Long-term application of organic fertilization causes the accumulation of antibiotic resistome in earthworm gut microbiota

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

Using cow dung to breed earthworms poses a risk of environmental transmission of antibiotic resistance genes (ARGs). The purpose of this study was to address the occurrence, persistence and environmental fate of ARGs during earthworm conversion of cow dung. The results showed that ARGs persisted through the whole process. Notably, earthworm conversion effectively reduced some ARGs in cow dung, but a definite concentration of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). We found that tet-ARGs were the most abundant in 15 earthworm farms (10^-6~10^-1 copies/16S copies) and some high-risk ARGs (i.e., bla_ampC, bla_OXA-1 and bla_TEM-1) were even prevalent in these farms. Interestingly, although ARGs differ widely in cow dung (10^-10~10^-1 copies/16S copies), the ARGs levels were comparable in vermicompost samples from different farms (10^-8~10^-2 copies/16S copies). Notably, earthworm conversion effectively reduced some ARGs in cow dung, but significant level of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). Nevertheless, the concentrations of some heavy metals (Cu, Zn and Ni), the abundance of mobile genetic elements (MGEs) and total nitrogen content were confirmed to be correlated to the enrichment of some ARGs. Overall, this study demonstrated the high prevalence of ARGs contamination in earthworm farms, and also highlighted the dissemination risk of ARGs during the earthworm conversion of cow dung.

Effects of Partial Organic Substitution for Chemical Fertilizer on Antibiotic Residues in Peri-Urban Agricultural Soil in China

Recycling of organic wastes in agricultural ecosystems to partially substitute chemical fertilizer is recommended to improve soil productivity and alleviate environmental degradation. However, livestock manure- and sewage sludge-derived amendments are widely known to potentially carry antibiotic residues. The aim of this study is to investigate how substituting organic fertilizer for chemical fertilizer affects soil quality and antibiotic residues in agricultural soil, as well as their tradeoffs. A field experiment was conducted with the different treatments of pig manure and sewage sludge as typical organic fertilizers at equal total nitrogen application rates. The analysis of variance showed that the increments on the levels of residual antibiotics in the agricultural soils due to organic substitution for chemical fertilizer by pig manure and sewage sludge were observed. The antibiotic residues ranged from 13.73 to 76.83 ng/g for all treatments. Partial organic substitution significantly increased the sequestration of antibiotics in agricultural soil by 138.1~332.5%. Organic substitution will also significantly improve soil quality, especially for nutrient availability. Based on principal component analysis, organic substitution will strongly affected soil quality and antibiotic contamination. Pearson's correlation showed that soil physicochemical properties had significant correlations with concentrations of antibiotics in soil, indicating organic fertilizers can promote the persistence of antibiotics in soil by modifying soil quality. To balance the benefits and risks, appropriate management practices of organic fertilizers should be adopted.

Insights into the Role of the Fungal Community in Variations of the Antibiotic Resistome in the Soil Collembolan Gut Microbiome

Fertilization is known to affect antibiotic-resistance gene (ARG) patterns in the soil, even in the gut of soil fauna. Here, we conducted a microcosm experiment to investigate differences of effects of different fertilizers on collembolan gut ARG profiles and to further explore the microecological mechanisms that cause the differences. Although fertilization increased the abundance of ARGs, compared with the conventional manure, the application of antibiotic-reduced manure and vermicompost all curbed the enrichment of ARGs in the gut of collembolans. The results of the structural equation model revealed that changes in the microbial community caused by fertilizations have an important contribution to variations in the ARGs. We further found that the fungal community, like bacterial community, is also an important driver of ARG patterns in the collembolan gut. The fungi belonging to Dokmaia and Talaromyces were significantly correlated with the ARGs in the gut of collembolans. In addition, the application of vermicompost significantly increased the abundance of agricultural beneficial microbes in the soil environment. Together, our results provide an insight into the role of the fungal community on ARG patterns in the soil collembolan gut microbiome and highlight environmental friendliness of vermicomposting.

Metagenomic Exploration of Bacterial Community Structure of Earthworms’ Gut

Living organisms are naturally bestowed with unique and imitable qualities for maintaining ecological balance and earthworms are no exceptions. These so-called keystone species of terrestrial ecosystems are equipped with wonderful machinery, allowing them to nurture soil beautifully. Earthworm gut represents a potential microbial reservoir, having a complex interdependence with the host. The study aimed to profile bacterial community structure of three earthworm species belonging to two different life forms; Perionyx excavatus and Eudrilus eugeniae (epigeic), Polypheretima elongata (endogeic) respectively. Diversity analysis using 16S amplicon sequencing revealed that the dominant phyla were Proteobacteria (34.17-77.88) followed by Actinobacteria (13.43-35.54%), Firmicutes (1.69-15.45%) and Bacteroidetes (0.51-8.12%). The alpha diversity indices explicit similar gut microbiota of Perionyx excavatus and Eudrilus eugeniae and while higher alpha diversity was recorded in comparison to Polypheretima elongata gut. The taxonomic to the phenotypic annotation of 16S rRNA metagenomes revealed that dominance of Gram-negative bacterial community in all earthworm species while, Polypheretima elongata comprises higher percentage (78%) of Gram-negative bacterial community to Perionyx excavatus (32.3%) and Eudrilus eugeniae (38.3%). The oxygen requirement phenotypic analysis showed that all earthworm species were abundant with aerobic followed by anaerobic bacterial groups. Furthermore, functional metabolism phenotypic analysis revealed that a high abundance of ammonia oxidizers (29.3-80.2%), the gut microbiomes showed the relative abundance of sulphate reducer (22.6-78.7%), nitrite reducer (19.8-73.2%), dehalogenators (12.6-25.1%), illustrating in the role of these microbial communities in various degradation and bioremediation processes. The present study signifies the intrinsic gut microbiota of earthworm species for intensified biodegradation.

Agricultural land-use change exacerbates the dissemination of antibiotic resistance genes via surface runoffs in Lake Tai Basin, China

Agricultural runoff is an important antibiotic resistance genes (ARGs) dissemination pathway from farmlands to water environment, however few studies have focused on the influence of agricultural land-use change on the pattern of ARGs in runoff and assess the health risk to public. Lake Tai Basin which experiences agricultural land-use change was selected to elucidate this concern. Our findings revealed that the pattern of ARGs was more diverse and the gene abundance was higher in orchard runoffs by comparison with conventional cropland runoffs. Co-occurrence network analysis between mobile genetic elements and ARGs demonstrated that after agricultural land-use change, ARG dissemination via runoffs became more threatened. In addition, this study illustrated the correlations between the antibiotic resistome and microbiome in runoffs, finding that non-dominant microbial taxa were the limiting factor which determined the pattern of ARGs in surface runoffs. In summary, the pattern and dissemination risk of ARGs in the surface runoff after agricultural land-use change in Lake Tai Basin were clarified via this study.

Tracking antibiotic resistance gene transfer at all seasons from swine waste to receiving environments

Antibiotic resistance genes (ARGs) in livestock farms have attracted a growing attention with potential effects on human health. As one of the most important organic fertilizer, swine waste provided an ideal environment for understanding the dissemination and accumulation of ARGs in agricultural ecosystems. Here we conducted a year-round follow-up trace from swine waste to receiving environments, with the purpose of revealing the contamination profiles and ecological risks of ARGs at different seasons. Results indicated that a variety of common ARGs and even high-risk ARGs (i.e., bla_ampC, bla_OXA-1, bla_TEM-1 and mcr-1) were prevalent from swine waste to farmland soil, with changing in various degrees from season to season. Regarding the occurrence pattern of ARGs, tetracycline resistance genes (tet-ARGs) were predominant genes at four seasons in all fresh pig feces, swine manure, manured soil and wastewater. The levels of most ARGs in solid waste were reduced at a different degree via natural composting, and the removal effect was best in summer, while ARGs decreased poorly after wastewater treatment, especially in winter (up to 10^-1 copies/16S copies in the residual level), which increased the possibility of propagation to receiving environment. This concern was also validated by the investigation on farmland environment with long-term application of manure, where causing an increase in ARG abundances in soils (approximately 0.9-32.7 times). To our knowledge, this study is the first to demonstrate the distribution pattern of ARGs from swine waste to its receiving farmland environment at all seasons on this integrity chain.

Heavy metal could drive co-selection of antibiotic resistance in terrestrial subsurface soils

Terrestrial surface ecosystems are important sinks for antibiotic resistance genes (ARGs) due to the continuous discharge of contaminants from human-impacted ecosystems. However, the abundance and resistance types of ARGs and their influencing factors in terrestrial subsurface soils are not well known. In this study, we investigated the abundance and diversity of ARGs, and their correlations with metal resistance genes (MRGs), mobile genetic elements (MGEs), bacteria, and heavy metals in subsurface soils using high throughput quantitative PCR and metagenomic sequencing approaches. Abundant and diverse ARGs were detected with high spatial heterogeneity among sampling sites. Vertically, there was no significant difference in ARG profiles between the aquifer and non-aquifer soils. Heavy metals were key factors shaping ARG profiles in soils with high heavy metal contents, while they showed no significant effect in low contents. Moreover, heavy metals could trigger the proliferation of antibiotic resistance by increasing MGE abundance or influencing bacterial communities. Metagenomic analysis also revealed the widespread co-occurrence of ARGs and MRGs, with heavy metals possibly enhancing the co-selection of ARGs and MRGs in soils with high heavy metal contents. This study highlighted the heavy metal-driven co-selection of ARGs and revealed the occurrence of ARG pollution in terrestrial subsurface soils.

An insight into the exploration of proliferation of antibiotic resistance genes in high-fat diet induced obesity mice

Using mice as an animal model, we first demonstrated the significant proliferation of ARGs and the change of mobile genetic elements (MGEs) in high-fat diet induced obesity (DIO) mice, which the ermB and tnpA-03 genes mostly increased, illuminating that DIO could enrich the abundance of ARGs. Additionally, Lactobacillus sharply increased in the DIO mice and might contribute to the proliferation of ARGs and dramatical change of MGEs in the HFD groups. Finally, procrustes analysis showed the explanatory variables of the MGEs, the metabolites, and the microbial communities for the ARGs accounted for 94.3%, 53.4%, and 68.1%, respectively, and implying that MGEs might be the most direct factor affecting ARGs, and microbiota could be the main driver of the proliferation of ARGs in the DIO mice.

Deciphering Potential Roles of Earthworms in Mitigation of Antibiotic Resistance in the Soils from Diverse Ecosystems

Earthworms are capable of redistributing bacteria and antibiotic resistance genes (ARGs) through soil profiles. However, our understanding of the earthworm gut microbiome and its interaction with the antibiotic resistome is still lacking. Here, we characterized the earthworm gut and soil microbiome and antibiotic resistome in natural and agricultural ecosystems at a national scale, and microcosm studies and field experiments were also employed to test the potential role of earthworms in dynamics of soil ARGs. The diversity and structure of bacterial communities were different between the earthworm gut and soil. A significant correlation between bacterial community dissimilarity and spatial distance between sites was identified in the earthworm gut. The earthworm gut consistently had lower ARGs than the surrounding soil. A significant reduction in the relative abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs was observed in the earthworm gut compared to the surrounding soil, which might contribute to the decrease of ARGs in the earthworm gut. The microcosm studies and field experiments further confirmed that the presence of earthworms significantly reduced the number and abundance of ARGs in soils. Our study implies that earthworm-based bioremediation may be a method to reduce risks associated with the presence of ARGs in soils.

Agricultural land-use change and rotation system exert considerable influences on the soil antibiotic resistome in Lake Tai Basin

In this study, we use high-throughput quantitative polymerase chain reaction approaches to comprehensively assess the effects of agricultural land-use change on the antibiotic resistome of agricultural runoffs after rainfalls in Lake Tai Basin. For the first time in this region, our findings show that orchard runoffs harbored more diverse and abundant antibiotic resistance genes (ARGs) than traditional cropland runoffs. Network analysis demonstrated that orchard runoffs possessed a strong ability for ARG dissemination via horizontal gene transfer. These results suggest that residents might be exposed to a higher public health threat than before. Moreover, the present study confirmed that the rice-wheat rotation system plays a key role in regulating the soil antibiotic resistome profile. Using 16S rRNA high-throughput sequencing technology, this study clarified the relationships between the antibiotic resistome and soil microbiome composition. Finally, we discuss the key environmental factors driving changes in the soil antibiotic resistome. In summary, this study gives insight into the dissemination of environmental ARGs to the people living in the Lake Tai Basin.

Seasonal change is a major driver of soil resistomes at a watershed scale

Soils harbor the most diverse naturally evolved antibiotic resistomes on Earth that threaten human health, ecosystem processes, and food security. Yet the importance of spatial and temporal variability in shaping the distribution of soil resistomes is not well explored. Here, a total of 319 topsoil samples were collected at a watershed scale during four seasons (spring to winter) and high-throughput quantitative PCR (HT-qPCR) was used to characterize the profiles of soil antibiotic resistance genes (ARGs). A significant and negative correlation was observed between soil ARG profiles and seasonal dissimilarity, which along with seasonally dependent distance-decay relationships highlight the importance of seasonal variability in shaping soil antibiotic resistomes. Significant, though weak, distance-decay relationships were identified in spring, summer and winter, for ARG similarities with geographic distances. There were also strong interactions between specific soil ARGs and Actinobacteria, Firmicutes and Proteobacteria. Moreover, we found that the relative abundance of soil Actinobacteria, Firmicutes and Proteobacteria correlated significantly with annual mean temperature and annual mean precipitation at a watershed scale. A random forest model showed that seasonal change rather than spatial variation was the most important predictor of the composition of soil ARGs. Together, these results constitute an advance in our understanding of the relative importance of spatial and temporal variability in shaping soil ARG profiles, which will provide novel insights allowing us to forecast their distribution under a changing environment.

Impacts of earthworm introduction and cadmium on microbial communities composition and function in soil

Heavy metal contamination of soil has become a public concern. Earthworms are key players in the functioning and service of soil ecosystems, with comprehension of their introduction in the polluted soil offering new insights into the protection of soil resources. In the present study, we evaluated the effects of earthworm (Eisenia fetida) introduction and Cd (0, 10, 30, and 60 mg kg^-1 of Cd) exposure upon soil microbial community using 16S rRNA gene amplicon sequencing. Our research demonstrated that Gemmatimonadetes and Deinococcus-Thermus upregulated significantly, while Chryseolinea showed an obvious decreasing trend after earthworm introduction. In Cd contaminated soil, many genera exhibited a greater presence of Cd-dependent bacteria, namely Cd-tolerant bacteria such as Altererythrobacter and Luteimonas, and a decrease of sensitive bacteria, such as Amaricoccus and Haliangium. Moreover, functional prediction analysis of soil microbiota indicated that earthworm introduction and Cd exposure changed functional pathways of soil microorganisms. The results obtained in this study are beneficial for understanding soil microbial community impacted by earthworm, and for exploring Cd resistant or tolerant bacteria, with potentially significant findings for soil biodiversity and Cd bioremediation.

Elimination of antibiotic resistance genes from excess activated sludge added for effective treatment of fruit and vegetable waste in a novel vermireactor

Elimination of antibiotic resistance genes (ARGs) from excess activated sludge (EAS) mixed for effective treatment of different fruit and vegetable waste (FVW) by using a novel vermireactor consisted of substrate and bed compartments was investigated. ARGs (tet G, tet M and sul 1) and mobile genetic element gene (intl 1) were targeted and, through quantitative analysis of their abundances in both the compartments and the fresh cast of earthworms, significant reductions in substrate compartments were confirmed for the treatments for FVW added with EAS and EAS alone even if the reduction extents differed among the types of FVW. Apparent reductions were not found in the bed compartment where the final products accumulated. For the fresh cast, the relative abundances of ARGs and intl 1 against to the total bacterial 16S rDNA decreased markedly. The present study provided an insight for proper controlling of ARGs during vermicomposting of FVW and EAS.

Effect of chlorpyrifos on the earthworm Eudrilus euginae and their gut microbiome by toxicological and metagenomic analysis

The earthworms are important soil invertebrates and play a crucial role in pedogenesis. The application of pesticides and prolonged exposure to pesticides causes mortality of earthworms apart from profoundly affecting the resident gut microbiome. The microbiome plays a significant effect on the metabolic processes associated with earthworms. The pesticide Chlorpyrifos (CPF) was studied for its toxicity on Eudrilus euginae by toxicity studies. The LC₅₀ value of filter paper contact test and acute toxicity test was 3.8 mg/mL and 180 mg/kg. The prolonged exposure of earthworms to pesticide on reproductive toxicity resulted in the mortality of earthworms and absence of cocoon formation. Further, the effects of CPF on the whole gut microbiome of E. euginae was analyzed using a long amplicon Nanopore sequencing. Results indicated no fluctuations with Firmicutes and Bacteroidetes, that were found to be dominant at bacterial phyla level while at the genus level, remarkable differences were noticed. Clostridium dominated the earthworm gut prior to CPF exposure while Bacillus dominated after exposure. Similarly, the fungal members such as Ascomycota and Basidiomycota were observed to dominate the gut of earthworm at the phyla level before and after exposure to CPF. In contrast, Clavispora (65%) was the dominant genus before CPF exposure and Taloromyces (42%) dominated after the CPF exposure. Our study demonstrates the effect of CPF on the mortality of E. euginae while the amplicon sequencing established the unique microbiome of the gut in response to the CPF exposure.

The changes in antibiotic resistance genes during 86 years of the soil ripening process without anthropogenic activities

This study aimed to reveal the baseline of natural variations in antibiotic resistance genes (ARGs) in soil without anthropogenic activities over the decades. Nine soil samples with different time of soil formation were taken from the Yancheng Wetland National Nature Reserve, China. ARGs and mobile genetic elements (MGEs) were characterized using metagenomic analysis. A total of 196 and 192 subtypes of ARGs were detected in bulk soil and rhizosphere, respectively. The diversity and abundance of ARGs were stable during 69 years probably due to the alkaline pH soil environment but not due to antibiotics. Increases in ARGs after 86 years were probably attributed to more migrant birds inhabited compared with other sampling sites. Multidrug was the most abundant type, and largely shared by soil samples. It was further shown that soil samples could not be clearly distinguished, suggesting a slow process of succession of ARGs in the mudflat. The variation partitioning analysis revealed that the ARG profile was driven by the comprehensive effects exhibited by the bacterial community, MGEs, and environmental factors. Besides, pathogenic bacteria containing ARGs mediated by migrant birds in the area with 86 years of soil formation history nearing human settlements needed special attention. This study revealed the slow variations in ARGs in the soil ripening process without anthropogenic activities over decades, and it provided information for assessing the effect of human activities on the occurrence and dissemination of ARGs.

Testosterone amendment alters metabolite profiles of the soil microbial community

Steroid hormones are prevalent in the environment and have become emerging pollutants, but little is known about their effects on soil microbial community composition and function. In the present study, three representative soils in China were amended with environmentally relevant concentrations of testosterone and responses of soil bacterial community composition and soil function were assessed using high-throughput sequencing and nontargeted metabolomics. Our results showed that testosterone exposure significantly shifted bacterial community structure and metabolic profiles in soils at Ningbo (NB) and Kunming (KM), which may reflect high bioavailability of the hormone. Abundances of several bacterial taxa associated with nutrient cycling were reduced by testosterone and metabolites related to amino acid metabolism were downregulated. A close connection between bacterial taxa and specific metabolites was observed and confirmed by Procrustes tests and a co-occurrence network. These results provide an insight into the effects of steroid hormones on soil microbial community and highlight that nontargeted metabolomics is an effective tool for investigating the impacts of pollutants.

Elevated CO2 concentration modifies the effects of organic fertilizer substitution on rice yield and soil ARGs

Antibiotic resistance and rising CO2 levels are considered among the most significant challenges we will face in terms of global development over the following decades. However, the impact of elevated CO2 on soil antibiotic resistance has rarely been investigated. We used a free-air CO2 enrichment system to investigate the potential risks posed by applying mineral and organic fertilizers to paddy soil at current CO2 concentration (370 ppm) and future elevated CO2 (eCO2, 570 ppm predicted for 2100). Organic fertilizer substitution (substituting the mineral fertilizer by 50% N) alone increased the plant uptake and soil residue of sulfamethazine, and enriched sulfonamide resistance genes (sul1, sul2), tetracycline resistance genes (tetG, tetM) and class 1 integron (intl1). But it decreased the rice grain yield (by 7.6%). Comparatively, eCO2 decreased the sul2, tetG and intl1 gene abundances by organic fertilizer substitution, and meanwhile increased grain yield (by 8.4%). Proteobacteria and Nitrospirae were potential hosts of antibiotic resistance genes (ARGs). Horizontal gene transfer via intl1 may play an important role in ARGs spread under eCO2. Results indicated that future elevated CO2 concentration could modify the effects of organic fertilizer substitution on rice yield and soil ARGs, with unknown implications for future medicine and human health.

Fates of Antibiotic Resistance Genes in the Gut Microbiome from Different Soil Fauna under Long-Term Fertilization

Applying organic fertilizers has been well documented to facilitate the dissemination of antibiotic resistance genes (ARGs) in soil ecosystems. However, the role of soil fauna in this process has been seldom addressed, which hampers our ability to predict the fate of and to manage the spread of ARGs. Here, using high-throughput quantitative polymerase chain reaction (HT-qPCR), we examined the effect of long-term (5-, 8-, and 10-year) fertilization treatments (control, inorganic fertilizers, and mixed fertilizers) on the transfer of ARGs between soil, nematodes, and earthworms. We found distinct fates for ARGs in the nematodes and earthworms, with the former having higher enriched levels of ARGs than the latter. Fertilization impacted the number and abundance of ARGs in soil, and fertilization duration altered the composition of ARGs. Shared ARGs among soil, nematodes, and earthworm guts supported by a fast expectation-maximization microbial source tracking analysis demonstrated the trophic transfer potential of ARGs through this short soil food chain. The transfer of ARGs was reduced by fertilization duration, which was mainly ascribed to the reduction of ARGs in the earthworm gut microbiota. This study identified the transfer of ARGs in the soil-nematode-earthworm food chain as a potential mechanism for a wider dissemination of ARGs in the soil ecosystem.

Exposure of CuO nanoparticles and their metal counterpart leads to change in the gut microbiota and resistome of collembolans

The widespread use of copper oxide nanoparticles (CuONPs) has dramatically increased their concentrations in soils and severely affected the health of soil organisms. The gut microbiota critically contributes to the metabolism and immune system of its host and is sensitive to environmental pollution. The toxic effect of CuONPs on the gut microbiota, especially in soil fauna, still needs further research. In the present study, a comprehensive toxicological test was performed to reveal the effects of CuONPs and their metal counterpart on the gut microbiota of soil collembolans using Illumina high throughput sequencing. Furthermore, the concomitant changes in the collembolans gut-associated antibiotic resistance genes (ARGs) and metabolism were investigated using high-throughput quantitative PCR and carbon and nitrogen stable isotope compositions. Both CuONPs and ionic copper (Cu) exposure disturbed the collembolan gut microbial community structure while only CuONPs reduced the gut microbial diversity. A total of 66 ARGs were detected in the collembolan guts, and CuONPs exposure induced a reduction in both diversity and abundance of ARGs. Additionally, CuONPs and ionic Cu exposure altered the C and N stable isotope compositions of the collembolans, indicating a change in their metabolism. Moreover, structural equation modeling indicated that 85.5% of the carbon stable isotope variations and 73.3% of the nitrogen stable isotope variations were explained by changes in Cu bioaccumulation and the gut microbiota. The results of the present study extend our knowledge regarding the comprehensive toxicity of metal oxide NPs on soil fauna.

Development and characterization of microsatellite markers in the earthworm Drawida gisti Michaelsen, 1931 and cross-amplification in two other congeners

The earthworm (Drawida gisti) is an ecologically important sentinel species for soils that is widely distributed throughout Eastern Asia; however, the molecular tools required for genetic diversity studies of this earthworm are still rare. The aim of the study was to develop and characterize microsatellite markers in D. gisti and to evaluate their transferability to other Drawida species. We employed a RAD-seq approach to develop 12 microsatellite markers for D. gisti. The characterization and analysis of loci was achieved using 24 individuals of D. gisti from a natural population. The number of alleles per locus ranged from four to eleven, with an average of 6.5. Observed and expected heterozygosities varied from 0.708 to 0.958, and from 0.568 to 0.883, respectively. No loci presented significant deviations from the Hardy-Weinberg equilibrium, while linkage disequilibrium was detected between three loci. Cross-species amplification tests suggested that the transferability of ten loci was positive for the two congeners D. japonica and D. ghilarovi. This set of microsatellite markers may be used to evaluate the genetic diversity and population structures of D. gisti and related species in the future.

Effects of ciprofloxacin exposure on the earthworm Eisenia fetida

The widespread use of the antibiotic ciprofloxacin (CIP) poses a serious risk to soil organisms. Here, earthworms (Eisenia fetida) were used to explore the effect of CIP exposure on growth, reproduction, mortality, antioxidant enzyme activity, DNA damage, and mRNA levels. The results showed that mortality, weight, and reproduction did not change in response to CIP exposure. The antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD), and glutathione (GSH) were inhibited after 10 mg/kg CIP exposure on day 21, and catalase (CAT) activity increased significantly on day 14. High concentrations (1-2 g/kg) of CIP pollution caused DNA damage in E. fetida on days 7 and 14. At a dose of 10 mg/kg, CIP altered antioxidant enzymes and gene expression, but was not harmful to the growth and reproduction of E. fetida. Moreover, mRNA expression of annetocin, metallothionein, heat shock protein 70, and translationally controlled tumor protein were significantly upregulated on day 28. These findings indicate that antioxidant enzymes, DNA damage, and mRNA levels of biomarkers are more sensitive than mortality, growth, and reproduction for detecting CIP pollution in the soil environment.

Dysbiosis in the Gut Microbiota of Soil Fauna Explains the Toxicity of Tire Tread Particles

Tread particles (TPs) from vehicle tires are widely distributed in soil ecosystems; therefore, there is an urgent need to evaluate their effects on soil biota. In the present study, the soil worm Enchytraeus crypticus was incubated for 21 days in soil microcosms containing increasing concentrations of TPs (0, 0.0048%, 0.024%, 0.12%, 0.6%, and 3% of dry soil weight). High concentrations of zinc (Zn, 9407.4 mg kg^-1) and polycyclic aromatic hydrocarbons (PAHs, 46.8 mg kg^-1) were detected in the TPs, which resulted in their increased concentrations in soils amended with TPs. We demonstrated that TPs had an adverse effect on the survival (decreased by more than 25%) and reproduction (decreased by more than 50%) of the soil worms. Moreover, TP exposure disturbed the microbiota of the worm guts and surrounding soil. In addition, a covariation between bacterial and fungal communities was observed in the worm guts after exposure to TPs. Further analysis showed that TP exposure caused an enrichment of microbial genera associated with opportunistic pathogenesis in the worm guts. The combined results from this study indicate that TPs might threaten the terrestrial ecosystem by affecting soil fauna and their gut microbiota.

World within world: Intestinal bacteria combining physiological parameters to investigate the response of Metaphire guillelmi to tetracycline stress

Due to the abusive usage of antibiotics in animal husbandry, a large amount of residual antibiotics has been released into the environment, therein posing great threat against both environment security and public health. Therefore, it is of great significance to investigate the toxicity of antibiotics on the widely-applied bioindicator-earthworm. In this work, the physiological parameters and the intestinal bacteria community of Metaphire guillelmi were monitored simultaneously to evaluate their sensitivity to the tetracycline (TC) exposure. As expected, the antioxidant enzyme activity and coelomocyte apoptosis acted fairly well as biomarkers for the TC toxicity. In contrast, the intestinal bacteria of Metaphire guillelmi responded varyingly to different TC doses. When TC concentration increased from 0 to 35.7 μg cm^-2, the percentage of the Proteobacteria phylum declined significantly from 85.5% to 34.4%, while the proportions of the Firmicutes, Planctomycetes and Atinomycete phyla clearly increased (p < 0.05). Meanwhile, the levels of TC resistance genes tetA, tetC, and tetW increased with the increasing TC concentration, in contrast to the declined abundance in denitrifying genes nirS and nosZ (p < 0.05). By analyzing the correlation between the antioxidant enzyme activity and the dominant intestinal bacteria in the worm gut, it is interesting to found that the four dominant bacteria genera Mesorhizobium, Aliihoeflea, Romboutsia, and Nitrospira are the promising bioindicator of TC stress due to their sensitive response. This work shed novel light on evaluating the ecotoxicological risks posed by residual TC in environment by using a combination of physiological parameters and intestinal bacterial activity in earthworms.

Characterization of antibiotic resistance genes and bacterial community in selected municipal and industrial sewage treatment plants beside Poyang Lake

Sewage treatment plants (STPs) are significant reservoirs of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Municipal STPs (MSTPs) and industrial STPs (ISTPs) are the two most important STP types in cities. In this study, the ARGs, mobile genetic elements (MGEs), and bacterial communities of selected STPs, including two MSTPs and one ISTP, in the vicinity of Poyang Lake were comprehensively investigated through high-throughput qPCR and high-throughput Illumina sequencing. The results showed that the profiles of ARGs, MGEs and bacteria differed between the ISTP and the two MSTPs, most likely due to differences in influent water quality, such as the Pb that characterized in the ISTP's influent. The longer hydraulic retention times (HRTs) of the two MSTPs than of the ISTP may also have accounted for the different profiles. Thus, a prolonged HRT in the CASS process seems to allow a more extensive removal of ARGs and bacteria in ISTPs with similar treatment process. By providing comprehensive insights into the characteristics of ARGs, MGEs and the bacterial communities of the selected MSTPs and ISTP, our study provides a scientific basis for controlling the propagation and diffusion of ARGs and ARB in different types of STPs.

Prevalence of Antibiotic Resistome in Ready-to-Eat Salad

Ready-to-eat salad harbors microorganisms that may carry various antibiotic resistance genes (ARGs). However, few studies have focused on the prevalence of ARGs on salad, thus underestimating the risk of ARGs transferring from salad to consumers. In this small-scale study, high-throughput quantitative PCR was used to explore the presence, prevalence and abundance of ARGs associated with serving salad sourced from two restaurant types, fast-food chain and independent casual dining. A total of 156 unique ARGs and nine mobile genetic elements (MGEs) were detected on the salad items assessed. The abundance of ARGs and MGEs were significantly higher in independent casual dining than fast-food chain restaurants. Absolute copies of ARGs in salad were 1.34 × 10⁷ to 2.71 × 10⁸ and 1.90 × 10⁸ to 4.87 × 10⁸ copies per g salad in fast-food and casual dining restaurants, respectively. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were the dominant bacterial phyla detected from salad samples. Pseudomonas, Acinetobacter, Exiguobacterium, Weissella, Enterobacter, Leuconostoc, Pantoea, Serratia, Erwinia, and Ewingella were the 10 most dominant bacterial genera found in salad samples. A significant positive correlation between ARGs and MGEs was detected. These results integrate knowledge about the ARGs in ready-to-eat salad and highlight the potential impact of ARGs transfer to consumers.

Host identity determines plant associated resistomes

Plant microbiome, as the second genome of plant, and the interface between human and environmental microbiome, represents a potential pathway of human exposure to environmental pathogens and resistomes. However, the impact of host identity on the profile of resistomes in plant phyllosphere is unclear and this knowledge is vital for establishing a framework to evaluate the dissemination of antibiotic resistance via the plant microbiome. Here, we explored the phyllosphere microbiome and resistomes in 12 selected plant species. By using High-throughput quantitative PCR, we identified a total of 172 unique resistance genes in plant phyllosphere microbiome, which was significantly divergent from the profile of resistomes in associated soils (Adonis, P < 0.01). Host identity had a significant effect on the plant resistome, which was mainly attributed to the dissimilarity of phyllosphere bacterial phylogeny across different plants. We identified a core set of plant resistomes shared in more than 80% of samples, which accounted for more than 64% of total resistance genes. These plant core resistomes conferred resistance to antibiotics that are commonly administered to humans and animals. Our findings extend our knowledge regarding the resistomes in plant phyllosphere microbiome and highlight the role of host identity in shaping the plant associated antibiotic resistance genes.

Does reduced usage of antibiotics in livestock production mitigate the spread of antibiotic resistance in soil, earthworm guts, and the phyllosphere?

The overuse of antibiotics in animal husbandry is widespread and believed to significantly contribute to the selection of antibiotic resistance genes (ARGs) in animals. Thus, there is a global drive to reduce antibiotic use in the agricultural sector. However, it has not been established whether a reduction in the use of antibiotics in livestock production would be effective in reducing the spread of ARGs. A microcosm approach was used to determine how the addition of manure with either reduced antibiotic levels or with typical antibiotic levels could affect the spread of antibiotic resistance genes between soil, earthworms and the phyllosphere. When compared to the control soil, earthworm and phyllosphere samples had the greater increase in ARG abundance in conventional manure treatments (P < 0.05). Reduced antibiotic manure also enriched the abundance of ARGs in the phyllosphere and soil but not earthworm guts when compared to the control (P < 0.05). In both soil and earthworm guts, the enrichment of ARGs was lower in reduced antibiotic manure than in conventional manure. This study has identified bacterial transfer through the soil-earthworm-phyllosphere system as a potential means to spread ARGs between habitats after fertilization with livestock derived manures.

Agricultural activities affect the pattern of the resistome within the phyllosphere microbiome in peri-urban environments

The plant microbiome represents a crucial pathway for human exposure to environmental antibiotic resistance. However, little information is available regarding the plant associated resistome in human-related environments at a larger scale. Here, by high-throughput quantitative-PCR chip-based array and amplicon sequencing, we characterized antibiotic resistance genes (ARGs) and bacterial communities in plant and soil microbiomes from human highly disturbed peri-urban farmland and less disturbed forest at a watershed scale. A total of 71 ARGs were detected in the phyllosphere, which covered almost all the major recognized classes of antibiotics that are administered commonly to humans and animals. The overall pattern of the plant associated resistome in intensive anthropogenic influenced farmland was significantly different from that of forest environments (PERMANOVA, P < 0.01), indicating that agricultural activities might be important drivers in shaping the plant resistome. A bipartite network analysis suggested that all ARGs detected in the plant microbiome were also present in the soil microbiome. Together, our findings provide a better understanding of the plant resistome and suggest that land use is a key contributor to the composition of ARG profiles in the plant phyllosphere, and that the soil resistome may represent a critical reservoir of plant associated ARGs.

Efficient reduction of antibiotic residues and associated resistance genes in tylosin antibiotic fermentation waste using hyperthermophilic composting

Insufficient removal of antibiotics and antibiotic resistance genes (ARGs) from waste products can increase the risk of selection for antibiotic resistance in non-clinical environments. While composting is an efficient way to reduce ARGs, most conventional methods are ineffective at processing highly contaminated antibiotic fermentation waste. Here we explored the efficacy and underlying mechanisms of hyperthermophilic composting at removing tylosin antibiotic fermentation residues (TFR) and associated ARGs and mobile genetic elements (MGEs; plasmids, integrons and transposon). Hyperthermophilic composting removed 95.0% of TFR, 75.8% of ARGs and 98.5% of MGEs and this reduction mainly occurred after extended exposure to temperatures above 60 °C for at least 6 days. Based on sequencing and culture-dependent experiments, reduction in ARGs and MGEs was strongly associated with a decrease in the number of bacterial taxa that were initially associated with ARGs and MGEs. Moreover, we found 94.1% reduction in plasmid genes abundances (ISCR1 and IncQ-oriV) that significantly correlated with reduced ARGs during the composting, which suggests that plasmids were the main carriers for ARGs. We verified this using direct culturing to show that ARGs were more often found in plasmids during the early phase of composting. Together these results suggest that hyperthermophilic composting is efficient at removing ARGs and associated resistance genes from antibiotic fermentation waste by decreasing the abundance of antibiotic resistance plasmids and associated host bacteria.

The persistence of antimicrobial resistance and related environmental factors in abandoned and working swine feedlots

Swine feedlots that have operated in the absence of adequate disposal facilities are being demolished under the new environmental protection policies in China. The environmental behavior and transmission risks of antimicrobial resistance genes (ARGs) are unclear for these abandoned swine feedlots. We examined 40 soil samples that originated from the soils adjacent to two abandoned and two working swine feedlots to explore: 1) the distribution patterns and vertical transmission of 17 ARGs and two integron genes and 2) the bacterial community as well as their correlation with environmental factors and target genes. We found that seven and nine out of forty-eight subtypes of veterinary antimicrobials (VAs) were detected in the soil near abandoned feedlots and working feedlots, respectively. Three tet genes (tetM, tetO and tetW) were particularly enriched in the soil adjacent to both abandoned and working feedlots. The tetM gene was a "hub" on the network of the topsoil. The relative abundance of Firmicutes ranged from 2.5 to 9% in the soil near two Beijing feedlots and was significantly higher than that in the upstream blank control (CK soil) (ANOVA, p < 0.05). Overall, the ARG distribution patterns in the soils adjacent to abandoned swine feedlots were similar to the working feedlots. This study offers basic information on the prevalence and transmission risk of ARGs in abandoned swine feedlots and provides a reference for the restoration and reuse of demolished feedlots.

The effects of tetracycline concentrations on tetracycline resistance genes and their bacterial hosts in the gut passages of earthworms (Eisenia fetida) feeding on domestic sludge

Vermi-composting is considered to be a feasible method for reducing tetracycline resistance genes (TRGs) in the sludge. Nevertheless, the way different gut passages of earthworm might affect the fates of TRGs and whether this process is affected by tetracycline (TC) concentrations need to be further investigated. In this study, we examined the effects of TC concentrations on changes in TRGs and bacterial communities in gut passages of earthworm were determined by using quantitative PCR and Illumina high-throughput sequencing. TRGs and intI1 were mainly reduced in the hindgut under the TC concentrations ranging from 0 to 25 mg/kg, while they were enriched under higher TC stress exposure. Consequently, we suggest the TC limitation of 25 mg/kg in the domestic sludge (DS) for vermi-composting. Although the predominant genera were TC sensitive under TC stress, many bacterial hosts harboring multiple TRGs (especially those in the hindgut) should be paid further attention to. In the foregut, five genera with abundant tetracycline-resistant bacteria (TRB) were specialized taxa. Among these genera, Unclassified_Solirubrobacterales and Pirellulaceae were probably related to the digestion processes. Other unclassified taxa related to the TRGs were probably derived from the DS. Five genera with abundant TRB were shared in the gut passages, and three specialized genera in the hindgut. These genera could spread TRGs and intI1 to the environment. These results suggest that vermi-composting is a feasible approach for TRG control in the DS containing TC concentration that does not exceed 25 mg/kg. Fates of TRGs and intI1 widely differ in the gut passages, showing inevitable connections with bacterial communities.

Development of antibiotic resistance genes in soils with ten successive treatments of chlortetracycline and ciprofloxacin

Antibiotic contamination caused by the long-term use of organic manure (OM) in greenhouse agricultural soils poses potential detrimental effects to the soil environment. By applying OM containing chlortetracycline (CTC) and/or ciprofloxacin (CIP) ten times in soil under laboratory conditions, we investigated the dissipation and accumulation characteristics of CTC and CIP in the soil, the changes in the microbial pollution-induced community tolerance (PICT), and the diversity and abundance of antibiotic resistance genes (ARGs) in the soil microbiome. The dissipation of CTC was rapid while CIP was accumulated in repeatedly treated soils; further, CIP could inhibit the dissipation of CTC. Meanwhile, the PICT to CTC and/or CIP significantly increased up to 15.0-fold after ten successive treatments compared to that in the first treatment. As the treatment frequency increased, significant upward trends in the abundances of tetracycline resistance genes tetA(G), tetX2, tetX, tetG, tetA(33), tetA, tetW, and tetA(P), fluoroquinolone resistance gene qnrA6, and multiple resistance gene mexF were revealed by both metagenomic and qPCR analyses. The findings demonstrated that repeated treatments with CTC and/or CIP can alter the dissipation rate, promote an increase in PICT to CTC and/or CIP, and increase the ARGs abundance in steps.

Heavy metal-induced co-selection of antibiotic resistance genes in the gut microbiota of collembolans

Heavy metal induced co-selection of antibiotic resistance genes (ARGs) has become an emerging environmental issue. The guts of soil fauna offer a unique habitat in the terrestrial ecosystem and harbor a variety of microorganisms. However, the effects of heavy metals on the gut-associated ARGs of soil fauna are poorly understood. In the present study, collembolans were cultivated with four types of heavy metals (Zn, Cu, Cd, and Cr) and one antibiotic (oxytetracycline), to investigate their impact on the gut-associated ARGs. High-throughput quantitative PCR and 16S rRNA gene amplicon sequencing were used to examine changes in the gut-associated ARGs and microbial composition caused by the metals and antibiotic. The results showed that heavy metals alone induced co-selection of ARGs in the collembolan gut, but the effects were weaker than selection by oxytetracycline. When Zn or Cu was present together with oxytetracycline, there was a strong synergistic effect between the compounds, which increased the selection of ARGs in the collembolan guts. Furthermore, redundancy analysis revealed that the gut microbiota and mobile genetic elements (MGEs) were significantly correlated with the ARG composition. These results extend our understanding on effects of heavy metals on the dispersal of ARGs in the soil food web.

Effects of biochar amendments on antibiotic resistome of the soil and collembolan gut

A diverse array of ARGs has been detected in the guts of soil fauna residing in farmland soil. Biochar has been widely used in farmland for soil remediation and improvement of soil quality; however, the effects of biochar amendment on the gut-associated ARGs of soil fauna remain unclear. In the present study, collembolans were cultivated in soils amended with 6 types of biochars. High-throughput qPCR was used to establish ARG profiles of the collembolan guts as well as the surrounding soils. A total of 73 and 162 subtypes of ARGs were detected in the collembolan guts and soils, respectively. Biochar amendment significantly altered the ARG compositions of the collembolan guts and soils, in a biochar quality-dependent manner. However, only manure-derived biochar, which contained elevated concentrations of heavy metals, increased the relative abundance of gut-associated ARGs. Changes in the gut microbial community, MGEs and biochar properties explained 84% of the total ARG variations in the collembolan guts. The findings of this study suggested that biochar properties should receive more attention, as high doses of heavy metals in biochar could increase the abundance of ARGs in collembolan guts, thereby contributing to the spread of ARGs in the environment through collembolan movement.

Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome

Although the effects of fertilization on the abundance and diversity of soil nematodes have been widely studied, the impact of fertilization on soil nematode microbiomes remains largely unknown. Here, we investigated how different fertilizers: no fertilizer, mineral fertilizer, clean slurry (pig manure with a reduced antibiotic burden) and dirty slurry (pig manure with antibiotics) affect the microbiome of a dominant soil nematode and its associated antibiotic resistance genes (ARGs). The results of 16S rRNA gene high throughput sequencing showed that the microbiome of the soil nematode Dorylaimus stagnalis is diverse (Shannon index: 9.95) and dominated by Proteobacteria (40.3%). Application of mineral fertilizers significantly reduced the diversity of the nematode microbiome (by 28.2%; P < 0.05) but increased the abundance of Proteobacteria (by 70.1%; P = 0.001). Microbial community analysis, using a null hypothesis model, indicated that microbiomes associated with the nematode are not neutrally assembled. Organic fertilizers also altered the diversity of the nematode microbiome, but had no impact on its composition as illustrated by principal coordinates analysis (PCoA). Interestingly, although no change of total ARGs was observed in the nematode microbiome and no significant relationship existed between nematode microbiome and resistome, the abundance of 48 out of a total of 75 ARGs was enriched in the organic fertilizer treatments. Thus, the data suggests that ARGs in the nematode microbiome still had a risk of horizontal gene transfer under fertilization and nematodes might be a potential refuge for ARGs.

Exposure to microplastics lowers arsenic accumulation and alters gut bacterial communities of earthworm Metaphire californica

Ubiquitous contamination of microplastics and arsenic in soil ecosystems can induce many health issues to nontarget soil organisms, and will also cause many potential threats to the gut bacterial communities of soil fauna. However, the changes in the gut bacterial communities of soil fauna after exposure to both microplastics and arsenic remain unknown. In this study, the toxicity and effects on the gut microbiota of earthworm Metaphire californica caused by the combined exposure of microplastics and arsenic were examined by using arsenic species analysis and high throughput sequencing of gut microbiota. Results showed that total arsenic and arsenic species in the earthworm gut and body tissues after exposure to combination of microplastics with arsenate (As(V)) were significantly different from that treated with As(V) alone. Microplastics lessened the accumulation of total arsenic and the transformation rate of As(V) to arsenite (As(III)). Microplastics alleviated the effect of arsenic on the gut microbiota possibly via adsorbing/binding As(V) and lowering arsenic bioavailability, thus prevented the reduction of As(V) and accumulation of total arsenic in the gut which resulted in a lower toxicity on the earthworm. The study broadens our understanding of the ecotoxicity of microplastics with other pollutants on the soil animals and on their gut microbiota.

Soil oxytetracycline exposure alters the microbial community and enhances the abundance of antibiotic resistance genes in the gut of Enchytraeus crypticus

Gut microbiota make an important contribution to the health of soil invertebrates. Many studies have focused on effects of antibiotics on soil invertebrates. Influence from antibiotics on the gut microbiota of non-target soil fauna is rarely reported and the abundance of antibiotics resistance genes (ARGs) in the gut is poorly understood. Here, 10 μg·g^-1 of oxytetracycline (OTC) (environmentally relevant concentration) was added in soil, used Enchytraeus crypticus as soil model worm was tested for the response to oxytetracycline. The results showed that although soil OTC exposure did not cause a change in E. crypticus growth, mortality or reproduction, it did result in bioaccumulation of OTC in E. crypticus body tissues. The OTC treatment induced a shift in the composition and diversity of the gut microbiota of E. crypticus when compared to the control treatment. Specifically, the relative abundance of Proteobacteria declined significantly from 52.2% to 32.4% after OTC exposure (P = 0.028), but the relative abundance of Planctomycetes was significantly elevated from 28.1% to 45.8% (P = 0.002). It is noteworthy that soil OTC exposure significantly enhanced the abundance and number of tetracycline-related ARGs in the E. crypticus gut. These results suggest that change in E. crypticus gut microbiota has potential as an indicator of soil antibiotic pollution, and E. crypticus gut may act as a receiver and mediator of ARGs resulting from soil antibiotic pollution.