Removal of antibiotic resistance genes during swine manure composting is strongly impaired by high levels of doxycycline residues

Elimination of antibiotic resistance genes and adaptive response of Firmicutes during chicken manure composting

Aerobic composting is an effective method for reducing the abundance of antibiotic resistance genes (ARGs), but its effectiveness is influenced by the complex conditions during the process. However, the impact of composting conditions on the fate of ARGs and the underlying mechanisms remains unclear. This study examined the profile of ARGs, their mobility potential, hosts, and the risk of antibiotic resistome under different chicken manure composting conditions. A total of 708 ARGs were identified, and composting reduced their relative abundance by 29.4 %-82.4 %. Composting amendments and aeration rates exhibited similar elimination efficiencies for ARGs at different levels. However, low initial moisture content (50 %) caused a rebound in ARG abundance during the maturation phase. ARGs were mainly located on plasmids. After composting, the percentage of plasmid-born ARGs decreased from 46.3 %-70.8 % to 28.4 %-49.0 %. ARGs co-localized with mobile genetic elements displayed similar trends. The tolerance of Firmicutes to low moisture content played a key role in the rebound of ARGs and variations in their mobility potential. Composting reduced antibiotic resistance and ARG mobility in pathogens. Conversely, low moisture content hindered this attenuation effect in Firmicutes, which increased antibiotic resistome risk. This study provides comprehensive insights into the fate of ARGs and highlights the environmental risks of ARGs during composting.

The new strategies for high efficiency removal of antibiotics and antibiotic resistance genes by direct bio-drying of biogas slurry: Microbiological mechanisms

High levels of antibiotics and antibiotic resistance genes (ARGs) still exist in biogas slurry after anaerobic digestion of cow manure. In this study, direct bio-drying strategies of cow manure biogas slurry without solid-liquid separation for the removal of antibiotics and ARGs were explored. The results showed that, after direct bio-drying of biogas slurry, the moisture contents decreased to 25.2 %-31.5 %. The maximum temperatures of the piles reached 76.1-77.4 °C, which is close to ultra-high temperatures (>80 °C). Direct biogas slurry bio-drying (CK treatment) achieved efficient removal of antibiotics, ARGs, and mobile genetic elements (MGEs) (95.4 %, 98.6 % and 86.7 % removal, respectively). Compared to the CK treatment, molecular membrane covering (MMC) alone was the most effective in further significantly decreasing the antibiotic concentration and the abundance of ARGs and MGEs in the final bio-dried samples, followed by food waste hydrochar (FHC) addition alone. Methanogenic archaea were identified as potential hosts for ARGs based on Network analysis. FHC addition-MMC increased the abundance of potential hosts for ARGs and promoted the expression of microbial methane metabolism function relative to the CK treatment during the later stages of bio-drying, thereby decreasing the removal efficiency of ARGs. The results of structural equation model and redundancy analysis showed that MGEs had the most significant direct effect on ARGs and moisture content had the highest relative contribution to changes in ARGs. In summary, direct bio-drying strategies were able to efficiently remove antibiotics and ARGs from cow manure biogas slurry and also achieve biological dewatering of the biogas slurry.

Vermicomposting significantly reduced antibiotic resistance genes in cow manure even under high tetracycline concentrations

Minimizing antibiotic resistance genes (ARGs) in livestock manure is crucial for curbing ARG dissemination. Vermicomposting can eliminate ARGs, but the effect of residual antibiotics on its reduction efficacy remains unclear. Herein, Eisenia foetida was employed to convert cow manure with varying concentrations of tetracycline (i.e., 0, 10, 100 mg/kg), aiming to explore the impact of tetracycline on ARG fate during vermicomposting for 35 days. Results showed that the total ARG abundance in vermicomposting (0.05 copies/16S rRNA copies) was significantly lower than that in natural composting (0.06 copies/16S rRNA copies) (p < 0.05). Notably, exposure to tetracycline increased total ARG abundance (p < 0.05) and stimulated microbial succession during vermicomposting, with some ARGs increasing and others decreasing. But ARGs removal in vermicomposting was still higher even under tetracycline stress than that in natural composting. Overall, vermicomposting is an effective method for reducing ARGs in cow manure even at high tetracycline levels.

The source and dissemination of ARGs in pristine environments: Elucidating the role of migratory birds in the Arctic

Antibiotic resistance genes (ARGs) are a class of emerging contaminants that significantly threaten public health. In this work, the profiles of ARGs and microbial communities in the soil, sediment, migratory bird, and local deer fecal samples collected from the Arctic were characterized using a metagenomic approach. The results retrieved the baseline profiles of ARGs and identified the role of migratory birds in disseminating ARGs in the Arctic. A total of 26 ARG types and 718 subtypes were determined, and 131 core ARGs were identified. All the samples were dominated by multidrug resistance genes, and some genes resistant to antibiotics commonly used in anthropogenic were also detected. Characterization of ARGs in bird fecal samples was significantly distinct from other media, with higher abundance, richness, and unique ARGs detected. Proteobacteria was the most predominant phylum in soil and fecal samples, while Thaumarchaeota was prevalent in sediment samples. Firmicutes harbored the majority of ARGs in all samples. The results of FEAST indicated that migratory birds were crucial allochthonous ARG sources in the Arctic. These significant findings shed light on the global spread of ARGs and should facilitate efforts to map baseline levels of ARGs before the era of antibiotics.

Ceftiofur in swine manure contributes to reducing pathogens and antibiotic resistance genes during composting

Aerobic composting is a common way for the disposal of feces produced in animal husbandry, and can reduce the release of antibiotic resistance genes (ARGs) from feces into the environment. In this study, we collected samples from two distinct treatments of swine manure compost with and without ceftiofur (CEF), and identified the ARGs, mobile genetic elements (MGEs), and bacterial community by metagenomic sequencing. The impacts of CEF on the bacterial community composition and fate of ARGs and MGEs were investigated. With increasing composting temperature and pH, the concentration of CEF in the manure decreased rapidly, with a degradation half-life of 1.12 d and a 100% removal rate after 10 d of aerobic composting. Metagenomics demonstrated that CEF in the manure might inhibit the growth of Firmicutes and Proteobacteria, thereby reducing some ARGs and MGEs hosted by these two bacteria, which was further confirmed by the variations of ARGs and MGEs. A further redundancy analysis suggested that pH and temperature are key environmental factors affecting ARG removal during composting, and intI1 and bacterial communities also have significant influence on ARG abundance. These results are of great significance for promoting the removal of some ARGs from animal manure by controlling some key environmental factors and the type of antibiotics used in animals.

Priority establishment of soil bacteria in rhizosphere limited the spread of tetracycline resistance genes from pig manure to soil-plant systems based on synthetic communities approach

The spread of antibiotic resistance genes (ARGs) in agroecosystems through the application of animal manure is a global threat to human and environmental health. However, the adaptability and colonization ability of animal manure-derived bacteria determine the spread pathways of ARG in agroecosystems, which have rarely been studied. Here, we performed an invasion experiment by creating a synthetic communities (SynCom) with ten isolates from pig manure and followed its assembly during gnotobiotic cultivation of a soil-Arabidopsis thaliana (A. thaliana) system. We found that Firmicutes in the SynCom were efficiently filtered out in the rhizosphere, thereby limiting the entry of tetracycline resistance genes (TRGs) into the plant. However, Proteobacteria and Actinobacteria in the SynCom were able to establish in all compartments of the soil-plant system thereby spreading TRGs from manure to soil and plant. The presence of native soil bacteria prevented the establishment of manure-borne bacteria and effectively reduced the spread of TRGs. Achromobacter mucicolens and Pantoea septica were the main vectors for the entry of tetA into plants. Furthermore, doxycycline stress promoted the horizontal gene transfer (HGT) of the conjugative resistance plasmid RP4 within the SynCom in A. thaliana by upregulating the expression of HGT-related mRNAs. Therefore, this study provides evidence for the dissemination pathways of ARGs in agricultural systems through the invasion of manure-derived bacteria and HGT by conjugative resistance plasmids and demonstrates that the priority establishment of soil bacteria in the rhizosphere limited the spread of TRGs from pig manure to soil-plant systems.

Community coalescence and plant host filtering determine the spread of tetracycline resistance genes from pig manure into the microbiome continuum of the soil-plant system

The spread of livestock manure-borne antibiotic resistance genes (ARGs) into agroecosystems through manure application poses a potential threat to human health. However, there is still a knowledge gap concerning ARG dissemination in coalescing manure, soil and plant microbiomes. Here, we examined the fate of tetracycline resistance genes (TRGs) originating from pig manure microbiomes and spread in the soil-A thaliana system and explored the effects of microbial functions on TRGs spread at different interfaces. Our results indicate that the TRGs abundances in all microbiome continuum of the soil-A. thaliana system were significantly increased with the application of a living manure microbiome, although the addition of manure with both an active and inactive microbiome caused a shift in the microbial community composition. This was attributed to the increasing relative abundances of tetA, tetL, tetM, tetO, tetW and tolC in the system. The application of living manure with DOX residues resulted in the highest relative abundance of total TRGs (3.30×10-3 copies/16S rRNA gene copies) in the rhizosphere soil samples. Community coalescence of the manure and soil microbiomes increased the abundance of Firmicutes in the soil and root microbiome, which directly explains the increase in TRG abundance observed in these interfaces. In contrast, the leaf microbiome differed markedly from that of the remaining samples, indicating strong plant host filtering effects on Firmicutes and TRGs from pig manure. The random forest machine learning model revealed microbial functions and their significant positive correlation with TRG abundance in the microbiome continuum of the system. Our findings revealed that community coalescence is the main driver of TRG spread from manure to the soil and root microbiomes. Plant host filtering effects play a crucial role in allowing certain microbial groups to occupy ecological niches in the leaves, thereby limiting the establishment of manure-borne TRGs in aboveground plant tissues.