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

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.

Soil metabolic processes influenced by rice roots co-regulates the environmental evolution of antibiotic resistome

Plant root activities lead to significant differences in metabolites between the rhizosphere and non-rhizosphere soil, profoundly affecting microbial distribution. However, how this process drives the migration and propagation of manure-derived antibiotic resistance genes (ARGs) in farmland ecosystems remains unclear. Herein, we used a rice pot microcosm experiment to explore the characteristics of antibiotic resistome and bacterial communities in rhizosphere and non-rhizosphere soils and the driving effects of rhizosphere metabolites on ARG propagation. The results showed significant differences in some ARGs and bacterial diversity in rhizosphere and non-rhizosphere soils with varied differential ARGs between different growth stages of rice (P < 0.05). The biosynthesis of secondary metabolites and glutathione metabolism were found to be the main pathways affecting ARG differences in rhizosphere and non-rhizosphere soils under manure application. Structural equation modeling (SEM) analysis further indicated that ARG distribution differences between rhizosphere and non-rhizosphere soils were mainly regulated by differential metabolites, which influenced the ARG distribution by altering the succession of soil microbial communities. These results demonstrate the role of differential metabolites resulting from rice root activities in co-regulating ARG distribution, providing new insights into the regulatory mechanisms of soil ARG dynamics in paddy fields.

Anthropogenic activities significantly interfered distribution and co-occurrence patterns of antibiotic resistance genes in a small rural watershed in Southwest China

The prevalence and spread of antibiotic resistance genes (ARGs) have been a significant concern for global public health in recent years. Small rural watersheds are the smallest units of factor mobility for agricultural production in China, and their ARG profiles are the best scale of the contamination status, but the mapping and the distribution and diffusion of ARGs in the water and soil of small rural watersheds are inadequate. In this study, based on microbial metagenomics, we invested prevalence maps of 209 ARGs corresponding to typical commonly used antibiotics (including multidrug, aminoglycoside, macrolide-lincosamide-streptogramin B (MLSB), and β-Lactamase) in water and soil in different agricultural types, as well as within water-soil interfaces in small rural watersheds in Southwest China. The results revealed that the most abundant ARGs in water and soil were consistent, but different in subtypes, and anthropogenic activities affect the transport of ARGs between water and soils. Livestock wastewater discharges influenced the diversity and abundance of ARGs in water, while in soil it is planting type and fertilizer management, and thus interfered with the co-occurrence patterns between bacteria and ARGs. Co-occurrence analysis revealed that Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant ARG hosts in water and soil, but soil exhibited a more intricate ARG-bacterial association. Overall, this study provides integrated profiles of ARGs in water and soil influenced by anthropogenic activities at the small watershed scale in a typical rural area and provides a baseline for comparisons of ARGs.

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.

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.

Is the application of organic fertilizers becoming an undeniable source of microplastics and resistance genes in agricultural systems?

The application of organic fertilizers is becoming an undeniable source of microplastics and antibiotic resistance genes (ARGs) in agricultural soils. The complex microbial activity further transfers resistance genes and their host bacteria to agricultural products and throughout the entire food chain. Therefore, the current main focus is on reducing the abundance of microplastics and ARGs in organic fertilizers at the source, as well as managing microplastics and ARGs in soil. The control of microplastic abundance in organic fertilizers is currently only achieved through pre-composting selection and other methods. However, there are still many shortcomings in the research on the distribution characteristics, propagation and diffusion mechanisms, and control technologies of ARGs, and some key scientific issues still need to be urgently addressed. The high-temperature composting of organic waste can effectively reduce the abundance of ARGs in organic fertilizers to a certain extent. However, it is also important to consider the spread of ARGs in residual antibiotic-resistant bacteria (ARB). This article systematically explores the pathways and interactions of microplastics and resistance genes entering agricultural soils through the application of organic fertilizers. The removal of microplastics and ARGs from organic fertilizers was discussed in detail. Based on the limitations of existing research, further investigation in this area is expected to provide valuable insights for the development and practical implementation of technologies aimed at reducing soil microplastics and resistance genes.