gene cassette arrays, showing increased abundance of integrons and antibiotic resistance upon manure application and decrease of the same with biochar. The use of biochar alone or in combination with manure could be a beneficial alternative to mitigate the spread of antimicrobial resistance and bacterial evolution in the environment, specifically in paddy soils.

Biochar can mitigate co-selection and control antibiotic resistant genes (ARGs) in compost and soil

Heavy metals (HMs) contamination raises the expression of antibiotic resistance (AR) in bacteria through co-selection. Biochar application in composting improves the effectiveness of composting and the quality of compost. This improvement includes the elimination and reduction of antibiotic resistant genes (ARGs). The use of biochar in contaminated soils reduces the bioaccessibility and bioavailability of the contaminants hence reducing the biological and environmental toxicity. This decrease in contaminant bioavailability reduces contaminants induced co-selection pressure. Conditions which favour reduction in HMs bioavailable fraction (BF) appear to favour reduction in ARGs in compost and soil. Biochar can prevent horizontal gene transfer (HGT) and can eliminate ARGs carried by mobile genetic elements (MGEs). This effect reduces maintenance and propagation of ARGs. Firmicutes, Proteobacteria, and Actinobacteria are the major bacteria phyla identified to be responsible for dissipation, maintenance, and propagation of ARGs. Biochar application rate at 2-10% is the best for the elimination of ARGs. This review provides insight into the usefulness of biochar in the prevention of co-selection and reduction of AR, including challenges of biochar application and future research prospects.

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.

Key factors driving the fate of antibiotic resistance genes and controlling strategies during aerobic composting of animal manure: A review

Occurrence of antibiotic resistance genes (ARGs) in animal manure impedes the reutilization of manure resources. Aerobic composting is potentially effective method for resource disposal of animal manure, but the fate of ARGs during composting is complicated due to the various material sources and different operating conditions. This review concentrates on the biotic and abiotic factors influencing the variation of ARGs in composting and their potential mechanisms. The dynamic variations of biotic factors, including bacterial community, mobile genetic elements (MGEs) and existence forms of ARGs, are the direct driving factors of the fate of ARGs during composting. However, most key abiotic indicators, including pH, moisture content, antibiotics and heavy metals, interfere with the richness of ARGs indirectly by influencing the succession of bacterial community and abundance of MGEs. The effect of temperature on ARGs depends on whether the ARGs are intracellular or extracellular, which should be paid more attention. The emergence of various controlling strategies renders the composting products safer. Four potential removal mechanisms of ARGs in different controlling strategies have been concluded, encompassing the attenuation of selective/co-selective pressure on ARGs, killing the potential host bacteria of ARGs, reshaping the structure of bacterial community and reducing the cell-to-cell contact of bacteria. With the effective control of ARGs, aerobic composting is suggested to be a sustainable and promising approach to treat animal manure.

Increase in arsenic methylation and volatilization during manure composting with biochar amendment in an aeration bioreactor

Biochar is widely used as an amendment to optimize the composting process. In this study, we firstly investigated the effects of biochar amendment on methylation and volatilization of arsenic (As), and the microbial communities during manure composting. Biochar amendment was found to increase the concentrations of monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA) during mesophilic (days 0-10) and early thermophilic (days 11-15) phases, and promote As volatilization during the maturing phase (days 60-80) of composting. In addition, the abundances of As(V) reductase (arsC) and As(III) S-adenosyl-L-methionine methyltransferase (arsM) genes were higher in the biochar treatment than that in the control. Moreover, biochar amendment influenced the microbial communities by promoting As methylation and volatilization via Ensifer and Sphingobium carrying arsC genes, and Rhodopseudomonas and Pseudomonas carrying arsM genes. This study emphasized the considerable role of biochar on methylation and volatilization of As during manure composting and provided an overall characterization of the community compositions of arsC and arsM genes during manure composting. It will broaden our insights in As biogeochemical cycle during manure composting with biochar amendment, which will facilitate the regulation of As during manure composting and its application in agricultural soil.

Dynamic bacterial assembly driven by Streptomyces griseorubens JSD-1 inoculants correspond to composting performance in swine manure and rice straw co-composting

The effect of Streptomyces griseorubens JSD-1 inoculant on composting performance and bacterial community assembly during the swine manure and rice straw co-composting was studied by a high-throughput pyrosequencing technology. The JSD-1 inoculant contributed to a higher temperature (maximum 66.8 °C), a longer thermophilic phase (46 days), and a lower bacterial diversity in JSD-1 compost. The principle component analysis confirmed that JSD-1 inoculant significantly reshaped the microbial communities. The difference in genera significantly increased during both composting processes. The predominant biomarkers were members of Bacteroidetes in JSD-1 composting. The network analysis also showed different chief "connecting" genera in both composts. Moreover, JSD-1 inoculant increased the total nitrogen, phosphorus, and potassium content in composts. The redundancy analysis showed that the bacterial community was mainly influenced by temperature; additionally, the nutrient contents were positively correlated with temperature. These results demonstrated that JSD-1 inoculant drove the bacterial assembly to induce physicochemical property changes in co-composting.

Spread of resistance genes from duck manure to fish intestine in simulated fish-duck pond and the promotion of cefotaxime and As

Integrated culture is a widespread culture mode in South China, in which resistance genes (RGs) also spread in the circulation system with nutrients. Accordingly, the aim of the present study was to investigate the spread of RGs in a fish-duck pond and the RGs and bacterial community of fish intestines. Five fish tanks, including a control tank and four experimental tanks (duck manure, duck manure + cefotaxime, duck manure + As, and duck manure + cefotaxime + As), were tested for 100 days. The results showed that duck manure increased both the diversity and relative abundance of RGs in fish intestines, and the addition of stress factors (cefotaxime, As) increased the relative abundance of RGs by one to two orders of magnitude. The stress-inducing effect of cefotaxime was greater than that of As. Tetracycline resistance genes were more sensitive to stress factors and were the predominant RGs in fish intestines. RGs in duck manure preferentially spread from the water to biofilm and then to fish intestines, whereas co-stress of cefotaxime and As obviously promoted the spread of RGs to fish intestines. In comparison to the control tank, duck manure and stress factors significantly changed the bacterial community of fish intestines. Correlation analysis also revealed that arsB, MOX, tetA and sul1 were significantly correlated with intI1 (P < 0.01), which hinted a potentially dissemination risk of RGs in fish intestines. These findings provide a theoretical basis for further investigating the dissemination of RGs in integrated culture systems and for evaluating the ecological risk of antibiotic and As use in aquaculture.

Manure as a Potential Hotspot for Antibiotic Resistance Dissemination by Horizontal Gene Transfer Events

The increasing demand for animal-derived foods has led to intensive and large-scale livestock production with the consequent formation of large amounts of manure. Livestock manure is widely used in agricultural practices as soil fertilizer worldwide. However, several antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria are frequently detected in manure and manure-amended soils. This review explores the role of manure in the persistence and dissemination of ARGs in the environment, analyzes the procedures used to decrease antimicrobial resistance in manure and the potential impact of manure application in public health. We highlight that manure shows unique features as a hotspot for antimicrobial gene dissemination by horizontal transfer events: richness in nutrients, a high abundance and diversity of bacteria populations and antibiotic residues that may exert a selective pressure on bacteria and trigger gene mobilization; reduction methodologies are able to reduce the concentrations of some, but not all, antimicrobials and microorganisms. Conjugation events are often seen in the manure environment, even after composting. Antibiotic resistance is considered a growing threat to human, animal and environmental health. Therefore, it is crucial to reduce the amount of antimicrobials and the load of antimicrobial resistant bacteria that end up in soil.

The profile of antibiotic resistance genes in pig manure composting shaped by composting stage: Mesophilic-thermophilic and cooling-maturation stages

The variation of antibiotic resistance genes (ARGs) and influential factors in pig manure composting were investigated by conducting simulated composting tests using four different supplement materials (wheat straw, corn straw, poplar sawdust and spent mushroom). The results show that the relative abundance of total ARGs increased by 0.19-1.61 logs after composting, and tetX, sulI, sulII, dfrA1 and aadA were the major contributors. The variations of ARG profiles and bacterial communities throughout the composting were clearly divided into mesophilic-thermophilic and cooling-maturation stages in all tests, while different supplement materials did not exert a noticeable influence. Network analysis demonstrated the diversity of bacterial hosts for ARGs, the existence of multiple antibiotic resistant bacteria, and the weak correlations between ARGs and physicochemical factors in the composting piles. Of note, integron intI1 and Mycobacterium (a potential pathogen) were positively correlated with eight and four ARGs, respectively, that displayed increased abundance after composting.

Co-composting of sewage sludge and Phragmites australis using different insulating strategies

Insulating strategies are indispensable for laboratory-scale composting reactors, however, current insulation methods interfere with the aerobic fermentation behaviors related to composting. To address this issue, a centre-oriented real-time temperature compensation strategy was designed in this study. Five 9 L reactors (R1-R5) with different insulation strategies were used for the co-composting of dewatered sludge and Phragmites australis and compared. The process performance was assessed by monitoring the temperature, O₂ and CO₂ emissions, the physical-chemical properties of the composting materials were evaluated by measuring the organic matter (OM), carbon nitrogen ratio (C/N), pH, electrical conductivity (EC), and fluorescence excitation-emission matrix (EEM) spectra. And a 16S rDNA analysis was used to quantify the evolution of bacterial community. The main findings are as follows. Compared with R1 as a control, the insulating strategies can increase the maximum temperature and prolong the thermophilic phase of composting. Comparing R1 and R3 showed that real-time temperature compensation can better restore the real fermentation of the compost. The results showed that R5 had the best composting effect, reaching 69.8 °C, which was 25.1%, 29.7%, 19.3%, and 17.3% higher than R1, R2, R3, and R4, respectively, and remaining in the thermophilic phase for 4.24 d, which is 1.4, 1.5, 1.3, and 0.2 times longer than R1, R2, R3, and R4, respectively. Furthermore, it can significantly reduce the temperature difference between the centre and edge of the reactor, which improved the composting material allocation efficiency and composting process control accuracy, further providing a basis for the actual full-scale composting operation.

Evolution and distribution of resistance genes and bacterial community in water and biofilm of a simulated fish-duck integrated pond with stress

Integrated fish-duck pond is a common circular farming model in South China, besides, it is also hot-spot for the co-selection of antibiotic resistance genes (ARGs). The aim of this study was to investigate the effects of duck manure, As and cefotaxime on the bacterial community, and the evolution and distribution of ARGs and metal(loid) resistance genes (MRGs) in water and biofilm. Five groups of fish tanks included a control and four test groups. The experimental period lasted for 100 days. Six ARGs (CIT, DHA, EBC, FOX, MOX, TEM), two MRGs (arsB, arsC), and two integron genes (intI1, intI2) were tracked and detected in water and biofilm. The results showed that duck manure brought ARGs and MRGs into fish tanks. Stress factors (cefotaxime, As) increased the relative abundance of resistance genes, and this was positively correlated with stress concentrations. The biofilm was visible significantly at the end of stage 3, and the total relative abundance of resistance genes in biofilm was higher than water from stage 5 onwards. Evolution of AmpC β-lactamase resistance genes was more obvious than MRGs, especially for MOX, which increased by 3 orders of magnitude. The abundance of Flavobacterium was higher in biofilm than in water. Moreover, correlation analysis showed that both arsB and MOX were significantly correlated with intI1 (p < 0.05), which suggested a potentially dissemination risk of resistance genes. This study provides a reference for health risk assessment in integrated aquaculture environment contaminated with duck manure, antibiotics and metalloids.

Changes of nutrients and potentially toxic elements during hydrothermal carbonization of pig manure

The effects of reaction temperature, residence time, sulfuric acid and potassium hydroxide on the total concentration and speciation of N and P, potentially toxic elements (salts and metal elements) of pig manure during its hydrothermal carbonization (HTC) were investigated. Concentrations of Cl, K, Na and Mg in the hydrochars were much lower but total N, P and nitrate-nitrogen (NO₃^--N) contents were significantly higher than in untreated pig manure. The acid-extractable fractions of Cu and Zn in hydrochars were 0.03-0.63 and 0.17-0.66 times lower than those in pig manure and decreased significantly with increasing reaction temperature. The addition of sulfuric acid (H2SO4) or potassium hydroxide (KOH) in HTC reduced the contents of P, Ca, Mg, Cl and heavy metal elements (HMEs) in hydrochars, and the removal rates of Cu and Zn were up to 55% and 59%, respectively. Overall, the rapid treatment of pig manure by HTC reduced the harm of salts and HMEs, and effectively recovered the nutrients in pig manure. The HTC under alkaline conditions was desirable for optimizing the main elemental composition of the hydrochars.

Heavy metals, antibiotics and nutrients affect the bacterial community and resistance genes in chicken manure composting and fertilized soil

Succession of bacterial communities involved in the composting process of chicken manure, including first composting (FC), second composting (SC) and fertilizer product (Pd) and fertilized soil (FS), and their associations with nutrients, heavy metals, antibiotics and antibiotic resistance genes (ARGs) were investigated. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla observed during composting. Overall, potential pathogenic bacteria decreased from 37.18% (FC) to 3.43% (Pd) and potential probiotic taxa increased from 5.77% (FC) to 7.12% (Pd). Concentrations of heavy metals increased after second composting (SC), however, no significant differences were observed between FS and CS groups. Alpha diversities of bacterial communities showed significant correlation with heavy metals and nutrients. All investigated antibiotics decreased significantly after the composting process. The certain antibiotics, heavy metals, or nutrients was significantly positive correlated with the abundance of ARGs, highlighting that they can directly or indirectly influence persistence of ARGs. Overall, results indicated that the composting process is effective for reducing potential pathogenic bacteria, antibiotics and ARGs. The application of compost lead to a decrease in pathogens and ARGs, as well as an increase in potentially beneficial taxa and nutrients in soil.

Effects of inoculation with lignocellulose-degrading microorganisms on antibiotic resistance genes and the bacterial community during co-composting of swine manure with spent mushroom substrate

Composting is usually employed to treat livestock manure, and inoculation with lignocellulose-degrading microorganisms can enhance the quality of compost. In this study, lignocellulose-degrading microorganisms were inoculated at two levels (uninoculated control = 0%, and T treatment = 10%) during co-composting of swine manure with spent mushroom substrate, and their effects on antibiotic resistance genes (ARGs) and the bacterial community were investigated. Inoculation with lignocellulose-degrading microorganisms caused greater decreases in 6/11 ARGs and 3/4 mobile genetic elements than the control. The total relative abundances of ARGs increased by 0.23 logs in the control but decreased by 0.08 logs in the T treatment after co-composting. The bacterial community was clustered according to the composting time in the two treatments, where inoculation mainly affected the bacterial community during the mesophilic phase. Redundancy analysis and network analysis showed that the bacterial community succession had important effects on the variations in ARGs. Inoculation with lignocellulose-degrading microorganisms led to the reduction of ARGs, which was significantly correlated with the abundances of potential host bacteria for ARGs. Thus, inoculation with lignocellulose-degrading microorganisms could decrease the risk of ARGs spreading and make compost products more security.

Application of metagenomic analysis for detection of the reduction in the antibiotic resistance genes (ARGs) by the addition of clay during poultry manure composting

The aim of the study was to reduce relative abundance of antibiotic resistant genes (ARGs) in the poultry manure (PM) compost by adding clay and to determine the mechanism of this effect. Five doses of clay additive [at 0% (T1), 2% (T2), 4% (T3), 6% (T4), 8% (T5) and 10% (T6) based on PM dry weight] were compared to explore the mechanism of reduction in ARGs in the PM compost by the addition of clay. The results confirmed that in the initial raw PM from the breeding farm, the ARG concentrations were 1.7-3.01 times higher than that in the domestic PM. High doses of the clay additive play an important role in reduction in the ARGs and are the main factor responsible for significant variations in ARG abundance between the treatment groups. Therefore, we recommend adding high doses of clay (HDC) as an effective means to reduce the maximum percentage of ARGs in PM compost. A heat map correlation study confirmed that HDC addition during the composting process reduced the bioavailable fractions of toxic metals originating from the chicken feed and significantly impacted ARG dispersion.

Dynamics of fungal diversity and interactions with environmental elements in response to wheat straw biochar amended poultry manure composting

The fungal dynamics and its correlation with physicochemical and gaseous emission were investigated using metagenomics and Heat map illustrator (HEMI). Five different concentrations of wheat straw biochar (WSB) were applied to poultry manure (PM) and composted for 50 days; those without the WSB treatment were used as a control. The results revealed the dominant phyla to be Chytridiomycota, Mucoromycota, Ascomycota and Basidiomycota, while Batrachochytrium, Rhizophagus, Mucor, and Puccinia were the superior genera. In particular, the diversity of Chytridiomycota and Ascomycota was more abundant among all of the treatments. Overall, the diversity of the fungal species was correspondent, but relative abundance varied significantly among all of the composts. Principle Coordinate Analysis (PCoA) and Non-Metric Multi- Dimensional Scaling (NMDS) indicated that different concentrations of WSB applied treatments have significantly distinct fungal communities. In addition, correlation analyses of fungal interactions with environmental elements via HEMI also indicate a clear difference among the treatments. Ultimately, the relative abundance of fungal composition significantly influenced the PM compost treated by the WSB.

Evaluating the effects of coal gasification slag on the fate of antibiotic resistant genes and mobile genetic elements during anaerobic digestion of swine manure

Coal gasification slag (GS) is an industrial solid waste with a highly developed pore structure, which can be used in anaerobic digestion (AD) to remove antibiotic resistance genes (ARGs) due to its structure, thereby utilizing this waste resource. This study evaluated the effects of three GS levels (0, 5, and 10 g/L) on the abundances of ARGs, mobile genetic elements, and the bacterial community. With GS added at 10 g/L, the removal rates for ARGs (dfrA7, sul2, tetW, ermF, and ermQ) were 24.81-90.48% after AD, and the removal rate for ISCR1 was 95.4%. In addition, 10 g/L GS was more effective at reducing the abundances of potential human pathogens. The variations in ARGs may have been affected by the succession of the microbial community. The results of this study demonstrate that supplementation with 10 g/L GS is more useful for reducing ARGs during AD.

Succession of bacteria diversity in the poultry manure composted mixed with clay: Studies upon its dynamics and associations with physicochemical and gaseous parameters

In this study, the bacterial community succession and variations were investigated in poultry manure (PM) compost by the using high-throughput sequencing in six different concentration of clay [at 0% (T1), 2% (T2), 4% (T3), 6% (T4), 8% (T5) and 10% (T6) on PM dry weight basis] applied compost. The results indicated that dominant phylum were Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes, while Bacillus, Paenibacillus, Virgibacillus, Oceanobacillus and Clostridium were the dominant genera in all the treatments. Correlation analyses provided useful tools for insight into the bacterial interactions with environmental factors and also extension of the compost maturation and resistance of bacteria. During the course of study, the diversity of bacteria similar but relative abundance variable in each treatments. However, the average and the normalized (to bacterial RAs or copies of sequences) both remained greater in higher dosage of clay applied treatments. Finally, the RAs of various bacterial community composition was affected in PM compost by the clay application.

Human and veterinary antibiotics during composting of sludge or manure: Global perspectives on persistence, degradation, and resistance genes

Wastewater treatment plant effluent, sludge and manure are the main sources of contamination by antibiotics in the whole environment compartments (soil, sediment, surface and underground water). One of the major consequences of the antibiotics discharge into the environment could be the prevalence of a bacterial resistance to antibiotic. In this review, four groups of antibiotics (Tetracyclines, Fluoroquinolones, Macrolides and Sulfonamides) were focused for the background on their wide spread occurrence in sludge and manure and for their effects on several target and non-target species. The antibiotics concentrations range between 1 and 136,000 μg kg^-1 of dry matter in sludge and manure, representing a potential risk for the human health and the environment. Composting of sludge or manure is a well-known and used organic matter stabilization technology, which could be effective in reducing the antibiotics levels as well as the antibiotic resistance genes. During sludge or manure composting, the antibiotics removals range between 17-100%. The deduced calculated half-lives range between 1-105 days for most of the studied antibiotics. Nevertheless, these removals are often based on the measurement of concentration without considering the matter removal (lack of matter balance) and very few studies are emphasized on the removal mechanisms (biotic/abiotic, bound residues formation) and the potential presence of more or less hazardous transformation products. The results from the few studies on the fate of the antibiotic resistance genes during sludge or manure composting are still inconsistent showing either decrease or increase of their concentration in the final product. Whether for antibiotic or antibiotic resistance genes, additional researches are needed, gathering chemical, microbiological and toxicological data to better understand the implied removal mechanisms (chemical, physical and biological), the interactions between both components and the environmental matrices (organic, inorganic bearing phases) and how composting process could be optimized to reduce the discharge of antibiotics and antibiotic resistance genes into the environment.

Targeted inactivation of antibiotic-resistant Escherichia coli and Pseudomonas aeruginosa in a soil-lettuce system by combined polyvalent bacteriophage and biochar treatment

High abundances of antibiotic-resistant pathogenic bacteria (ARPB) and antibiotic resistance genes (ARGs) in agricultural soil-plant systems have become serious threats to human health and environmental safety. Therefore, it is crucial to develop targeted technology to control existing antibiotic resistance (AR) contamination and potential dissemination in soil-plant systems. In this work, polyvalent bacteriophage (phage) therapy and biochar amendment were applied separately and in combination to stimulate ARPB/ARG dissipation in a soil-lettuce system. With combined application of biochar and polyvalent phage, the abundance of Escherichia coli K-12 (tetR) and Pseudomonas aeruginosa PAO1 (ampR + fosR) and their corresponding ARGs (tetM, tetQ, tetW, ampC, and fosA) significantly decreased in the soil after 63 days' incubation (p < 0.05). Similar results for endophytic K-12 and PAO1, and ARGs, were also obtained in lettuce tissues following combined treatment. Additionally, high throughput sequencing revealed that biochar and polyvalent phage synergetically improved the structural diversity and functional stability of the indigenous bacterial communities in soil and the endophytic ones in lettuce. Hence, this work proposes a novel biotechnology that combines biochar amendment and polyvalent phage therapy to achieve targeted inactivation of ARPB, which stimulates ARG dissipation in soil-lettuce systems.

Electron shuttles enhance the degradation of sulfamethoxazole coupled with Fe(III) reduction by Shewanella oneidensis MR-1

The ability of anthraquinone-2,6-disulfonate (AQDS) and riboflavin to enhance the sulfamethoxazole (SMX) degradation coupled with the Fe(III) reduction by Shewanella oneidensis MR-1 was investigated. The results indicated that the SMX degradation rate was 38.5% with an initial SMX concentration at 0.04 mM. For the overall performance of AQDS and riboflavin mediated SMX degradation and iron reduction, the SMX degradation rate was gradually increased with the enhancement of iron reduction. Riboflavin had a stronger enhancement on SMX degradation and iron reduction than AQDS, but the enhancement was not positively correlated with electron shuttles concentration. A quantitative characterization of the electron transfer capacity (ETC) of the electron shuttles showed that the ETC was higher for riboflavin than AQDS. The S. oneidensis MR-1 16S rRNA gene copies results indicated that electron shuttles had a positive effect on the microbial activity of S. oneidensis MR-1. The LCMS result indicated that the products of the SMX biodegradation were 3-amino-5-methylisoxazole and 4-aminobenzenesulfonic acid, which suggested that the SMX biodegradation was caused by SN bond cleavage. This study indicates that the biochemical mechanisms play a vital role in SMX transformation and Fe(II) generation in this system.

Influence of zeolite and superphosphate as additives on antibiotic resistance genes and bacterial communities during factory-scale chicken manure composting

Factory-scale chicken manure composting added with zeolite (F), superphosphate (G), or zeolite and ferrous sulfate (FL) simultaneously, were evaluate for their effects on the behaviors of antibiotic resistance genes (ARGs) and bacterial communities. After composting, ARGs in manure decreased by 67.3% in the control, whereas the reductions were 86.5%, 68.6% and 72.2% in F, G and FL, respectively. ARGs encoding ribosomal protection proteins (tetO, tetB(P), and tetM) were reduced to a greater extent than tetG, tetL, sul1 and sul2. Bacteria pathogens were also effectively removed by composting. Network analysis showed that Firmicutes were the important potential host bacteria for ARGs. The bacterial communities and environmental factors, as well as the intI gene, contributed significantly to the variation of ARGs. The ARGs and integrons were reduced more when zeolite was added than when superphosphate was added; thus, it may be useful for reducing the risks of ARGs in chicken manure.

Dynamics of bacterial composition and the fate of antibiotic resistance genes and mobile genetic elements during the co-composting with gentamicin fermentation residue and lovastatin fermentation residue

Dynamics in bacterial community composition, along with 13 antibiotic resistance genes (ARGs) and eight mobile genetic elements (MGEs), were assessed during co-composting with gentamicin and lovastatin fermentation residue (GFR and LFR, respectively). Using next generation sequencing, the key bacterial taxa associated with the different stages of composting were identified. Most importantly, Bacillus, belonging to Phylum Firmicutes, was associated with enhanced degradation of gentamicin, decomposition of organic matter (OM) and dissolved organic carbon (DOC), and also extension of the thermophilic phase of the composting cycle. During the course of composting, the patterns of different ARGs/MGEs varied. However, the total and the normalized (to bacterial numbers) copies both remained high. The abundance of various ARGs was related to bacterial abundance and community composition, and the changing pattern of individual ARGs was influenced by the selectivity of MGEs and bacteria.

Variation pattern of terrestrial antibiotic resistances and bacterial communities in seawater/freshwater mixed microcosms

The ocean is the final place where pollutants generated by human activities are deposited. As a result, the long-range transport of the ocean can facilitate the diffusion of terrestrial contaminants, including ARGs. However, to our knowledge, little research has been devoted to discussing the content change of terrestrial ARGs and the reason for the change in coastal area. This study established various microcosms, in which seawater and freshwater were mixed at different ratio to simulate the environmental conditions of different regions in coastal areas. Four ARGs were quantified, and 16S pyrosequencing was conducted. The results showed that the terrestrial ARGs influenced the concentration of the corresponding ARGs in coastal areas, and the content change pattern of each ARG was distinct. The influence of salinity on the ARG content was limited in most cases. Moreover, most dominant bacteria from freshwater had significant positive correlation (p < 0.05) with selected ARGs, except for bla_TEM. The dominant bacteria in freshwater diminished dramatically in microcosms with a high proportion of seawater. Freshwater may have a strong impact on the bacteria composition of seawater, and the materials from freshwater may prompt the growth of some bacteria (include potential hosts of ARGs) in coastal area.