Effects of shrimp shell powder on antibiotic resistance genes and the bacterial community during swine manure composting

Fe-Mn binary oxides improve the methanogenic performance and reduce the environmental health risks associated with antibiotic resistance genes during anaerobic digestion

Increasing evidence indicates that metal oxides can improve the methanogenic performance during anaerobic digestion (AD) of piggery wastewater. However, the impacts of composite metal oxides on the methanogenic performance and risk of antibiotic resistance gene (ARG) transmission during AD are not fully understood. In this study, different concentrations of Fe-Mn binary oxides (FMBO at 0, 250, 500, and 1000 mg/L) were added to AD to explore the effects of FMBO on the process. The methane yield was 7825.1 mL under FMBO at 250 mg/L, 35.2% higher than that with FMBO at 0 mg/L. PICRUSt2 functional predictions showed that FMBO promoted the oxidation of acetate and propionate, and the production of methane from the substrate, as well as increasing the abundances of most methanogens and genes encoding related enzymes. Furthermore, under FMBO at 250 mg/L, the relative abundances of 14 ARGs (excluding tetC and sul2) and four mobile gene elements (MGEs) decreased by 24.7% and 55.8%, respectively. Most of the changes in the abundances of ARGs were explained by microorganisms, especially Bacteroidetes (51.20%), followed by MGEs (11.98%). Thus, the methanogenic performance of AD improved and the risk of horizontal ARG transfer decreased with FMBO, especially at 250 mg/L.

Elucidating carbon conversion and bacterial succession by amending Fenon-like systems during co-composting of pig manure and branch

The essential point of current study was to investigate the effect of a Fenton-like system established by oxalic acid and Fe(II) on gas emission, organic matter decomposition and humification during composting. Branches were pretreated with Fenton reagents (0.02 M FeCl2·4H2O + 1.5 M H2O2) and then adding 10 % oxalic acid (OA). The treatments were marked as B1 (control), B2 (Fenton reagent), B3 (10% OA) and B4 (Fenton-like reagent). The results collected from 80 d of composting showed that adding Fenton-like reagent benefited the degradation of organic substances, as reflected by the total organic carbon and dissolved organic carbon, and the maximum decomposition rate was observed in B4. In addition, the Fenton-like reagent could improve the synthesis of humus characterized by complex and stable compounds, which was consistent with the spectral parameters (SUVA254, SUVA280, E253/E203 and Fourier transform-infrared indicators) of DOC. Furthermore, the functional microbial succession performance and linear discriminant effect size analyses provided microbial evidence of humification improvement. Notably, compared with the control, the minimum value of CH4 cumulation was reported in B4, which decreased by 30.44 %. Concluded together, the addition of a Fenton-like reagent composed by OA and Fe(II) is a practical way to improve the humification. Furthermore, the mechanisms related to the promotion of humification should be investigated from free radicals, functional genes, and metabolic pathways.

Tetracycline removal from soil by phosphate-modified biochar: Performance and bacterial community evolution

Since the remediation performance of soil tetracycline pollution by original biochar is not ideal, many modified methods have been proposed to improve its performance. Considering the cost, complex modification process and environmental friendliness, many modified biochar are difficult to be used in soil environments. In this work, biochar derived from corn stover was modified using phosphate to increase the adsorption ability of soil tetracycline and alleviate the negative effects caused by tetracycline. The results showed that pyrolysis temperatures and anion types of phosphate (PO43-, HPO42-, H2PO4-) played important roles in the performance of modified biochar. Compared with original biochar, phosphate modified biochar not only improved the adsorption capacity, but also changed the adsorption behavior of tetracycline. Via SEM, BET and FTIR techniques, the intrinsic reasons for the increase of adsorption capacity were explained by the change of morphological structures as well as functional groups of the modified biochar. K3PO4 and high temperature (800 °C) maximally improved the surface morphology, increased the pore structure, changed the surface functional groups of biochar, and then increased the adsorption capacity of tetracycline (124.51 mg/g). Subsequently, the optimal material (K3PO4-800) was selected and applied for tetracycline contaminated soil remediation. Compared to the soil without remediation, K3PO4-800 modified biochar effectively reduced the effective concentration of tetracycline in soil, and improved soil K and P nutrition, and reshaped microbial communities. Our study showed that K3PO4-800 modified biochar was not only a good tetracycline resistant material, but also a good soil amendment.

Performances of antibiotic resistance genes profile upon the action of biochar-activated peroxydisulfate in composting

In this study, the amendment of biochar-activated peroxydisulfate during composting to remove antibiotic resistance genes (ARGs) by direct (microbial community succession) and indirect methods (physicochemical factors) was analyzed. When implementing indirect methods, the synergistic effect of peroxydisulfate with biochar optimized the physicochemical habitat of compost, maintaining its moisture within a range of 62.95%-65.71%, and a pH of 6.87-7.73, and causing the compost to mature 18 days earlier than the control groups. The direct methods caused the optimized physicochemical habitat to adjust the microbial communities and reduce the abundance of most of the ARG host bacteria (Thermopolyspora, Thermobifida, and Saccharomonospora), thus inhibiting this substance's amplification. Heatmap analysis confirmed the necessary connection between physicochemical factors, microbial communities, and ARGs. Moreover, a mantel test confirmed the direct significant effect of the microbial communities on ARGs and the indirect significant effect of physicochemical factors on ARGs. The results showed that the abundance of more ARGs was down-regulated at the end of composting and regulated by biochar-activated peroxydisulfate, especially for the abundance of AbaF, tet(44), golS, and mryA, which was significantly decreased by 0.87-1.07 fold. These results provide new insights into the removal of ARGs during composting.

Profiles and key drivers of bacteria/phage co-mediated antibiotic resistance genes during swine manure composting amended with humic acid

Phages can promote the spread of antibiotic resistance genes (ARGs) in agricultural environments through transduction. However, studies on phage-mediated ARG profiles during composting have not been performed. This study investigated the effects of adding humic acid (HA) on the abundances of bacteria/phage co-mediated ARGs (b/pARGs) during swine manure composting and the key factors that affected the transmission of b/pARGs. The results showed that the addition of 5 % HA during composting could effectively reduce the absolute abundances of b/pARGs, inhibit the proliferation of pathogenic microorganisms (e.g., Corynebacterium and Streptococcus) that carried ARGs, and ultimately affect the fate of b/pARGs in the composting process by regulating key environmental factors to change the abundance of co-host bacteria. Overall, the findings of this study provided new information for understanding the main driving factors affecting the b/pARGs profile and provided a reference for the prevention and control of ARGs pollution during composting.

Leaching risk of antibiotic resistance contamination from organic waste compost in rural areas

Composting is an important decentralized technology for treating multiple biodegradable organic wastes in rural areas. However, compared to industrial composting (i.e., time and temperature protocols), rural composting is less well-controlled, and the risk of antibiotic resistance genes (ARGs) in these composts needs to be determined. We performed a quantitative determination of ARGs and both prokaryotes and eukaryotes to investigate the liquid-solid leaching ratio and the relationship between ARGs and microbial communities in solid and water extracts of composts collected from rural areas. We observed a high level of sulfonamides resistance genes and tetracyclines resistance genes (10^-4-10^-2 copies/16S copies). Tet-C and tet-X show the strongest leaching potential in rural organic waste composts with complex hosts in solid and liquid phases. This study showed high ARG abundances in compost solid and water extracts, highlighting the leaching risk of compost ARGs when exposed to runoff or groundwater during open storage and field application.

Metagenomic insights into role of red mud in regulating fate of compost antibiotic resistance genes mediated by both direct and indirect ways

In this study, the amendment of red mud (RM) in dairy manure composting on the fate of antibiotic resistance genes (ARGs) by both direct (bacteria community, mobile genetic elements and quorum sensing) and indirect ways (environmental factors and antibiotics) was analyzed. The results showed that RM reduced the total relative abundances of 10 ARGs and 4 mobile genetic elements (MGEs). And the relative abundances of total ARGs and MGEs decreased by 53.48% and 22.30% in T (with RM added) on day 47 compared with day 0. Meanwhile, the modification of RM significantly increased the abundance of lsrK, pvdQ and ahlD in quorum quenching (QQ) and decreased the abundance of luxS in quorum sensing (QS) (P < 0.05), thereby attenuating the intercellular genes frequency of communication. The microbial community and network analysis showed that 25 potential hosts of ARGs were mainly related to Firmicutes, Proteobacteria and Actinobacteria. Redundancy analysis (RDA) and structural equation model (SEM) further indicated that RM altered microbial community structure by regulating antibiotic content and environmental factors (temperature, pH, moisture content and organic matter content), which then affected horizontal gene transfer (HGT) in ARGs mediated by QS and MGEs. These results provide new insights into the dissemination mechanism and removal of ARGs in composting process.

Biochar-amended composting of lincomycin fermentation dregs promoted microbial metabolism and reduced antibiotic resistance genes

Improper disposal of antibiotic fermentation dregs poses a risk of releasing antibiotics and antibiotic resistant bacteria to the environment. Therefore, this study evaluated the effects of biochar addition to lincomycin fermentation dregs (LFDs) composting. Biochar increased compost temperature and enhanced organic matter decomposition and residual antibiotics removal. Moreover, a 1.5- to 17.0-fold reduction in antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) was observed. Adding biochar also reduced the abundances of persistent ARGs hosts (e.g., Streptomyces, Pseudomonas) and ARG-related metabolic pathways and genes (e.g., ATP-binding cassette type-2 transport, signal transduction and multidrug efflux pump genes). By contrast, compost decomposition improved due to enhanced metabolism of carbohydrates and amino acids. Overall, adding biochar into LFDs compost reduced the proliferation of ARGs and enhanced microbial community metabolism. These results demonstrate that adding biochar to LFDs compost is a simple and efficient way to decrease risks associated with LFDs composting.

Biological Control of Melon Continuous Cropping Obstacles: Weakening the Negative Effects of the Vicious Cycle in Continuous Cropping Soil

The continuous cropping obstacles of melons have become increasingly serious in recent years. To investigate this, we explored the effects and mechanisms of Bacillus subtilis C3 in control of the continuous cropping obstacles of melon. We provide a novel interaction model of the occurrence factors of continuous cropping obstacles. The dominant pathogen isolated from melon soil was Fusarium. Their hyphae were used as food to cultivate root-knot nematodes. The main phenolic acids in melon soil promoted the growth of Fusarium and indirectly increased the number of root-knot nematodes, but they also had direct toxic effects on melon root-knot nematodes. The simultaneous inoculation of the three had the strongest inhibitory effect on melon seedlings, while the inhibitory effect of paired inoculation was weaker than that of single inoculation. Therefore, the three balance each other, forming a vicious cycle. Bacillus subtilis C3 weakened the negative effects of this cycle on melon by eliminating phenolic acids and inhibiting the growth of Fusarium and root-knot nematodes. Simultaneously, they also alleviated the continuous cropping obstacles of melon by improving the composition and structure of the rhizosphere microbial community. Our results might be useful for the effective control of the continuous cropping obstacles of melon. IMPORTANCE The soil environment, crop growth and fruit quality of melons are negatively affected by long-term continuous cropping. It is important to study the mechanism of continuous cropping obstacles and their biological control. In this study, we propose a novel interaction model of the occurrence factors of continuous cropping obstacles. The dominant phenolic acids, pathogenic fungi, and root-knot nematodes from melon soil balance each other, forming a vicious cycle. Bacillus subtilis C3 weakened the negative effects of this cycle on melon by eliminating phenolic acids and inhibiting the growth of Fusarium and root-knot nematodes. In addition, C3 also improved the composition and structure of the melon rhizosphere microbial community. These results advance the study of the occurrence mechanism of continuous cropping obstacles and demonstrate an efficient and environmentally friendly biological control scheme.

Three-dimensional printed bulking agents reduce antibiotic resistance genes in swine manure aerobic composting by regulating oxygen concentration to alter host microorganisms and mobile genetic elements

Antibiotic resistance genes (ARGs) in manure aerobic composting are a potential environmental pollutant. Therefore, reducing the abundance of ARGs is crucial. The effects of adding three-dimensional printed bulking agents (3DBAs) on ARGs in aerobic composting of swine manure were investigated in this study. Compared with the control group, 3DBAs with different addition dosages can greatest reduce the total ARGs by 5.98%, tetracycline resistance genes by 14.02%, macrolide resistance genes by 9.65%, and sulfonamide resistance genes by 20.59%. By further combining physicochemical parameters, host microorganisms, and mobile genetic elements (MGEs) for analysis, it was found that oxygen concentration was vital for ARGs reduction, and 3DBAs with regular porosity and uniform size indirectly regulate the activity of host microorganisms and MGEs abundance by changing the oxygen consumption, finally reducing vertical or horizontal ARGs transfer risks. Overall, 3DBAs addition is an effective strategy to reduce the abundance of ARGs in aerobic composting.

Enhancing microplastics biodegradation during composting using livestock manure biochar

Biodegradation of microplastics (MPs) in contaminated biowastes has received big scientific attention during the past few years. The aim here is to study the impacts of livestock manure biochar (LMBC) on the biodegradation of polyhydroxyalkanoate microplastics (PHA-MPs) during composting, which have not yet been verified. LMBC (10% wt/wt) and PHA-MPs (0.5% wt/wt) were added to a mixture of pristine cow manure and sawdust for composting, whereas a mixture without LMBC served as the control (CK). The maximum degradation rate of PHA-MPs (22-31%) was observed in the thermophilic composting stage in both mixtures. LMBC addition significantly (P < 0.05) promoted PHA-MPs degradation and increased the carbon loss and oxygen loading of PHA-MPs compared to CK. Adding LMBC accelerated the cleavage of C-H bonds and oxidation of PHA-MPs, and increased the O-H, CO and C-O functional groups on MPs. Also, LMBC addition increased the relative abundance of dominant microorganisms (Firmicutes, Proteobacteria, Deinococcus-Thermus, Bacteroidetes, Ascomycota and Basidiomycota) and promoted the enrichment of MP-degrading microbial biomarkers (e.g., Bacillus, Thermobacillus, Luteimonas, Chryseolinea, Aspergillus and Mycothermus). LMBC addition further increased the complexity and connectivity between dominant microbial biomarkers and PHA-MPs degradation characteristics, strengthened their positive relationship, thereby accelerated PHA-MPs biodegradation, and mitigated the potential environmental and human health risk. These findings provide a reference point for reducing PHA-MPs in compost and safe recycling of MPs contaminated organic wastes. However, these results should be validated with other composting matrices and conditions.

Dynamics and key drivers of antibiotic resistance genes during aerobic composting amended with plant-derived and animal manure-derived biochars

Plant-derived and animal manure-derived biochars have been used to improve the quality of compost but the differences in their effects on antibiotic resistance genes (ARGs) during composting are unclear. This study selected two types of biochar (RB and PB) produced from abundant agricultural waste to be added to the compost. Adding plant-derived RB performed better in ARGs, mobile genetic elements, and human pathogenic bacteria removal during aerobic composting, whereas adding manure-derived PB even increased ARGs abundance. Vertical gene transfer was possibly the key mechanism for persistent ARGs, and easily removed ARGs were regulated by horizontal and vertical gene transfer. Adding plant-derived RB reduced the abundances of persistent ARG hosts (e.g., Pseudomonas and Longispora) and ARG-related metabolic pathways and genes. The higher nitrogen content of manure-derived PB may have promoted the proliferation of ARG hosts. Overall, adding manure-derived biochar during composting may not be the optimal option for eliminating ARGs.

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.

Insights into the associations of copper and zinc with nitrogen metabolism during manure composting with shrimp shell powder

The application of shrimp shell powder (SSP) in manure composting can promote the maturation of compost and reduce the associated environmental risk. This study investigated the response of adding SSP at different levels (CK: 0, L: 5%, M: 10%, and H: 15%) on heavy metal resistance genes (MRGs), nitrogen functional genes, enzymes, and microorganisms. SSP inhibited nitrification and denitrification via decreasing the abundances of functional genes and key enzymes related to Cu, Zn, and MRGs. The nitrate reductase and nitrous-oxide reductase in the denitrification pathway were lower under H. Phylogenetic trees indicated that Burkholderiales sp. had strong relationships with OTU396 and OTU333, with important roles in the nitrogen cycle and plant growth. Redundancy analysis and structural equation modeling showed the complex response between heavy metal and nitrogen that bio-Cu and bio-Zn had positive significantly relationships with nirK-type and amoA-type bacteria, and amoA-type bacteria might be hotspot of cueO.

Intraspecific and interspecific quorum sensing of bacterial community affects the fate of antibiotic resistance genes during chicken manure composting under penicillin G stress

In this study, the effects of penicillin G (PENG) on the fate of bacterial communities and β-lactamase antibiotic resistance genes (ARGs) during chicken manure composting were assessed, to illustrate the roles of PENG in ARGs behavior. The results showed that the total absolute abundances of 9 ARGs and 4 mobile genetic elements (MGEs) was significantly increased by PENG (P < 0.05). Dozens of potential hosts for ARGs were predominantly affiliated with Firmicutes, Proteobacteria, and Actinobacteria. Meanwhile, the higher concentration of PENG significantly increased the abundance of luxI and luxS in quorum sensing (QS) (P < 0.05), which enhanced the frequency of inter/intraspecific gene "communication." Redundancy analysis and structural equation modeling further revealed that QS had a strong regulatory role in horizontal gene transfer of ARGs mediated via MGEs. These results provide new insight into the mechanism of ARGs propagation in aerobic composting modified by PENG.

The fate of antibiotic resistance genes and their influential factors in swine manure composting with sepiolite as additive

Manures are storages for antibiotic resistance genes (ARGs) entering the environment. This study investigated the effects of adding sepiolite at 0%, 2.5%, 5%, and 7.5% (CK, T1, T2, and T3, respectively) on the fates of ARGs during composting. The relative abundances (RAs) of the total ARGs in CK and T3 decreased by 0.23 and 0.46 logs, respectively, after composting. The RAs of 10/11 ARGs decreased in CK, whereas they all decreased in T3. The reduction in the RA of the total mobile genetic elements (MGEs) was 1.26 times higher in T3 compared with CK after composting. The bacterial community accounted for 47.93% of the variation in the abundances of ARGs. Network analysis indicated that ARGs and MGEs shared potential host bacteria (PHB), and T3 controlled the transmission of ARGs by reducing the abundances of PHB. Composting with 7.5% sepiolite is an effective strategy for reducing the risk of ARGs proliferating.

Effects of H3PO4 modified biochar on heavy metal mobility and resistance genes removal during swine manure composting

In this research, static composting treatments of swine manure with forced ventilation were conducted to study the effects of biochar (BC) and H₃PO₄ modified biochar (BP) addition on heavy metals (HMs) stabilization, profiles of antibiotic resistance genes (ARGs), heavy metals resistance genes (MRGs) and bacterial communities during swine manure composting. After 42 days of the composting, compared to control (CK), BC and BP decreased the concentration of diethylenetriamine pentaacetic acid extractable Cu and Zn by 12.04%, 15.15% and 26.91%, 36.50%, respectively. Furthermore, BC and BP treatments reduced the total abundances of nine ARGs by 4.02% and 66.21%, and five MRGs by 53.66% and 58.81%, compared to CK in the compost product. Network analysis and square structural equation model analysis revealed that the decrease of ARGs and MRGs in BP treatment was related tothe change in bacterial community during the composting, rather than differences in co-selection pressure.

Effects of microplastics on humification and fungal community during cow manure composting

The effect of microplastics (MPs) on the biological treatment of organic waste has been extensively studied, but little is known about the influence of different MPs on composting humification and the fungal community. In this study, PE, PVC, and PHA MPs were individually mixed with cow dung and sawdust and then composted. The results showed that different MPs had various influences on humification, and the humic acid to fulvic acid ratio of all MP-added treatments (0.44-0.83) was lower than that of the control (0.91). During the composting process, Ascomycota (26.32-89.14%) and Basidiomycota (0.47-4.78%) are the dominant phyla in all treatments and all microplastics decreased the diversity and richness of the fungal community at the thermophilic stage of composting. Exposure to MPs had an obvious effect on the fungal community at the genus level, and the addition of PHA and PE MPs increased the relative abundance of phytopathogenic fungi. LEfSe and network analysis indicated that MPs reduced the number of biomarkers and led to a simpler and more unstable fungal community structure compared to the control. This study has important implications for assessing microplastic pollution and organic waste disposal.

Insights into the beneficial effects of woody peat for reducing abundances of antibiotic resistance genes during composting

Antibiotic resistance genes (ARGs) in manure endangered human health, while heavy metals in manure will pose selective pressure on ARGs. This study explored the effects on ARGs of adding woody peat during composting at different ratios (0 (CK), 5% (T1), and 15% (T2)). After composting, the relative abundances of 8/11 ARGs were 6.97-38.09% and 10.73-54.31% lower in T1 and T2, respectively, than CK. The bioavailable Cu content was 1.40% and 18.40% lower in T1 and T2, respectively, than CK. Network analysis showed that ARGs, mobile genetic elements (MGEs), and metal resistance genes possessed common potential host bacteria, such as Streptococcus, Dietzia, and Corynebacterium_1. Environmental factors, especially bioavailable Cu, and MGEs accounted for 80.75% of the changes in the abundances of ARGs. In conclusion, 15% Woody peat is beneficial to decrease the bioavailable Cu content and weaken horizontal gene transfer for controlling the spread of ARGs during composting.

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.