Cow manure simultaneously reshaped antibiotic and metal resistome in the earthworm gut tract by metagenomic analysis

Significant effects of earthworm species on antibiotic resistome in livestock manure as revealed by metagenomic analysis

Animal-derived antibiotic resistance genes (ARGs) have emerged as a critical threat, while vermicomposting has been recognized as an effective strategy for reducing ARGs. However, the efficacy of different earthworm species in reducing ARGs remains poorly understood. In this study, 72 vermicompost and earthworm gut samples were collected from various earthworm farms to evaluate the impact of vermicomposting with different earthworm species on ARGs via metagenomic analysis. Approximately 28 ARG types were detected in gut and vermicompost samples. There were significant differences in ARGs among the four species of earthworm composting systems (p < 0.05), and each species possessed its dominant ARGs and microbes. Proteobacteria represented the predominant bacterial phylum within the gut microbiota of Pheretima guillelmi (46.89 %) and Eisenia fetida (48.42 %), whereas Euryarchaeota (36.71 %) and Actinobacteria (39.42 %) were the most abundant in Perionyx excavatus and Eudrilus eugeniae, respectively. The overall abundance of ARGs in vermicompost processed by Eisenia fetida (0.18 copies16S rRNA gene copies) was lower than that observed in other earthworm species (0.23-0.39 copies/16S rRNA gene copies), with gut microbial identified as a key determinant of variations in ARG reduction. These findings provide valuable insights into selecting suitable earthworm species to promote ARG degradation, thus contributing to the decrease in ARG dissemination risks in agricultural ecosystems.

The Mechanisms of Tetracycline in Shaping Antibiotic Resistance Gene Dynamics in Earthworm Casts During Vermicomposting

Earthworm gut digestion plays a crucial role in reducing antibiotic resistance genes (ARGs) during vermicomposting, offering significant potential for controlling ARG dissemination in livestock manure. However, the impact of residual tetracycline antibiotics on this process remains poorly understood. Herein, this study systematically evaluated the impact of tetracycline of three concentrations (0, 10, and 100 mg/kg) on ARG dynamics and microbial community evolution during 35-day vermicomposting of cattle manure. The results demonstrated that earthworm intestinal digestion effectively eliminated over 96% of initial ARG load in raw manure. Noticeably, tetracycline stress significantly enhanced total ARG abundance in the casts (p < 0.05), with distinct response patterns observed among different ARG types. Mechanistic analysis revealed that tetracycline potentially enhanced ARG persistence through two pathways: (1) promoting horizontal transfer via mobile genetic elements, and (2) altering gut microbial succession patterns that influence ARG host-microbe relationships. These discoveries contribute to our comprehension of antibiotic interference in vermi-remediation processes and provide insights for optimizing ARG mitigation strategies in contaminated livestock manure.

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.

Evolution of the Black solider fly larvae gut antibiotic resistome during kitchen waste disposal

Kitchen waste (KW) is an important reservoir of antibiotic resistance genes (ARGs). Black solider fly larvae (BSFL) are extensively employed in KW disposal, closely linking to their robust gut microbes. However, antibiotic resistome in BSFL gut during the KW disposal processes and the mechanism remain unclear. In the present study, the antibiotic resistome in BSFL gut within the 12 days KW disposal processes were investigated. Results showed that, ARGs abundance initially increased and subsequently decreased, the five most prevalent core ARG classes were tetracycline, aminoglycoside, cephalosporin, lincosamide and multidrug. A total of 7 MGE types were observed and the horizontal gene transfer (HGT) of ARGs was predominantly mediated by plasmids. Host microbes were mainly categorized into Proteobacteria (98.12 %) and their assemblies were mainly classified into the deterministic processes. To elucidate the driving mechanisms, the mantel test and the structural equation model (SEM) were developed. Results indicated that microbial functions (0.912, p < 0.0001) and microbial community (1.014, p = 0.036), consistently showed very significant relationships with the patterns of ARGs, which presented higher direct effects than indirect effects. Overall, this study makes an initial contribution to a more deepgoing comprehension of the gut antibiotic resistome of BSFL during KW disposal.

Are earthworms the victim, facilitator or antidote of antibiotics and antibiotic resistance at the soil-animal-human interface? A One-Health perspective

The transfer of antibiotics and antibiotic resistance (AR) to the soil systems poses ecological hazards to various organisms, including earthworms. Understanding the complex interactions between earthworms, antibiotics, and AR in the soil system requires a comprehensive assessment. Hence, the present review investigates the behaviour, fate, impacts, and mechanisms involved in the interaction of earthworms with antibiotics and AR. The antibiotics and AR detected in earthworms and their associated media, such as vermicompost, are presented, but several other antibiotics and AR widely detected in soils remain understudied. As receptors and bioassay organisms, earthworms are adversely affected by antibiotics and AR causing (1) acute and chronic toxicity, and (2) emergence of AR in previously susceptible earthworm gut microbiota, respectively. The paper also highlights that, apart from this toxicity, earthworms can also mitigate against antibiotics, antibiotic-resistant bacteria and antibiotic-resistance genes by reducing bacterial diversity and abundance. The behaviour and fate processes, including biodegradation pathways, biomarkers of antibiotics and AR in earthworms, are discussed. In addition, the factors controlling the behaviour and fate of antibiotics and AR and their interactions with earthworms are discussed. Overall, earthworms mitigate antibiotics and AR via various proximal and distal mechanisms, while dual but contradictory functions (i.e., mitigatory and facilitatory) were reported for AR. We recommend that future research based on the One-World-One-Health approach should address the following gaps: (1) under-studied antibiotics and AR, (2) degradation mechanisms and pathways of antibiotics, (3) effects of environmentally relevant mixtures of antibiotics, (4) bio-augmentation in earthworm-based bioremediation of antibiotics, (5) long-term fate of antibiotics and their metabolites, (6) bio-transfers of antibiotics and AR by earthworms, (7) development of earthworm biomarkers for antibiotics and AR, (8) application of earthworm-based bioremediation of antibiotics and AR, (9) cascading ecological impacts of antibiotics and AR on earthworms, and (10) pilot-scale field applications of earthworm-based bioremediation systems.

Overlooked volcanic effect during transmission of antibiotic resistance genes induced by copper and zinc

Adding heavy metals such as copper and zinc to animal feeds is common practice to promote growth, but meanwhile has side consequence of enhancing spread of antibiotic resistance genes (ARGs) in soil. This presents a global challenge to food security and human health. We in this study investigated the transmission of typical ARGs, i. e. β-lactamase genes (β-RGs), in dairy farm environments where dietary Cu and Zn were present in a wide range of concentration. The β-RGs were demonstrated to be highly prevalent across environmental media, with a relative abundance of 94.55%, dominated by mechanisms of antibiotic deactivation (93.75%) and cellular protection (6.25%). More importantly, we first found the transmission of ARGs to be highly dependent on the overlooked volcanic effect, i. e. low-concentration Cu (12-22 mg/kg) and Zn (45-80 mg/kg) acted as micronutrients necessary for microbial growth but facilitated ARGs transfer, whereas higher-concentration Cu (22-39 mg/kg) and Zn (80-153 mg/kg) became toxic to microbial communities and gene expression patterns. Notably, the specific microbial phyla Proteobacteria (2.28-82.94%), Bacteroidetes (0.02-56.48%) and Actinobacteria (1.62-12.92%) exhibited resistance at low concentration of Cu and Zn, which enhanced the transmission of β-RGs. However, this process was inhibited at higher concentration due to inactivation of microbes by Cu and Zn. The increase in resistance was first observed in class Gammaproteobacteria (2.02-88.51%) and Alphaproteobacteria (0.68-10.1%) with increased Cu and Zn concentration. This resulted in heightened transfer of ARGs by tnpA-07 (80.35%) due to protection of thicker cell membrane by chelation with Cu and Zn. This study not only offers mechanistic insights into the volcanic effect of dietary metals on dissemination of ARGs, but also has important implications for safe management of agricultural settings.

Impact of earthworms on antibiotic resistance genes removal in ampicillin-contaminated soil through bacterial community alteration

The emergence of antibiotic resistance genes (ARGs) as contaminants in soil poses a significant threat to public health. Earthworms (Eisenia foetida), which are common inhabitants of soil, have been extensively studied for their influence on ARGs. However, the specific impact of earthworms on penicillin-related ARGs remains unclear. In this study, we investigate the role of earthworms in mitigating ARGs, specifically penicillin-related ARGs, in ampicillin-contaminated soil. Utilizing high-throughput quantitative PCR (HT-qPCR), we quantified a significant reduction in the relative abundance of penicillin-related ARGs in soil treated with earthworms, showing a decrease with a p-value of <0.01. Furthermore, high-throughput 16S rRNA gene sequencing revealed that earthworm intervention markedly alters the microbial community structure, notably enhancing the prevalence of specific bacterial phyla such as Proteobacteria, Firmicutes, Chloroflexi, and Tenericutes. Our findings not only demonstrate the effectiveness of earthworms in reducing the environmental load of penicillin-related ARGs but also provide insight into the alteration of microbial communities as a potential mechanism. This research contributes to our understanding of the role of earthworms in mitigating the spread of antibiotic resistance and provides valuable insights for the development of strategies to combat this global health issue.

Occurrence characteristics and influencing factors of antibiotic resistance genes in rural groundwater in Henan Province

This study determined the antibiotic-resistant gene (ARG) contents of 34 groundwater samples in Henan Province collected from September to October 2022, then assessed the roles of both water quality parameters and intI1 in ARG propagation in groundwater. The results show that there existed universal ARG pollution in groundwater, and sulfonamides-, β-lactem-, and tetracycline-resistance genes were the most prevalent gene types during the time. Sul1 contributed the majority proportion of the total resistance genes (TARGs). The prevalence of ESBLs gene blaTEM and the occurrence of Carbapenems resistant gene blaOXA-1 suggests the pollution of high-risk ARGs in groundwater demands more attention. IntI1 is prevalent and had a significantly positive correlation with almost 50% ARGs, indicating its contribution to ARG propagation in groundwater. Well types contribute little to ARG propagation in rural groundwater of Henan, which means the protective facilities established by the local government for public wells can effectively prevent contamination from exogenous ARGs. However, the economic level has no impact on the abundance of ARGs in rural groundwater, which suggests the local government should pay greater attention to investment in controlling ARG pollution in Henan rural areas.

Antibiotic resistance profiles of gut microbiota across various primate species in Guangxi

Introduction

Understanding the gut microbiota and antibiotic resistance gene (ARG) profiles in non-human primates (NHPs) is crucial for evaluating their potential impact on human health and the environment.

Methods

In this study, we performed metagenomic analysis of 203 primate fecal samples, including nine NHP species and humans, to comprehensively characterize their gut microbiota and ARGs.

Results

Our study reveals the prevailing phyla in primates as Firmicutes, Bacteroidetes, Euryarchaeota, and Proteobacteria. The captive NHPs exhibited higher ARG abundance compared to their wild counterparts, with tetracycline and beta-lactam resistance genes prevailing. Notably, ARG subtypes in Trachypithecus leucocephalus (T. leucocephalus) residing in karst limestone habitats displayed a more dispersed distribution compared to other species. Interestingly, ARG profiles of NHPs clustered based on geographic location and captivity status. Co-occurrence network analysis revealed intricate correlations between ARG subtypes and bacterial taxa. Procrustes analysis unveiled a significant correlation between ARGs and microbial phylogenetic community structure. Taxonomic composition analysis further highlighted differences in microbial abundance among NHPs and humans.

Discussion

Our study underscores the impact of lifestyle and geographical location on NHP gut microbiota and ARGs, providing essential insights into the potential risks posed by NHPs to antibiotic resistance dissemination. This comprehensive analysis enhances our understanding of the interplay between NHPs and the gut resistome, offering a critical reference for future research on antibiotic resistance and host-microbe interactions.

A Critical Review on the Vermicomposting of Organic Wastes as a Strategy in Circular Bioeconomy: Mechanism, Performance, and Future Perspectives

AbstractTo meet the current need for sustainable development, vermicomposting (VC), a natural, eco-friendly, and cost-effective technology, can be a wise selection for the bioconversion of organic wastes into value-added by-products. However, no one has tried to establish the VC technology as an economically sustainable technology by exploring its linkage to circular bioeconomy. Even, no researcher has made any effort to explore the usability of the earthworms (EWs) as a protein supplement while assessing the economic perspectives of VC technology. Very few studies are available on the greenhouse gas (GHG) emission potential of VC technology. Still, the contribution of VC technology towards the non-carbon waste management policy is not yet explored. In the current review, a genuine effort has been made to inspect the contribution of VC technology towards the circular bioeconomy, along with evaluating its capability to bioremediate the organic wastes generated from domestic, industrial, and agricultural premises. The potential of the EWs as a protein source has also been explored to strengthen the contribution of VC technology towards the circular bioeconomy. Moreover, the linkage of the VC technology to the non-carbon waste management policy has been comprehensively demonstrated by highlighting its carbon sequestration and GHG emission potentials during the treatment of organic wastes. It has been observed that the cost of food production was reduced by 60--70% by replacing chemical fertilizers with vermicompost. The implication of the vermicompost significantly lessened the harvesting period of the crops, thereby helping the farmers attain higher profits by cultivating more crops in a single calendar year on the same plot. Furthermore, the vermicompost could hold the soil moisture for a long time, lessening the water demand up to 30-40%, which, in turn, reduced the frequency of irrigation. Also, the replacement of the chemical fertilizers with vermicompost resulted in a 23% increment in the grapes' yield, engendering an extra profit of up to 110000 rupees/ha. In Nepal, vermicompost has been produced at a cost of 15.68 rupees/kg, whereas it has been sold to the local market at a rate of 25 rupees/kg as organic manure, ensuring a net profit of 9.32 rupees/kg of vermicompost. EWs embraced 63% crude protein, 5-21% carbohydrates, 6-11% fat, 1476 kJ/100 g of metabolizable energy, and a wide range of minerals and vitamins. EWs also contained 4.11, 2.04, 4.43, 2.83, 1.47, and 6.26  g/kg (on protein basis) of leucine, isoleucine, tryptophan, arginine, histidine, and phenylalanine, respectively, enhancing the acceptability of the EW meal (EWM) as the protein supplement. The inclusion of 3 and 5% EWM in the diet of broiler pullets resulted in a 12.6 and 22.5% increase in their feed conversion ratio (FCR), respectively after one month. Similarly, when a 100% fish meal was substituted by 50% EWM and 50% fish meal, the FCR and growth rate of Parachanna obscura were increased substantially. The VC of maize crop residues mixed with pig manure, cow dung, and biochar, in the presence of Eisenia fetida EWs, yielded only 0.003-0.081, 0-0.17, and 130.40-189.10 g CO₂-eq.kg^-1 emissions of CO₂, CH₄, and N₂O, respectively. Similarly, the VC of tomato stems and cow dung ensured 2.28 and 5.76 g CO₂-eq.kg^-1 CO₂ emissions of CH₄ and N₂O, respectively. Additionally, the application of vermicompost at a rate of 5 t/ha improved the soil organic carbon proportion and aggravated carbon sequestration. The land application of vermicompost improved micro-aggregation and cut down the tillage, reducing GHG emissions and triggering carbon sequestration. The significant findings of the current review suggest that VC technology potentially contributes to the concept of circular bioeconomy, substantially negotiates potential GHG emissions, and complies with the non-carbon waste management policy, reinforcing its acceptability as an economically sound and environmentally benevolent organic waste bioremediation alternative.