Species-specific response of the soil collembolan gut microbiome and resistome to soil oxytetracycline pollution

Glyphosate Disorders Soil Enchytraeid Gut Microbiota and Increases Its Antibiotic Resistance Risk

Pesticides promote the stable development of intensive global agriculture. Nevertheless, their residues in the soil can cause ecological and human health risks. Glyphosate is a popular herbicide and is generally thought to be ecologically safe and nontoxic, but this conclusion has been questioned. Herein, we investigated the interaction among soil fauna (Enchytraeus crypticus) exposed to glyphosate and found that glyphosate induced oxidative stress and detoxification responses in E. crypticus and disturbed their lipid metabolism and digestive systems. We further demonstrated that glyphosate disordered the gut microbiota of E. crypticus and increased the abundance of resistance determinants with significant human health risks. Empirical tests and structural equation models were then used to confirm that glyphosate could cause E. crypticus to generate reactive oxygen species, indirectly interfering with their gut microbiota. Our study provides important implications for deciphering the mechanisms of the ecotoxicity of pesticides under the challenge of worldwide pesticide contamination.

Effects of Zinc Thiazole and Oxytetracycline on the Microbial Metabolism, Antibiotic Resistance, and Virulence Factor Genes of Soil, Earthworm Gut, and Phyllosphere

Pesticides and antibiotics are believed to increase the incidence of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), constituting a serious threat to global health. However, the impact of this combined pollution on the microbiome and that of the related ARGs and VFGs on soil-plant-animal systems remain unknown. In this study, a 60-day microcosm experiment was conducted to reveal the effects of zinc thiazole (ZT) and oxytetracycline (OTC) on microbial communities, antibiotic resistomes, and virulence factors in soil, earthworm gut, and phyllosphere samples using metagenomics. ZT exposure perturbed microbial communities and nutrient metabolism and increased the abundance of ARGs and VFGs in the gut. Combined exposure changed the profiles of ARGs and VFGs by decreasing microbial diversity in the phyllosphere. Host-tracking analysis identified some genera, such as Citrobacter and Aeromonas, as frequent hosts of ARGs and VFGs in the gut. Notably, some co-occurrence patterns of ARGs and MGEs were observed on the metagenome-assembled contigs. More importantly, ZT markedly increased the abundance of potentially drug-resistant pathogens Acinetobacter soli and Acinetobacter junii in the phyllosphere. Overall, this study expands our current understanding of the spread of ARGs and VFGs in soil-plant-animal systems under pollutant-induced stress and the associated health risks.

Overview of Direct and Indirect Effects of Antibiotics on Terrestrial Organisms

Antibiotics (ABs) have made it possible to treat bacterial infections, which were in the past untreatable and consequently fatal. Regrettably, their use and abuse among humans and livestock led to antibiotic resistance, which has made them ineffective in many cases. The spread of antibiotic resistance genes (ARGs) and bacteria is not limited to nosocomial environments, but also involves water and soil ecosystems. The environmental presence of ABs and ARGs is a hot topic, and their direct and indirect effects, are still not well known or clarified. A particular concern is the presence of antibiotics in agroecosystems due to the application of agro-zootechnical waste (e.g., manure and biosolids), which can introduce antibiotic residues and ARGs to soils. This review provides an insight of recent findings of AB direct and indirect effects on terrestrial organisms, focusing on plant and invertebrates. Possible changing in viability and organism growth, AB bioaccumulation, and shifts in associated microbiome composition are reported. Oxidative stress responses of plants (such as reactive oxygen species production) to antibiotics are also described.

Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome

Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.

Joint effects of bacterium and biochar in remediation of antibiotic-heavy metal contaminated soil and responses of resistance gene and microbial community

Soils containing both veterinary antibiotics (VAs) and heavy metals necessitate effective remediation approaches, and microbial and molecular levels of the results should be further examined. Here, a novel material combining waste fungus chaff-based biochar (WFCB) and Herbaspirillum huttiense (HHS1) was established to immobilize copper (Cu) and zinc (Zn) and degrade oxytetracycline (OTC) and enrofloxacin (ENR). Results showed that the combined material exhibited high immobilization of Cu (85.5%) and Zn (64.4%) and great removals of OTC (41.9%) and ENR (40.7%). Resistance genes including tet(PB), tetH, tetR, tetS, tetT, tetM, aacA/aphD, aacC, aadA9, and czcA were reduced. Abundances of potential hosts of antibiotic resistance genes (ARGs) including phylum Proteobacteria and genera Brevundimonas and Rhodanobacter were altered. Total phosphorus and pH were the factors driving the VA degrading microorganisms and potential hosts of ARGs. The combination of WFCB and HHS1 can serve as an important bioresource for immobilizing heavy metals and removing VAs in the contaminated soil.

Animal gut microbiome mediates the effects of antibiotic pollution on an artificial freshwater system

The antibiotic pollution has become an emerging environmental problem worldwide, but the ecological outcomes remain to be elucidated, especially very little is known about the interactions between antibiotics and different ecological elements. In this study, the long-term influences of three representative antibiotics, i.e., tetracycline, erythromycin, and sulfamethoxazole, were investigated focusing on a simplified artificial freshwater system composed of amphibian tadpoles, gut and environmental bacterial and fungi communities, and water parameters. Results demonstrated that antibiotic exposure reduced tadpole's fitness with increased mortality and physiological abnormality, and altered the water quality, particularly the nitrogen homeostasis. Sequential analyses at organism, symbiont, and systematic levels revealed that antibiotics disrupted tadpole metabolome (e.g., tetrahydrobiopterin metabolism) directly by off-target effects. Antibiotics also reshaped the tadpole gut bacterial and fungi diversity and composition, which partly accounted for the tadpole's health condition. Moreover, changes of tadpole gut microbiome (i.e., Cyanobacteria and Basidiomycota OTUs) partly explained the variations of water parameters. In contrast, environmental microbiota and metagenome stayed relatively stable, and didn't contribute to the environmental variations. These results highlighted the pivotal role of gut microbiome in mediating the effects of antibiotics on the host and the environment, which would extend our understanding on the ecological outcomes caused by antibiotic pollution.

Mite gut microbiome and resistome exhibited species-specific and dose-dependent effect in response to oxytetracycline exposure

The importance of the gut microbiome to host health is well recognized, but the effects of environmental pressures on the gut microbiome of soil fauna are poorly understood. Here, Illumina sequencing and high-throughput qPCR were applied to characterize the gut microbiomes and resistomes of two mites, Nenteria moseri and Chiropturopoda sp. AL5866, exposed to different concentrations of oxytetracycline (0, 0.01, 0.1 and 1 μg mg^-1). Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant phyla in the gut microbiomes of both studied mite species, but the relative abundance of them was different between mites. After exposure to oxytetracycline, there was no variation in the gut microbiome and resistome of C. sp. AL5866, whereas the gut microbiome and resistome of N. moseri were altered significantly. The relative abundance of Proteobacteria significantly decreased, and those of Bacteroidetes and Firmicutes significantly increased at the high-concentration antibiotic treatments. Excepting the 0.01 μg mg^-1 treatment, gut microbial diversity increased with ascending concentrations. A significant resistome enrichment of relative abundance in N. moseri gut microbiome at low-dose antibiotic treatment was noted. These results indicated that the gut microbiome in N. moseri was potentially more sensitive to antibiotics than C. sp. AL5866, which was supported by the greater relative abundance of key tetracycline-resistant genes in the gut microbiome of C. sp. AL5866 compared to N. moseri. Mite gut microbiomes were correlated with their associated resistomes, demonstrating the consistent changes between microbiome and resistome. Thus, this study showed that oxytetracycline amendment resulted in a dose-dependent and species-specific effect on the gut microbiomes and resistomes of two mite species. It will contribute to understanding the relationship between the soil mite gut microbiome and resistome under antibiotic exposure, and extend our knowledge regarding the emergence and transfer of resistomes in soil food webs.

Oral azoxystrobin driving the dynamic change in resistome by disturbing the stability of the gut microbiota of Enchytraeus crypticus

Pesticides are continually entering the soil ecosystem because of safety assurance of high-yield food in agricultural intensification. It is highly urgent to evaluate their effects on the soil biota. This study characterized the dose-dependent changes in the gut bacterial and fungal community of Enchytraeus crypticus after oral exposure to an environmental dose of the fungicide azoxystrobin (AZ; 0.5, 1, and 10 mg/L) for 21 days. AZ not only induced the growth opportunistic pathogens and reduced the relative abundance of beneficial bacteria in the E. crypticus gut, but also destroyed the stability of the gut microecology of E. crypticus. Meanwhile, the dose-dependent effects of AZ were observed on the number and normalized abundance of antibiotic resistance genes (ARGs; copies/bacterial cell), and trace dose of AZ (> 0 and < 0.085 μg/individual) might enrich the ARG numbers in the gut of E. crypticus. Moreover, we used structural equation modeling to speculate that apart from mobile genetic elements and the bacterial community, the microbial interaction of E. crypticus gut might be another key contributor that drived the emergence and dissemination of ARGs. This study provides new perspectives in assessing the gut health of soil fauna under pesticide pollution in intensive agricultural production.

Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants

BACKGROUND

The ubiquitous gut microbiotas acquired from the environment contribute to host health. The gut microbiotas of soil invertebrates are gradually assembled from the microecological region of the soil ecosystem which they inhabit, but little is known about their characteristics when the hosts are under environmental stress. The rapid development of high-throughput DNA sequencing in the last decade has provided unprecedented insights and opportunities to characterize the gut microbiotas of soil invertebrates. Here, we characterized the core, transient, and rare bacterial taxa in the guts of soil invertebrates using the core index (CI) and developed a new theory of global microbial diversity of soil ecological microregions.

RESULTS

We found that the Gammaproteobacteria could respond indiscriminately to the exposure to environmental concentrations of soil pollutants and were closely associated with the physiology and function of the host. Meanwhile, machine-learning models based on metadata calculated that Gammaproteobacteria were the core bacteria with the highest colonization potential in the gut, and further identified that they were the best indicator taxon of the response to environmental concentrations of soil pollution. Gammaproteobacteria also closely correlated with the abundance of antibiotic resistance genes.

CONCLUSIONS

Our results determined that Gammaproteobacteria were an indicator taxon in the guts of the soil invertebrates that responded to environmental concentrations of soil pollutants, thus providing an effective theoretical basis for subsequent assessments of soil ecological risk. The results of the physiological and biochemical analyses of the host and the microbial-community functions, and the antibiotic resistance of Gammaproteobacteria, provide new insights for evaluating global soil ecological health. Video abstract.

Toxic effects of norfloxacin in soil on fed and unfed Folsomia candida (Isotomidae: Collembola) and on gut and soil microbiota

Soils contaminated with antibiotics may exert effects on soil-dwelling animals. A systematic ecological toxicity assessment of norfloxacin on the soil collembolan Folsomia candida (F. candida) was therefore conducted in soil and Petri dish systems with and without feeding at the population, individual and cellular levels. The indicators survival, reproduction, antioxidant enzyme activities peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD), malondialdehyde (MDA) contents and gut microbiota were studied. The surrounding soil microbiota were also investigated because F. candida can ingest soil microbiota that may have effects on the gut microbiota. In general, the toxicity of norfloxacin to F. candida in contaminated soil without food addition was higher than in contaminated soil with food addition. Norfloxacin had little effect at population and individual levels but antioxidant enzyme activities changed significantly in treatments with longer exposure times or higher norfloxacin concentrations. CAT was more sensitive than SOD or POD. The diversity indices and composition at phylum level of the gut microbiota showed little change. However, the operational taxonomic units in the gut decreased in the presence of norfloxacin. The relative abundance of Wolbachia, the predominant bacterial genus in the gut, decreased significantly with increasing soil norfloxacin concentration. Wolbachia may therefore be a promising bioindicator in the assessment of norfloxacin pollution of soils at environmental concentrations.

The fate of tetracycline in vegetated mesocosmic wetlands and its impact on the water quality and epiphytic microbes

The fate of antibiotics and their impact on antibiotic resistance genes (ARGs) and microbial communities are far from clear in wetlands. The fate and impact of tetracycline (TC) on the nutrient degradation of wetlands and epiphytic microbes were investigated. This study showed that after TC spiking, 99.7% of TC were removed from the surface water of wetlands containing Vallisneria spiralis within 4 days post-treatment. TC spiking impaired the nutrient removal capacity and disrupted epiphytic microbial community structure while enhancing the abundance of 11 ARGs subtypes, including tetracycline resistance genes, tetX, tetM, tetO, tetQ, tetS, and tet36. TC decreased bacterial biodiversity but amplified the relative abundance of Proteobacteria and Firmicutes by 4% and 61%, respectively, and increased eukaryotic diversity. 16 metabolic pathways including Carbohydrate, Energy, Amino acid, 'cofactor and vitamins' metabolisms were significantly (p < 0.01) increased in TC treatment. Phylogenetic, functional prediction analysis indicated that Flavobacterium was positively related with xenobiotics, cell motility, 'terpenoids and polyketides' metabolism but negatively related to nucleotide metabolism, while Rhodobacter showed a reverse trend but positively related with nucleotide and 'glycan biosynthesis' and metabolism. These data highlighted that TC has negative impacts on epiphytic microbial community and nutrients removal in wetlands.

Copper stimulates the incidence of antibiotic resistance, metal resistance and potential pathogens in the gut of black soldier fly larvae

The black soldier fly larvae (BSFL) have been successfully applied to treat various organic wastes. However, the impacts of heavy metals on antibiotic resistance in the BSFL guts are poorly understood. Here, we investigated the effect of copper (exposure concentrations of 0, 100 and 800 mg/kg) on the antibiotic and metal resistance profiles in BSFL guts. A total of 83 antibiotic resistance genes (ARGs), 18 mobile genetic elements (MGEs) and 6 metal resistance genes (MRGs) were observed in larval gut samples. Exposure to Cu remarkably reduced the diversity of ARGs and MGEs, but significantly enhanced the abundances of gut-associated ARGs and MRGs. The levels of MRGs copA, czcA and pbrT were dramatically strengthened after Cu exposure as compared with CK (increased by 2.8-13.5 times). Genera Enterococcus acted as the most predominant potential host of multiple ARG, MGE and MRG subtypes. Meanwhile, high exposure to Cu aggravated the enrichment of potential pathogens in BSFL guts, especially for Escherichia, Enterococcus and Salmonella species. The mantel test and procrustes analysis revealed that the gut microbial communities could be a key determinant for antibiotic and metal resistance. However, no significant positive links were observed between MGEs and ARGs or MRGs, possibly suggesting that MGEs did not play a crucial role in shaping the ARGs or MRGs in BSFL guts under the stress of Cu. These findings extend our understanding on the impact of heavy metals on the gut-associated antibiotic and metal resistome of BSFL.

Arthropod-Microbiota Integration: Its Importance for Ecosystem Conservation

Recent reports indicate that the health of our planet is getting worse and that genuine transformative changes are pressing. So far, efforts to ameliorate Earth's ecosystem crises have been insufficient, as these often depart from current knowledge of the underlying ecological processes. Nowadays, biodiversity loss and the alterations in biogeochemical cycles are reaching thresholds that put the survival of our species at risk. Biological interactions are fundamental for achieving biological conservation and restoration of ecological processes, especially those that contribute to nutrient cycles. Microorganism are recognized as key players in ecological interactions and nutrient cycling, both free-living and in symbiotic associations with multicellular organisms. This latter assemblage work as a functional ecological unit called "holobiont." Here, we review the emergent ecosystem properties derived from holobionts, with special emphasis on detritivorous terrestrial arthropods and their symbiotic microorganisms. We revisit their relevance in the cycling of recalcitrant organic compounds (e.g., lignin and cellulose). Finally, based on the interconnection between biodiversity and nutrient cycling, we propose that a multicellular organism and its associates constitute an Ecosystem Holobiont (EH). This EH is the functional unit characterized by carrying out key ecosystem processes. We emphasize that in order to meet the challenge to restore the health of our planet it is critical to reduce anthropic pressures that may threaten not only individual entities (known as "bionts") but also the stability of the associations that give rise to EH and their ecological functions.

Macleaya cordata extract, an antibiotic alternative, does not contribute to antibiotic resistance gene dissemination

The abuse of antibiotics and their associated health risks are receiving global attention. The use of antibiotic additives in fodder has been banned in the European Union since 2006 and in China since 2020. Antibiotic alternatives are being developed, but their risks to the soil ecosystem remain poorly understood. Here, we compared the effects of the antibiotic oxytetracycline (OTC10, 10 mg/kg) with those of a Macleaya cordata extract (MCE, 10 and 100 mg/kg), the major antibiotic substitute. All tested concentrations of MCE and OTC10 exerted slight effects on the soil microbiome, but OTC10 and MCE100 could interfere with the structures and functions of the gut microbiome and might thus affect the soil ecological functions of Enchytraeus crypticus. Furthermore, OTC10 exposure inevitably increased the antibiotic resistance gene (ARG) abundance by 213%, whereas MCE did not induce ARG dissemination, which explains why MCE is considered to be associated with a low ecological risk. Our research provides the first demonstration of the risks posed by antibiotic alternatives to soil animals from the perspective of environmental toxicology and explores the potential development of antibiotic alternatives associated with a low ecological risk from a new perspective.

The equine hindgut as a reservoir of mobile genetic elements and antimicrobial resistance genes

Antibiotic resistance in bacterial pathogens is a growing problem for both human and veterinary medicine. Mobile genetic elements (MGEs) such as plasmids, transposons, and integrons enable the spread of antibiotic resistance genes (ARGs) among bacteria, and the overuse of antibiotics drives this process by providing the selection pressure for resistance genes to establish and persist in bacterial populations. Because bacteria, MGEs, and resistance genes can readily spread between different ecological compartments (e.g. soil, plants, animals, humans, wastewater), a "One Health" approach is needed to combat this problem. The equine hindgut is an understudied but potentially significant reservoir of ARGs and MGEs, since horses have close contact with humans, their manure is used in agriculture, they have a dense microbiome of both bacteria and fungi, and many antimicrobials used for equine treatment are also used in human medicine. Here, we collate information to date about resistance genes, plasmids, and class 1 integrons from equine-derived bacteria, we discuss why the equine hindgut deserves increased attention as a potential reservoir of ARGs, and we suggest ways to minimize the selection for ARGs in horses, in order to prevent their spread to the wider community.

Influence of long-term biosolid applications on communities of soil fauna and their metal accumulation: A field study

Amendment with sewage sludge or biosolids can increase soil fertility but may also transfer biosolid-borne pollutants to the soil and the possible effects on the soil ecosystem are poorly understood, especially long-term effects. A long-term experiment was therefore established to assess the effects of repeated applications of different types of biosolids (fresh domestic, dried domestic and fresh industrial sludges) in field conditions. Nine years of sludge application led to changes in soil chemical and biological properties and generally contributed little to soil nutrient status. However, soil concentrations of potentially toxic elements (PTEs) were elevated by amendment, especially with industrial biosolids. Soil fauna are usually used to decipher the underlying effects of biosolid applications on the soil ecosystem. Here, collembolans (50.9%), nematodes (41.6%) and enchytraeid worms (7.50%) were collected and differentiated into different ecological and trophic groups and their body lengths and PTE concentrations in the body tissues were investigated. The animals showed different responses to the biosolids at population and individual levels. There were substantial changes in epigeic collembolan communities and bacterivorous nematodes increased significantly after biosolid amendment. Biosolid-borne PTEs were major factors and Redundancy (RDA) analysis indicates that collembolan communities were strongly influenced by zinc (Zn). The three groups of soil animals showed similar trends in accumulation of PTEs in the sequence cadmium (Cd) > Zn > copper (Cu), and the bioaccumulation factor (BAF) values of the PTEs were significantly higher in the industrial sludge treatment than in other two treatments with a similar trend of decreasing body length of nematodes. The results indicate that it is potentially risky to use industrial biosolids in the long term, and different species and ecological groups of collembolans and different trophic groups of nematodes should be examined when assessing soil health.

The fungicide azoxystrobin perturbs the gut microbiota community and enriches antibiotic resistance genes in Enchytraeus crypticus

The use of pesticides to ensure global food security is the most important pest control strategy in modern agriculture but causes extensive soil pollution. This pollution involves potential risks to human health and ecosystems. In addition to soil animal growth, the adverse impact of pesticides on the gut microbiomes of nontarget soil fauna remains largely unknown. Here, the effect of the fungicide azoxystrobin (AZ) on soil and the gut microbiota of soil animals (Enchytraeus crypticus) was studied. The tested concentrations of AZ altered the bacterial community in the soil and E. crypticus gut and were slightly toxic with respect to E. crypticus adult mortality and reproduction. The most abundant bacterial phylum, Proteobacteria, significantly increased in response to the 2 and 5 mg/kg AZ treatments, which implied a disordered unhealthy gut bacterial community. Furthermore, bacterial community analysis between the soil and gut showed that the main effect of AZ on the gut microbiota was directly through AZ, not soil microbiota. In addition, AZ exposure significantly enhanced the number and total abundance of antibiotic resistance genes (ARGs) in the E. crypticus gut; these genes may enter the soil food web to affect higher trophic levels and cause a more serious ecological risk. Our study reported the effect of pesticides on the gut of soil animals and on the enrichment of ARGs as global emerging contaminants, revealing unknown potential impacts of fungicides on ecosystem services and sustainable food production.