Tracking antibiotic resistance genes (ARGs) during earthworm conversion of cow dung in northern China

Vermicompost: In situ retardant of antibiotic resistome accumulation in cropland soils

The dissemination of antibiotic resistance genes (ARGs) in soil has become a global environmental issue. Vermicomposting is gaining prominence in agricultural practices as a soil amendment to improve soil quality. However, its impact on soil ARGs remains unclear when it occurs in farmland. We comprehensively explored the evolution and fate of ARGs and their hosts in the field soil profiles under vermicompost application for more than 3 years. Vermicompost application increased several ARG loads in soil environment but decreased the high-risk bla-ARGs (blaampC, blaNDM, and blaGES-1) by log(0.04 - 0.43). ARGs in soil amended with vermicompost primarily occurred in topsoil (approximately 1.04-fold of unfertilized soil), but it is worth noting that their levels in the 40-60 cm soil layer were the same or even less than in the unfertilized soil. The microbial community structure changed in soil profiles after vermicompost application. Vermicompost application altered the microbial community structure in soil profiles, showing that the dominant bacteria (i.e., Proteobacteria, Actinobacteriota, Firmicutes) were decreased 2.62%-5.48% with the increase of soil depth. A network analysis further revealed that most of ARG dominant host bacteria did not migrate from surface soil to deep soil. In particular, those host bacteria harboring high-risk bla-ARGs were primarily concentrated in the surface soil. This study highlights a lower risk of the propagation of ARGs caused by vermicompost application and provides a novel approach to reduce and relieve the dissemination of ARGs derived from animals in agricultural production.

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.

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

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

Mitigation of antibiotic resistome in swine manure by black soldier fly larval conversion combined with composting

The increasing prevalence of antibiotic resistance genes (ARGs) in animal manure has attracted considerable attention because of their potential contribution to the development of multidrug resistance worldwide. Insect technology may be a promising alternative for the rapid attenuation of ARGs in manure; however, the underlying mechanism remains unclear. This study aimed to evaluate the effects of black soldier fly (BSF, Hermetia illucens [L.]) larvae conversion combined with composting on ARGs dynamics in swine manure and to uncover the mechanisms through metagenomic analysis. Compared to natural composting (i.e. without BSF), BSFL conversion combined with composting reduced the absolute abundance of ARGs by 93.2 % within 28 days. The rapid degradation of antibiotics and nutrient reformulation during BSFL conversion combined with composting indirectly altered manure bacterial communities, resulting in a lower abundance and richness of ARGs. The number of main antibiotic-resistant bacteria (e.g., Prevotella, Ruminococcus) decreased by 74.9 %, while their potential antagonistic bacteria (e.g., Bacillus, Pseudomonas) increased by 128.7 %. The number of antibiotic-resistant pathogenic bacteria (e.g., Selenomonas, Paenalcaligenes) decreased by 88.3 %, and the average number of ARGs carried by each human pathogenic bacterial genus declined by 55.8 %. BSF larvae gut microbiota (e.g., Clostridium butyricum, C. bornimense) could help reduce the risk of multidrug-resistant pathogens. These results provide insight into a novel approach to mitigate multidrug resistance from the animal industry in the environment by using insect technology combined with composting, in particular in light of the global "One Health" requirements.

Insights into the panorama of antibiotic resistome in cropland soils amended with vermicompost in China

The accumulation and propagation of animal-derived antibiotic resistance genes (ARGs) pose great challenges to agricultural ecosystems. Vermicompost has drawn global attention as a new type of eco-friendly organic fertilizer. However, the effects of vermicompost application on ARGs in soil are still unclear. Here, we conducted a nationwide large-scale survey to explore the impact of vermicompost application on ARGs and the host in cropland fields as well as their regional differences. Vermicompost application was found to alter the pattern of ARGs, reduce the transfer of mobile genetic elements (MGEs), and mitigate the proliferation of high-risk bla-ARGs in soil. Regional differences in vermicompost-derived ARGs were observed in croplands, with less ARG-spreading risk in brown and yellow-brown soils. Total ARG abundance was present at the lowest level (1.24 × 10⁵-3.57 × 10⁷ copies/g) in vermicomposted soil compared with the croplands using animal manure (e.g., swine, chicken, and cow manure). Furthermore, vermicompost application increased the abundance of beneficial bacteria like Ilumatobacter and Gaiella, while reducing the abundance of Acidobacteria and Pseudarthrobacter. Network analysis showed that vermicompost altered ARG host bacteria and reduced the numbers of potential ARG hosts in soil. Microbes played a key role in ARG changes in vermicompost-treated soil. Our study provides valuable insight into the response of soil ARGs and the host to vermicompost in cropland ecosystem, and also provides a novel pathway for controlling the propagation of animal-derived ARGs.

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

Earthworm conversion is an eco-friendly biological process that converts livestock waste into a benign nutrient-rich organic fertilizer. However, little is known about the impacts of earthworm-converted livestock manure on the antibiotic resistome in the earthworm gut microbiota. Herein, lab-scale vermicomposting was performed to comprehensively evaluate the shift of antibiotic resistance genes (ARGs) in the earthworm gut-feeding on cow manure (CM)-by metagenomic analysis. The effects of copper (Cu) as a food addictive were also evaluated. CM substantially enriched the antibiotic resistome in the foregut and midgut, while it decreased in the hindgut. A similar trend was observed for metal resistance genes (MRGs). Notably, Cu in the CM had little effect on composition of ARGs and MRGs in earthworm gut. The earthworm gut microbiome altered by CM was responsible for the shift of ARGs and MRGs. In wormcast, Cu (100 and 300 mg/kg) significantly increased the abundance of ARGs and MRGs. Our study provides valuable insight into the response of ARGs and MRGs to CM in earthworm gut, and underscores the need for the judicious use of heavy metals as feed additives in livestock and poultry farming.

Response of Antibiotic Resistance Genes and Related Microorganisms to Arsenic during Vermicomposting of Cow Dung

Antibiotic resistance pollution in livestock manure is a persistent issue that has drawn public attention. Vermicomposting is an ecofriendly biological process that can render livestock manure harmless and resourceful. However, little is known about the impact of vermicomposting on antibiotic resistance in livestock manure under stress caused by potentially toxic arsenic levels. Herein, lab-scale vermicomposting was performed to comprehensively evaluate the shift in antibiotic resistance genes (ARGs) and related microorganisms in fresh earthworm casts as well as vermicompost product health (i.e., nutrient availability and enzyme activity) when they were fed on arsenic-contaminated cow manure. The results showed that the earthworms' interaction with cow dung led to a significant reduction in ARG concentrations, especially for tetracycline ARGs (tet-ARGs), β-lactam ARGs (bla-ARGs), and quinolone ARGs (qnr-ARGs). However, arsenic significantly enhanced ARG accumulation in earthworm casts in a dose-dependent manner. Moreover, vermicomposting increased the percentage of Bacteroidota in the converted products. Furthermore, arsenic exposure at low concentrations promoted the proliferation of Proteobacteria, whereas high concentrations had little effect on Proteobacteria. Our study provides valuable insight into the changes in the antibiotic resistome and related microorganisms during vermicomposting of arsenic-amended cow manure, and it is crucial to explain the environmental impact of earthworms and improve our understanding of the reciprocal benefits of soil invertebrates.

Does Plant Identity Affect the Dispersal of Resistomes Above and Below Ground?

Resistomes are ubiquitous in natural environments. Previous studies have shown that both the plant phyllosphere and soil-borne nematodes were reservoirs of above- and below-ground resistomes, respectively. However, the influence of plant identity on soil, nematode, and phyllosphere resistomes remains unclear. Here, a microcosm experiment was used to explore the characteristics of bacterial communities and resistomes in soil, nematode, and phyllosphere associated with six different plant identities (Lactuca sativa, Cichorium endivia, Allium fistulosum, Coriandrum sativum, Raphanus sativus, and Mesembryanthemum crystallinum). A total of 222 antibiotic resistance genes (ARGs) and 7 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR from all samples. Plant identity not only significantly affected the diversity of resistomes in soil, nematode, and phyllosphere but also influenced the abundance of resistomes in nematodes. Shared bacteria and resistomes indicated a possible pathway of resistomes transfer through the soil-nematode-phyllosphere system. Structural equation models revealed that plant identity had no direct effect on phyllosphere ARGs, but altered indirectly through complex above- and below-ground interactions (soil-plant-nematode trophic transfer). Results also showed that bacteria and MGEs were key factors driving the above- and below-ground flow of resistomes. The study extends our knowledge about the top-down and bottom-up dispersal patterns of resistomes.

Cow Dung-Based Biochar Materials Prepared via Mixed Base and Its Application in the Removal of Organic Pollutants

Cow dung (CD) is a waste product of livestock production. Improper disposal of a large amount of CD will cause environmental pollution. In this work, three biochar materials based on CD (BMCD) were prepared by using three types of base, including KOH, NaOH, and mixed base (MB, a mixture of equal mass NaOH and KOH) as activators to investigate the different physicochemical properties of BMCDs (BMCD-K, BMCD-Na, and BMCD-MB). The objective was to verify the effectiveness of MB activation in the preparation of biochar materials. The results show that MB has an effect on the structural characteristics of BMCDs. In particular, the surface area and total pore volume, the specific surface area, and the total pore volume of BMCD-MB (4081.1 m² g⁻¹ and 3.0118 cm³ g⁻¹) are significantly larger than those of BMCD-K (1784.6 m² g⁻¹ and 1.1142 cm³ g⁻¹) and BMCD-Na (1446.1 m² g⁻¹ and 1.0788 cm³ g⁻¹). While synthetic dye rhodamine B (RhB) and antibiotic tetracycline hydrochloride (TH) were selected as organic pollutant models to explore the adsorption performances, the maximum adsorption capacities of BMCD-K, BMCD-NA and BMCD-MB were 951, 770, and 1241 mg g⁻¹ for RhB, 975, 1051, and 1105 mg g⁻¹ for TH, respectively, which were higher than those of most adsorbents. This study demonstrated that MB can be used as an effective activator for the preparation of biochar materials with enhanced performance.

β-lactamase genes transmission influenced by tetracycline, sulfonamide and β-lactams antibiotics contamination in the on-site farm soil

The prevalence of antibiotic resistance genes (ARGs), which have been identified as emerging environmental pollutants that pose a considerable risk to human health is widespread. The formation and transmission of ARGs are mainly associated with the antibiotic stress in an environment. And the abundance of ARGs also influenced by other categories antibiotics. The geographic information system was used to visualize the relative abundance of 28 types of ARGs and concentration of 18 types of antibiotics. The concentration of tetracycline antibiotics (TCs) and sulfonamide antibiotics (SAs) decreased gradually with increasing soil depth, while that of β-lactams (β-Ls) showed an increasing trend. The results revealed that TCs accounted for the largest proportion of all antibiotics. Furthermore, the abundance of β-lactam ARGs (β-RGs) increased with TCs and β-Ls increased. The abundance of tetracycline ARGs (TRGs) remained relatively stable with increasing concentrations of all antibiotics, while that of sulfonamide ARGs (SRGs) showed a decreasing trend. Although the abundance of β-RGs significantly increased with increasing levels of TCs and β-Ls. However, β-RGs were not significantly correlated with β-Ls, but with TCs. This study provided visual and comprehensive insights into the correlation between the distribution of typical antibiotics and ARGs and analyzed the synergy or antagonism between different antibiotics and ARGs. It is significant for soil remediation to reduce the likelihood of ARGs entering into and spreading in the human food chain via milk and beef consumption.

Manure application: A trigger for vertical accumulation of antibiotic resistance genes in cropland soils

The application of livestock manure increases the dissemination risk of antibiotic resistance genes (ARGs) in farmland soil environment. However, the vertical migration behavior and driving factor of ARGs in manured soil under swine manure application remains undefined. Here, the dynamics of ARGs, mobile genetic elements (MGEs) and bacterial communities in different soil depths (0 - 80 cm) with long-term swine manure application were tracked and conducted using real-time qPCR. Results showed that long-term application of swine manure remarkably facilitated the vertical accumulation of ARGs and MGEs, in particular that the relative abundance of bla_ampC showed significant enrichment with increasing depth. ARGs abundance was similar in the three fields with long-term application of swine manure. (p＞0.05). Procrustes analysis indicated that microbial communities were the dominant drivers of ARGs variation in topsoil, and the changes of environmental factors played a vital role in vertical migration ARGs in cropland soils. Additionally, the variation patterns of high-risk ARGs (i.e., bla_ampC, bla_TEM-1) were influenced by the dominant bacteria (Actinomycetes) and pH. This study illustrated that the swine manure application promoted the vertical migration of ARGs, including multidrug resistance determinants, highlighting the ecological risk caused by long-term manure application.

A Review of Current Bacterial Resistance to Antibiotics in Food Animals

The overuse of antibiotics in food animals has led to the development of bacterial resistance and the widespread of resistant bacteria in the world. Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in food animals are currently considered emerging contaminants, which are a serious threat to public health globally. The current situation of ARB and ARGs from food animal farms, manure, and the wastewater was firstly covered in this review. Potential risks to public health were also highlighted, as well as strategies (including novel technologies, alternatives, and administration) to fight against bacterial resistance. This review can provide an avenue for further research, development, and application of novel antibacterial agents to reduce the adverse effects of antibiotic resistance in food animal farms.