Ecological role of earthworm intestinal bacteria in terrestrial environments: A review

The interaction between biochar and earthworms: Revealing the potential ecological risks of biochar application and the feasibility of their co-application

Biochar's interaction with soil-dwelling organisms, particularly earthworms, is crucial in ensuring the effective and secure utilization of biochar in the soil. This review introduces the application of biochar in soil, summarizes how earthworms respond to biochar-amended soil and the underlying factors that can influence their response, discusses the synergistic and antagonistic impacts of earthworm activity on the efficacy of biochar, and considers the feasibility of applying them together. A review of existing research has identified uncertainty in the effect of biochar exposure on earthworms, with biochar derived from animal wastes, produced at higher pyrolysis temperatures, and used at higher doses of biochar having more negative effects on earthworms. Habitat modification, toxicity release, particle effects, and contaminant immobilization are underlying factors in how biochar affects earthworm indicators. While biochar in contaminated soils may alleviate the stress of pollutants on earthworms by decreasing their bioaccumulation, this remedial effect is not always effective. Additionally, earthworm bioturbation can enhance the migration, fragmentation, and oxidation of biochar, while also stimulating extracellular enzymes that convert biochar into 'vermichar'. Earthworms and biochar can synergize well to improve soil fertility and remediate soil organic pollution, yet exhibit contrasting roles in soil C sequestration and immobilizing heavy metals in soil. These findings highlight both the advantages and risks of their co-application. Therefore, when considering the use of biochar alone or with earthworms, it is crucial to thoroughly assess its potential ecotoxicity on earthworms and other soil organisms, as well as the influence of bioturbation, such as that caused by earthworms, on the effectiveness of biochar.

Comparative Analysis of Bacterial Community Structures in Earthworm Skin, Gut, and Habitat Soil across Typical Temperate Forests

Earthworms are essential components in temperate forest ecosystems, yet the patterns of change in earthworm-associated microbial communities across different temperate forests remain unclear. This study employed high-throughput sequencing technology to compare bacterial community composition and structure in three earthworm-associated microhabitats (skin, gut, and habitat soil) across three typical temperate forests in China, and investigated the influence of environmental factors on these differential patterns. The results indicate that: (1) From warm temperate forests to cold temperate forests, the soil pH of the habitat decreased significantly. In contrast, the physicochemical properties of earthworm skin mucus exhibited different trends compared to those of the habitat soil. (2) Alpha diversity analysis revealed a declining trend in Shannon indices across all three microhabitats. (3) Beta diversity analysis revealed that the transition from warm temperate deciduous broad-leaved forest to cold temperate coniferous forest exerted the most significant impact on the gut bacterial communities of earthworms, while its influence on the skin bacterial communities was comparatively less pronounced. (4) Actinobacteria and Proteobacteria were the predominant phyla in earthworm skin, gut, and habitat soil, but the trends in bacterial community composition differed among the three microhabitats. (5) Mantel tests revealed significant correlations between bacterial community structures and climatic factors, physicochemical properties of earthworm habitat soil, and physicochemical properties of earthworm skin mucus. The findings of this study offer novel perspectives on the interplay between earthworms, microorganisms, and the environment within forest ecosystems.

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale

Earthworms are critical in regulating soil processes and act as filters for antibiotic resistance genes (ARGs). Yet, the geographic patterns and main drivers of earthworm gut ARGs remain largely unknown. We collected 52 earthworm and soil samples from arable and forest ecosystems along a 3000 km transect across China, analyzing the diversity and abundance of ARGs using shotgun metagenomics. Earthworm guts harbored a lower diversity and abundance of ARGs compared to soil, resulting in a stronger distance-decay rate of ARGs in the gut. Greater deterministic assembly processes of ARGs were found in the gut than in soil. The earthworm gut had a lower frequency of co-occurrence patterns between ARGs and mobile genetic elements (MGEs) in forest than in arable systems. Viral diversity was higher in the gut compared to soil and was negatively correlated with bacterial diversity. Bacteria such as Streptomyces and Pseudomonas were potential hosts of both viruses and ARGs. Viruses had negative effects on the diversity and abundance of ARGs, likely due to the lysis on ARG-bearing bacteria. These findings provide new insights into the variations of ARGs in the earthworm gut and highlight the vital role of viruses in the regulation of ARGs in the soil ecosystem.

Earthworm gut bacteria facilitate cadmium immobilization through the formation of CdS nanoparticles

Gut bacteria of earthworm Amynthas hupeiensis exhibit significant potential for the in-situ remediation of cadmium (Cd)-contaminated soil. However, the mechanisms by which these gut bacteria immobilize and tolerate Cd remain elusive. The composition of the gut bacterial community was characterized by high-throughput sequencing. Cd-tolerant bacteria were isolated from the gut, and their roles in Cd immobilization, as well as their tolerance mechanisms, were explored through chemical characterization and transcriptome analysis. The predominant taxa in the gut bacterial community included unclassified Enterobacteriaceae, Citrobacter, and Bacillus, which were distinctly different from those in the surrounding soil. Notably, the most Cd-tolerant gut bacterium, Citrobacter freundii DS strain, immobilized 63.61% of Cd2+ within 96 h through extracellular biosorption and intracellular bioaccumulation of biosynthetic CdS nanoparticles, and modulation of solution pH and NH4+ concentration. Moreover, the characteristic signals of CdS were also observed in the gut content of A. hupeiensis when the sterilized Cd-contaminated soil was inoculated with C. freundii. The primary pathways involved in the response of C. freundii to Cd stress included the regulation of ABC transporters, bacterial chemotaxis, cell motility, oxidative phosphorylation, and two-component system. In conclusion, C. freundii facilitates Cd immobilization both in vitro and in vivo, thereby enhancing the host earthworm's adaptation to Cd-contaminated soil.

Insights into tolerance mechanisms of earthworms (Eisenia fetida) in copper-contaminated soils by integrating multi-omics analyses

Earthworms can resist high levels of soil copper (Cu) contamination and play an essential role in absorbing them effectively. However, the molecular mechanisms underlying Cu tolerance in earthworms are poorly understood. To address this research gap, we studied alterations of Eisenia fetida in antioxidant enzymes, gut microbiota, metabolites, and genes under varying levels of Cu exposure soils (0, 67.58, 168.96, 337.92 mg/kg). Our results revealed a reduction in antioxidant enzyme activities across all treatment groups, indicating an adaptive response to alleviate Cu-induced oxidative stress. Analysis of gut microbiota revealed a significant increase in the abundance of bacteria associated with nutrient uptake and Cu2+ excretion under Cu stress. Furthermore, metabolomic analysis discovered an increase in certain metabolites associated with energy metabolism, such as pyruvic acid, L-malic acid, and fumaric acid, as Cu concentration escalated. These results suggested that enhanced energy supply contributes to the elevated tolerance of E. fetida towards Cu. Additionally, transcriptome analysis not only identified crucial detoxification genes (Hsp70, CTSL, GST, CHAC, and GCLC), but also confirmed the critical role of glutathione metabolism as a key pathway in E. fetida Cu detoxification processes. These findings provide a new perspective on the molecular mechanisms of Cu tolerance in earthworms.

Soil health hazards of di(2-ethylhexyl) phthalate: New perspectives on earthworms from different ecological niches DNA damage, gut microbial disruption and soil enzyme changes

Di(2-ethylhexyl) phthalate (DEHP) is perceived an emerging threat to terrestrial ecosystem, however, clear and accurate studies to fully understander ecotoxicity and underlying mechanisms of DEHP on the soil fauna remain poorly understood. Therefore, this study conducted a microcosm experiment of two earthworm ecotypes to investigate the ecological hazards of DHEP from multiple perspectives. The results showed that DEHP significantly increased the 8-hydroxy-deoxyguanosine (8-OHdG) content both in Eisenia foetida (13.76-133.0%) and Metaphire guillelmi (11.01-49.12%), leading to intracellular DNA damage. Meanwhile, DEHP negatively affected the expression of functional genes (ATP-6, NADH1, COX), which may be detrimental to mitochondrial respiration and oxidative stress at the gene level. The two earthworm guts shared analogous dominant bacteria however, the incorporation of DEHP drastically suppressed the homogeneity and diversity of the gut microbes, which further disrupted the homeostasis of the gut microbial ecological network. The keystone species in the gut of E. foetida decreased under DEHP stress but increased in the gut of M. guillelmi. Moreover, DEHP presented detrimental effects on soil enzyme activity, which is mainly associated with pollutant levels and earthworm activity. Collectively, the findings expand the understanding of soil ecological health and reveal the underlying mechanisms of the potential exposure risk to DEHP.

Effects of biochar-derived dissolved organic matter on the gut microbiomes and metabolomics in earthworm Eisenia fetida

The ecological risks of biochar-derived dissolved organic matter (DOM) to soil invertebrates at different organismal levels remains limited. This study comprehensively explored the ecological risks of biochar-derived DOM on earthworm gut through assessments of enzyme activity response, histopathology, gut microbiomes, and metabolomics. Results demonstrated that DOM disturbed the digestive enzymes in earthworm, especially for 10% DOM300 groups. The integrated biomarker response v2 (IBRv2) indicated that the perturbation of earthworm digestive enzymes induced by DOM was both time-dependent and dose-dependent. Pathological observations revealed that 10% DOM300 damaged intestinal epithelium and digestive lumen of earthworms. The significant damage and injury to earthworms caused by DOM300 due to its higher concentrations of heavy metal ions and organic substrates (e.g., toluene, hexane, butanamide, and hexanamide) compared to DOM500 and DOM700. Analysis of 16S rRNA from the gut microbiota showed a significant decrease in genera (Verminephrobacter, Bacillus, and Microbacteriaceae) associated with inflammation, disease, and detoxification processes. Furthermore, 10% DOM300 caused the abnormality of metabolites, such as glutamate, fumaric acid, pyruvate, and citric acid, which were involved in energy metabolism, These findings contributed to improve our understanding of the toxic mechanism of biochar DOM from multiple perspectives.

Low-density polyethylene enhances the disturbance of microbiome and antibiotic resistance genes transfer in soil-earthworm system induced by pyraclostrobin

Non-antibiotic chemicals in farmlands, including microplastics (MPs) and pesticides, have the potential to influence the soil microbiome and the dissemination of antibiotic resistance genes (ARGs). Despite this, there is limited understanding of the combined effects of MPs and pesticides on microbial communities and ARGs transmission in soil ecosystems. In this study, we observed that low-density polyethylene (LDPE) microplastic enhance the accumulation of pyraclostrobin in earthworms, resulting in reduced weight and causing severe oxidative damage. Analysis of 16 S rRNA amplification revealed that exposure to pyraclostrobin and/or LDPE disrupts the microbial community structure at the phylum and genus levels, leading to reduced alpha diversity in both the soil and earthworm gut. Furthermore, co-exposure to LDPE and pyraclostrobin increased the relative abundance of ARGs in the soil and earthworm gut by 2.15 and 1.34 times, respectively, compared to exposure to pyraclostrobin alone. It correlated well with the increasing relative abundance of genera carrying ARGs. Our findings contribute novel insights into the impact of co-exposure to MPs and pesticides on soil and earthworm microbiomes, highlighting their role in promoting the transfer of ARGs. This knowledge is crucial for managing the risk associated with the dissemination of ARGs in soil ecosystems.

Characterization of a blaNDM-1-positive Citrobacter freundii strain isolated from earthworms

OBJECTIVES

Earthworms are one of the key components of soil, and they play a crucial role in the transformation of various nutrients and pollutants in the soil. The purpose of this study is to characterize the NDM-1-producing C. freundii isolated from soil-dwelling earthworms near a hospital, exploring their potential role as carriers of carbapenem-resistant genes.

METHODS

Isolates were isolated from the intestines of earthworms and identified by MALDI-TOF MS. The presence of NDM enzyme was verified through the CARBA-5 Assay. Whole genome sequencing was conducted using the Illumina NovaSeq PE150 platform. Antimicrobial susceptibility testing and conjugation experiment were performed for phenotypic analysis.

RESULTS

This isolate exhibited a multidrug-resistant profile, including resistance to imipenem, meropenem, and ertapenem and successfully transferred blaNDM-1 gene to Escherichia coli. Whole genomic sequencing showed that blaNDM-1 gene was located on an IncFIIY-type plasmid. Phylogenetic analysis revealed a close relationship between the QY221001 strain obtained from earthworms and the human isolate F2021 in the NCBI database, both of which were collected in Hangzhou, China.

CONCLUSION

To our knowledge, this is the first report of an NDM-1-producing bacteria isolated from the intestine of an earthworm. Our finding suggested that earthworms could be a potential reservoir of carbapenem resistance genes, emphasizing the importance of enhanced environmental monitoring of antimicrobial resistance.

Biotransformation of roxarsone by earthworms and subsequent risk of soil arsenic release: The role of gut bacteria

The organoarsenical feed additive roxarsone (ROX) is a ubiquitous threat due to the unpredictable levels of arsenic (As) released by soil bacteria. The earthworms representing soil fauna communities provide hotspots for As biotransformation genes (ABGs). Nonetheless, the role of gut bacteria in this regard is unclear. In this study, the changes in As speciation, bacterial ABGs, and communities were analyzed in a ROX-contaminated soil (50 mg/kg As in ROX form) containing the earthworm Eisenia feotida. (RE vs. R treatment). After 56 d, earthworms reduced the levels of both ROX and total As by 59 % and 17 %, respectively. The available As content was 10 % lower in the RE than in R treatment. Under ROX stress, the total ABG abundance was upregulated in both earthworm gut and soil, with synergistic effects observed following RE treatment. Besides, the enrichment of arsM and arsB genes in earthworm gut suggested that gut bacteria may facilitate As removal by enhancing As methylation and transport function in soil. However, the bacteria carrying ABGs were not associated with the ABG abundance in earthworm gut indicating the unique strategies of earthworm gut bacteria compared with soil bacteria due to different microenvironments. Based on a well-fit structural equation model (P = 0.120), we concluded that gut bacteria indirectly contribute to ROX transformation and As detoxification by modifying soil ABGs. The positive findings of earthworm-induced ROX transformation shed light on the role of As biomonitoring and bioremediation in organoarsenical-contaminated environments.

Water balance analysis in a novel pilot-scale of the Worm-sludge treatment reed bed (W-STRB) planted with Arundo donax

A one-year study of sludge treatment reed bed assisted with earthworms (W-STRB) was conducted in a temperate climate. The effects of using Eisenia fetid and Arundo donax on W-STRB water balance (WB) and dewatering efficiency (DE) were investigated. Four different bed configurations were tested: worm-planted (WP), planted (P), worm-control (W), and control (C), duplicated resulting in a total of eight units. The beds received a total of 24 cycles of mixed sewage sludge twice per month (average loading rate: 43.59 kg.DS. m-2.year-1). It was found seasonal variation played a significant role in WB and DE. During the dry season, the thickness of the residual sludge (RS) layer was less than 1 cm, with a dry solid (DS) content of over 80%, in contrast, the wet season indicated an increase in RS thickness to nearly 30 cm (DS < 15 % for all units). The WP unit exhibited the lowest RS accumulation, 22% less than the P, W, and C units. The subsurface layer had a 5% lower volatile solids (VS) content compared to the surface layers. After 132 days of a final resting, WP unit had the highest RS volume reduction of 65 % (DS = 71 % and VS = 53 %) and a RS thickness of 6 cm indicating a 10 % higher stabilization compared to P unit. The population of earthworms was 30% higher in the WP unit compared to the W unit. As the subsurface DS exceeded 20 % during the dry season, the population increased. The WP unit showed a 43% higher above-ground plant biomass compared to the P unit. In WB analysis, evapotranspiration (ET) was 46% higher in the WP unit (average daily ET = 5.44 mm in the dry season). The main process of water loss was through drainage and Awhile water content in RS layer was 57 % during feeding period. The water percolation rate of all units decreased by 99%, particularly during the wet season, reaching less than 0.1 m.day-1.

Functional similarity, despite taxonomical divergence in the millipede gut microbiota, points to a common trophic strategy

BACKGROUND

Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting) and the temperate millipede Glomeris connexa (small, non-methane emitting), fed on an identical diet, were studied using comparative metagenomics and metatranscriptomics.

RESULTS

The results showed that the microbial load in E. pulchripes is much higher and more diverse than in G. connexa. The microbial communities of the two species differed significantly, with Bacteroidota dominating the hindguts of E. pulchripes and Proteobacteria (Pseudomonadota) in G. connexa. Despite equal sequencing effort, de novo assembly and binning recovered 282 metagenome-assembled genomes (MAGs) from E. pulchripes and 33 from G. connexa, including 90 novel bacterial taxa (81 in E. pulchripes and 9 in G. connexa). However, despite this taxonomic divergence, most of the functions, including carbohydrate hydrolysis, sulfate reduction, and nitrogen cycling, were common to the two species. Members of the Bacteroidota (Bacteroidetes) were the primary agents of complex carbon degradation in E. pulchripes, while members of Proteobacteria dominated in G. connexa. Members of Desulfobacterota were the potential sulfate-reducing bacteria in E. pulchripes. The capacity for dissimilatory nitrate reduction was found in Actinobacteriota (E. pulchripes) and Proteobacteria (both species), but only Proteobacteria possessed the capacity for denitrification (both species). In contrast, some functions were only found in E. pulchripes. These include reductive acetogenesis, found in members of Desulfobacterota and Firmicutes (Bacillota) in E. pulchripes. Also, diazotrophs were only found in E. pulchripes, with a few members of the Firmicutes and Proteobacteria expressing the nifH gene. Interestingly, fungal-cell-wall-degrading glycoside hydrolases (GHs) were among the most abundant carbohydrate-active enzymes (CAZymes) expressed in both millipede species, suggesting that fungal biomass plays an important role in the millipede diet.

CONCLUSIONS

Overall, these results provide detailed insights into the genomic capabilities of the microbial community in the hindgut of millipedes and shed light on the ecophysiology of these essential detritivores. Video Abstract.

Earthworms mediate the influence of polyethylene (PE) and polylactic acid (PLA) microplastics on soil bacterial communities

There is a growing body of evidence that suggests that both biodegradable and conventional (non-degradable) microplastics (MP) are hazardous to soil health by affecting the delivery of key ecological functions such as litter decomposition, nutrient cycling and water retention. Specifically, soil fauna may be harmed by the presence of MPs while also being involved in their disintegration, degradation, migration and transfer in soil. Therefore, a comprehensive understanding of the interactions between MPs and soil fauna is essential. Here, we conducted a 120-day soil microcosm experiment applying polyethylene (PE) and polylactic acid (PLA), in the absence/presence of the earthworm Eisenia nordenskioldi to estimate the relative singular and combined impact of MPs and earthworms on the soil bacterial community. Our findings revealed contrasting effects of PE and PLA on the composition and diversity of soil bacteria. All treatments affected the community and network structure of the soil bacterial community. Compared to the control (no MPs or earthworms), PE decreased bacterial alpha diversity, while PLA increased it. Patescibacteria were found to be significantly abundant in the PE group whereas Actinobacteria and Gemmatimonadetes were more abundant in PE, and PLA and earthworms groups. The presence of earthworms appeared to mediate the impact of PE/PLA on soil bacteria, potentially through bacterial consumption or by altering soil properties (e.g., pH, aeration, C availability). Earthworm presence also appeared to promote the chemical aging of PLA. Collectively, our results provide novel insights into the soil-fauna-driven impact of degradable/nondegradable MPs exposure on the long-term environmental risks associated with soil microorganisms.

Exploring the toxicity of biodegradable microplastics and imidacloprid to earthworms (Eisenia fetida) from morphological and gut microbial perspectives

Biodegradable microplastics (BMPs) pose serious environmental problems to soil organisms, and their adsorption capacity might make pesticides more dangerous for soil organisms. Therefore, in this study, polylactic acid (PLA) BMPs and imidacloprid (IMI) were used as a representative of BMPs and pesticides, respectively. Eisenia fetida was used as a test animal to investigate the effects of environmentally relevant concentrations of single and compound contaminated PLA BMPs and IMI on mortality, growth, number of offspring, tissue damage, and gut microorganisms of E.fetida. Exposure to PLA BMPs treatment and PLA BMPs + IMI treatment resulted in a sustained increase in E.fetida mortality, reaching 16.7% and 26.7%, respectively. The growth inhibition rate of single treatments was significantly increased. The compound contamination had the greatest effect on E.fetida offspring compared to the control. PLA BMPs and IMI cause histological damage to E.fetida, with the compound treatment causing the most severe damage. Based on the results of 16S sequencing, the bacterial communities in E.fetida gut and soil treated to PLA BMPs and IMI were significantly different. PLA BMPs + IMI treatment suppresses the abundance and diversity of E.fetida gut microorganisms, disrupting the homeostasis of bacterial communities and causing immune and metabolic dysfunction. These findings highlight the more severe damage of combined PLA BMPs and IMI pollution to E.fetida, and help to assess the risk of earthworm exposure to environmentally relevant concentrations of PLA BMPs and IMI.

Soil fauna-microbial interactions shifts fungal and bacterial communities under a contamination disturbance

The aim of this study was to determine whether the soil faunal-microbial interaction complexity (SFMIC) is a significant factor influencing the soil microbial communities and the willow growth in the context of PAH contamination. The SFMIC treatment had eight levels: just the microbial community, or the microbial community with nematodes, springtails, earthworms and all the possible combinations. SFMIC affected the height and biomass of willows after eight weeks or growth. SFMIC affected the structure and the composition of the bacterial, archaeal and fungal communities, with significant effects of SFMIC on the relative abundance of fungal genera such as Sphaerosporella, a known willow symbiont during phytoremediation, and bacterial phyla such as Actinobacteriota, containing many polycyclic aromatic hydrocarbons (PAH) degraders. These SFMIC effects on microbial communities were not clearly reflected in the community structure and abundance of PAH degraders, even though some degraders related to Actinobacteriota and the diversity of Gram-negative degraders were affected by the SFMIC treatments. Over 95% of PAH was degraded in all pots at the end of the experiment. Overall, our results suggest that, under our experimental conditions, SFMIC changes willow phytoremediation outcomes.

Integrated microbiome and multi-omics analysis reveal the molecular mechanisms of Eisenia fetida in response to biochar-derived dissolved and particulate matters

At present, most ecotoxicological studies are still confined to focusing on the harmful effects of biochar itself on soil fauna. However, the potential ecotoxicity of different components separated from biochar to terrestrial invertebrates remains poorly understood. In this study, the dissolved matter (DM) and particulate matter (PM) were separated from biochar (BC) and then introduced into the soil-earthworm system to investigate the response mechanism of earthworms at the molecular level. The results showed that BC and DM exposure caused an increase in the abundance of Proteobacteria in the cast bacterial community, suggesting the dysbiosis of intestinal microbiota. It was also observed that the cast bacterial communities were more sensitive to DM exposure than PM exposure. Transcriptomic analysis showed that BC and DM exposure induced significant enrichment of functional pathways related to infectious and neuropathic diseases. Metabolomic profiling manifested that DM exposure caused metabolic dysfunction, antioxidant and detoxification abilities recession. Furthermore, significant differences in the responses of earthworms at transcriptomic and metabolic levels confirmed that DM exhibited greater ecotoxicity than PM. This study highlighted the significant contributions of dissolved matter to the ecotoxicity of biochar from the perspective of transcriptomic and metabolomic profiles.

Coupling multifactor dominated the biochemical response and the alterations of intestinal microflora of earthworm Pheretima guillelmi due to typical herbicides

The excessive application of herbicides on farmlands can substantially reduce labor costs and increase crop yields, but can also have undesirable effects on terrestrial ecosystems. To evaluate the ecological toxicity of herbicides, metolachlor and fomesafen, two typical herbicides that are extensively used worldwide were chosen as target pollutants, and the endogeic earthworm Pheretima guillelmi, which is widely distributed in China, was selected as the test organism. A laboratory-scale microcosmic experiment was set, and energy resources, enzymes, and the composition and connections of intestinal microorganisms in earthworms were determined. Both herbicides depleted the energy resources of the earthworms, especially glycogen contents; increased the levels of antioxidant enzymes; and inhibited acetylcholinesterase. Moreover, the richness and diversity of the intestinal bacterial community of the earthworms were suppressed. Additionally, the bacterial composition at the genus level changed greatly and the connections between dominant bacteria increased dramatically. Most interactions among the bacterial genera belonging to the same and different phyla showed mutualism and competition, respectively. Importantly, metolachlor with higher toxicity had a transitory effect on these indicators in earthworms, whereas fomesafen, with lower toxicity but stronger bioaccumulation potential, exerted a sustaining impact on earthworms. Collectively, these results indicate that the toxic effects of herbicides on terrestrial organisms should be comprehensively considered in combination with biological toxicity, persistence, bioaccumulation potential, and other factors.

Phages in vermicomposts enrich functional gene content and facilitate pesticide degradation in soil

Organic fertilizer microbiomes play substantial roles in soil ecological functions, including improving soil structure, crop yield, and pollutant dissipation. However, limited information is available about the ecological functions of phages and phage-encoded auxiliary metabolic genes (AMGs) in orga9nic fertilizers. Here we used a combination of metagenomics and phage transplantation trials to investigate the phage profiles and their potential roles in pesticide degradation in four organic fertilizers from different sources. Phage annotation results indicate that the two vermicomposts made from swine (PV) and cattle (CV) dung had more similar phage community structures than the swine (P) and cattle (C) manures. After vermicomposting, the organic fertilizers (PV and CV) exhibited enriched phage-host pairings and phage AMG diversity in relative to the two organic fertilizers (P and C) without composting. In addition, the number of broad-host-range phages in the vermicomposts (182) was higher than that in swine (153) and cattle (103) manures. Notably, phage AMGs associated with metabolism and pesticide biodegradation were detected across the four organic fertilizers. The phage transplantation demonstrated that vermicompost phages were most effective at facilitating the degradation of pesticide precursor p-nitrochlorobenzene (p-NCB) in soil, as compared to swine and cattle manures (P < 0.05). Taken together, our findings highlight the significance of phages in vermicompost for biogeochemical cycling and biodegradation of pesticide-associated chemicals in contaminated soils.

Earthworms synergize with indigenous soil functional microorganisms to accelerate the preferential degradation of the highly toxic S-enantiomer of the fungicide imazalil in soil

The roles of soil and earthworm gut microorganisms in the degradation of the chiral fungicide imazalil (IMA) enantiomers were systemically studied in soil-earthworm systems. S-IMA degraded slower than R-IMA in soil without earthworms. After the addition of earthworms, S-IMA degraded faster than R-IMA. Methylibium was the potential degradative bacterium likely related to the preferential degradation of R-IMA in soil. However, the addition of earthworms significantly decreased the relative abundance of Methylibium, especially in R-IMA-treated soil. Meanwhile, a new potential degradative bacterium Aeromonas first appeared in soil-earthworm systems. Compared with enantiomer-treated soil, the relative abundance of indigenous soil bacterium Kaistobacter significantly boomed in enantiomer-treated soil with earthworms. Interestingly, Kaistobacter in the earthworm gut also obviously increased after exposure to enantiomers, particularly in S-IMA-treated soil, which was associated with the significant increase in Kaistobacter in soil. More importantly, the relative abundances of Aeromonas and Kaistobacter in S-IMA-treated soil were obviously higher than those in R-IMA-treated soil after the addition of earthworms. Moreover, these two potential degradative bacteria were also potential bacterial hosts of the biodegradation genes p450 and bph. Collectively, gut microorganisms are important helpers in soil pollution remediation by participating in the preferential degradation of S-IMA mediated by indigenous soil microorganisms.

Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes

The earthworm gut virome influences the structure and function of the gut microbiome, which in turn influences worm health and ecological functions. However, despite its ecological and soil quality implications, it remains elusive how earthworm intestinal phages respond to different environmental stress, such as soil pollution. Here we used metagenomics and metatranscriptomics to investigate interactions between the worm intestinal phages and their bacteria under different benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg^-1) stress stimulated microbial metabolism (1.74-fold to control), and enhanced the antiphage defense system (n = 75) against infection (8 phage-host pairs). Low-level BaP exposure resulted in the highest proportion of lysogenic phages (88%), and prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level BaP exposure (200 mg kg^-1) disrupted microbial metabolism and suppressed the antiphage systems (n = 29), leading to the increase in phage-bacterium association (37 phage-host pairs) and conversion of lysogenic to lytic phages (lysogenic ratio declined to 43%). Despite fluctuating phage-bacterium interactions, phage-encoded AMGs related to microbial antioxidant and pollutant degradation were enriched, apparently to alleviate pollution stress. Overall, these findings expand our knowledge of complex phage-bacterium interactions in pollution-stressed worm guts, and deepen our understanding of the ecological and evolutionary roles of phages.

Microplastic pollution destabilized the osmoregulatory metabolism but did not affect intestinal microbial biodiversity of earthworms in soil

Metabolomic and gut microbial responses of soil fauna to environmentally relevant concentrations of microplastics indicate the potential molecular toxicity of microplastics; however, limited data exist on these responses. In this study, earthworms (Eisenia fetida) were exposed to spherical (25-30 μm diameter) polystyrene microplastic-contaminated soil (0.02%, w:w) for 14 days. Changes in weight, survival rate, intestinal microbiota and metabolic responses of the earthworms were assessed. The results showed that polystyrene microplastics did not influence the weight, survival rate, or biodiversity of the gut microbiota, but significantly decreased the relative abundance of Bacteroidetes at the phylum level. Moreover, polystyrene microplastics disturbed the osmoregulatory metabolism of earthworms, as indicated by the significantly decreased betaine, myo-inositol and lactate, and increased 2-hexyl-5-ethyl-furan-3-sulfonic acid at the metabolic level. This study provides important insights into the molecular toxicity of environmentally relevant concentrations of polystyrene microplastics on soil fauna.

Ecological adaptation of earthworms for coping with plant polyphenols, heavy metals, and microplastics in the soil: A review

In recent years, soil pollution by massive accumulation of heavy metals (HMs), microplastics, and refractory hydrocarbon chemicals has become an emerging and global concern, drawing worldwide attention. These pollutants influence soil diversity by hindering the reproduction, abundance, thereby affecting aboveground productivity. The scientific community has recently emphasized the contribution of earthworms to heavy metal accumulation, microplastic degradation, and the decomposition of organic matter in the soil, which helps maintain the soil structure. This review paper aimed to compile scientific facts on how earthworms cope with the effect of HMs, microplastics, and plant polyphenols so that vermiremediation could be widely applied for well-being of the soil ecosystem by environmentalists. Earthworms have special surface-active metabolites in their guts called drilodefensins that help them defend themselves against the oxidative action of plant polyphenols. They also combat the effects of toxic microplastics, and other oxidative compounds by elevating the antioxidant activities of their enzymes and converting them into harmless compounds or useful nutrients. Moreover, earthworms also act as biofilters, bioindicators, bioaccumulators, and transformers of oxidative polyphenols, microplastics, toxic HMs, and other pollutant hydrocarbons. Microorganisms (fungi and bacteria) in earthworms' gut of also assist in the fixation, accumulation, and transformation of these toxicants to prevent their effects. As a potential organism for application in ecotoxicology, it is recommended to propagate earthworms in agricultural fields; isolate, and culture enormously in industry, and inoculate earthworms in the polluted soil, thereby abate toxicity and minimizing the health effect caused by these pollutants as well enhance the productivity of crops.

Multi-omics analysis reveals copper-induced growth inhibition mechanisms of earthworm (Eisenia fetida)

Exposure to high concentrations of copper can cause toxic effects on the growth and development of organisms, but the relevant toxic mechanisms are far from fully understood. This study investigated the changes of metabolites, genes, and gut microorganisms in earthworms (Eisenia fetida) exposed to 0 (control), 67.58 (low), 168.96 (medium), and 337.92 (high) mg/kg of Cu in soil for 60 days. Differentially expressed genes (DEGs) and differential metabolites (DMs) at the low-, medium-, and high-level Cu exposure groups were identified and introduced into Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Integrated metabolomic and transcriptomic analysis revealed that amino acid metabolism, lipid metabolism, and carbohydrate metabolism are the major metabolic pathways disturbed by Cu exposure. Furthermore, Cu exposure significantly decreased the diversity of the intestinal bacterial community and affected the relative abundance (increased or decreased) of intestinal colonizing bacteria. This resulted in high energy expenditure, inhibited nutrient absorption and fatty acid synthesis, and weakened antioxidant and detoxification abilities, ultimately inhibiting the growth of E. fetida. These findings offer important clues and evidence for understanding the mechanism of Cu-induced growth and development toxicity in E. fetida and provide further data for risk assessment in terrestrial ecosystems.

Evaluation of the treatment performance and reuse potential in agriculture of organized industrial zone (OIZ) wastewater through an innovative vermifiltration approach

Vermifiltration (VF) is a natural and sustainable biofilter that has many advantages, including being energy-free, cost-effective, and allowing ease of application and maintenance. In this study, the effectiveness of a lab-scale VF system was assessed by the removal efficiency of total suspended solids, electrical conductivity, chemical oxygen demand, total nitrogen, total phosphorus, fecal coliform, and heavy metals in organized industrial zones (OIZ) and domestic wastewater (DW) for the first time. Additionally, the reuse suitability of the treated wastewater was determined by comparing different countries' and global irrigational criteria. The lab systems were built with four layers: one worm-bed and three varying filtering materials, and operated at an optimum hydraulic loading rate of 1.8-2 m³/m²/day for 45 days with Eisenia fetida as the earthworm species. The results demonstrated that removal efficiencies of total suspended solids and chemical oxygen demand were found to be 95% and 80% in OIZ wastewater and 90% and 88% in DW, respectively. Total nitrogen and total phosphorus were removed at rates of 69% and 67% in OIZ wastewater, respectively, and 84% and 74% in DW. Besides, the VF system has shown satisfactory removal performance for heavy metals ranging from 51% to 77% in OIZ wastewater that has met Turkish national wastewater discharge limits. Although the final characterization of treated wastewater was suitable, heavy metal and fecal coliform levels have not met many countries' irrigation water quality criteria. To meet global irrigation standards and to enhance the VF performance, further experimental studies should be carried out, including parameters such as bed material type in the reactor, worm type, and different operating conditions.

Bioresponses of earthworm-microbiota symbionts to polychlorinated biphenyls in the presence of nano zero valent iron in soil

Both earthworms and nano zero-valent iron (nZVI) have been recently regarded as important approaches for in-situ remediation of polychlorinated biphenyls (PCBs) in soil. However, the combined action of earthworms and nZVI toward PCBs, and the biological responses of earthworm-microbiota symbionts to nZVI-PCBs co-exposure in soil remediation systems remain unclear. In this study, a 28-d exposure with different levels of polychlorinated biphenyls (PCBs) and nZVI was applied to earthworm Eisenia fetida in an agricultural soil. Both physiological responses of earthworms and their surrounding microbiota in gut and soil were examined. Kinetic modelling parameters showed a doubled PCB accumulation in earthworms with the presence of nZVI. Meanwhile, nZVI-PCBs coexposure synergistically stimulated the activities of superoxide dismutase (SOD) and catalase (CAT), along with the elevated levels of reactive oxygen species (ROS), malondialdehyde (MDA) and glutathione (GSH) in earthworms. Based on integrated metabolomic and 16S rRNA analysis, it was found that earthworms provided certain metabolites, e.g., S-(2-hydroxyethyl)glutathione, 16-hydroxypalmitic acid, and formamide, beneficial to PCB-degrading microbiota (Novosphingobium and Achromobacter) in the intestine. Our findings of nZVI-enhanced PCB bioaccumulation and the defense mechanism afforded by the earthworm-microbiota symbionts toward PCB-nZVI exposure show the promise of combining earthworms with nZVI for the remediation of PCBs-contaminated soil.

Removal of sulfamethoxazole and antibiotic resistance genes in paddy soil by earthworms (Pheretima guillelmi): Intestinal detoxification and stimulation of indigenous soil bacteria

Vermiremediation, which use earthworms to remove contaminants from soil, has been proven to be an alternative, low-cost technology. However, the effects of earthworm activity, especially the degraders in earthworm intestines, on the fate of sulfamethoxazole (SMX), and the effects of intestinal bacteria on degrading bacteria in soil are unclear. In this study, the effects of earthworms on the fate of SMX and related antibiotic resistance genes (ARGs) were investigated. Special attention was paid to the impact of earthworms on SMX degradation efficiency, degradation products, related ARGs, and degraders in both soil and earthworm intestines; the effect of intestinal bacteria on soil bacteria associated with SMX was also studied. Earthworms significantly accelerated SMX degradation by both intestinal detoxification and the stimulation of indigenous soil bacteria. Compared with the treatment without earthworms, the treatment with earthworms reduced SMX residues by 25.1 %, 49.2 %, 35.7 %, 34.2 %, and 35.7 % on the 10th, 20th, 30th, 60th, and 90th days, respectively. Compared with those in soil (treated with earthworms), the SMX residues in wormcasts were further reduced by 12.2-29.0 % from the 2nd to the 20th day, producing some unique anaerobic degradation products that were distinct from those in the soil. In earthworm intestines, SMX degradation was enhanced by bacteria of the genera Microvirga, Sphingomonas, Methylobacterium, Bacillus, and Tumebacillus. All of these bacteria (except Bacillus spp.) entered and colonised the soil with wormcasts, further promoting SMX degradation. Additionally, earthworms removed a significant number of ARGs by increasing the fraction of potential SMX degraders and inhibiting the potential hosts of ARGs and int1. This study demonstrated that earthworms could remediate SMX-contaminated soil by enhancing the removal of SMX and ARGs.

Microplastic pollution in soils, plants, and animals: A review of distributions, effects and potential mechanisms

Increasing production of synthetic plastics and poor management of plastic wastes have dramatically increased the amount of plastics in the environment. In 2014, at the first United Nations Environment Assembly, marine plastic waste pollution was listed as one of the 10 most pressing environmental issues. In addition, there is much plastic waste in terrestrial ecosystems due to substantial residues from agricultural mulching and packing. As a recently recognized pollutant, microplastics (MPs) have attracted significant attention from the public and various governments. Concentrations of MPs in the environment vary among locations, from <100 to >1 × 10⁶ particles per cubic meter. Many studies have addressed the impacts and potential mechanisms of MPs on the environment and organisms. Humans and other organisms can ingest or carry MPs in a variety of passive ways and these MPs can have a range of negative effects on metabolism, function, and health. Additionally, given their large surface area, MPs can sorb various pollutants, including heavy metals and persistent organic pollutants, with serious implications for animals and human wellbeing. However, due to their complexity and a lack of accurate determination methods, the systematic impacts of MP pollution on whole foodwebs are not clearly established. Therefore, this review summarizes current research advances in MP pollution, particularly the impact of MPs on soils, plants, and animals, and proposes potential future research prospects to better characterize MPs.

Bacterial Keystone Taxa Regulate Carbon Metabolism in the Earthworm Gut

As important ecosystem engineers in soils, earthworms strongly influence carbon cycling through their burrowing and feeding activities. Earthworms do not perform these roles in isolation, because their intestines create a special habitat favorable for complex bacterial communities. However, how the ecological functioning of these earthworm-microbe interactions regulates carbon cycling remains largely unknown. To fill this knowledge gap, we investigated the bacterial community structure and carbon metabolic activities in the intestinal contents of earthworms and compared them to those of the adjacent soils in a long-term fertilization experiment. We discovered that earthworms harbored distinct bacterial communities compared to the surrounding soil under different fertilization conditions. The bacterial diversity was significantly larger in the adjacent soils than that in the earthworm gut. Three statistically identified keystone taxa in the bacterial networks, namely, Solirubrobacterales, Ktedonobacteraceae, and Jatrophihabitans, were shared across the earthworm gut and adjacent soil. Environmental factors (pH and organic matter) and keystone taxa were important determinants of the bacterial community composition in the earthworm gut. Both PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) and FAPROTAX (Functional Annotation of Prokaryotic Taxa) predicted that carbon metabolism was significantly higher in adjacent soil than in the earthworm gut, which was consistent with the average well color development obtained by the Biolog assay. Structural equation modeling combined with correlation analysis suggested that pH, organic matter, and potential keystone taxa exhibited significant relationships with carbon metabolism. This study deepens our understanding of the mechanisms underlying keystone taxa regulating carbon cycling in the earthworm gut. IMPORTANCE The intestinal microbiome of earthworms is a crucial component of the soil microbial community and nutrient cycling processes. If we could elucidate the role of this microbiome in regulating soil carbon metabolism, we would make a crucial contribution to understanding the ecological role of these gut bacterial taxa and to promoting sustainable agricultural development. However, the ecological functioning of these earthworm-microbe interactions in regulating carbon cycling has so far not been fully investigated. In this study, we revealed, first, that the bacterial groups of Solirubrobacterales, Ktedonobacteraceae, and Jatrophihabitans were core keystone taxa across the earthworm gut and adjacent soil and, second, that the environmental factors (pH and organic carbon) and keystone taxa strongly affected the bacterial community composition and exhibited close correlations with microbial carbon metabolism. Our results provide new insights into the community assembly of the earthworm gut microbiome and the ecological importance of potential keystone taxa in regulating carbon cycling dynamics.

Indigenous earthworms and gut bacteria are superior to chemical amendments in the remediation of cadmium-contaminated seleniferous soils

The natural selenium (Se)-rich areas in China are generally characterized by high geological background of cadmium (Cd) which poses potential risks to human health. Therefore, immobilization of Cd is the prerequisite to ensure the safe utilization of natural seleniferous soil resources. A pot experiment was conducted to compare the effects of indigenous earthworm (Amynthas hupeiensis) and its gut bacteria (Citrobacter freundii DS strain) on the remediation of Cd-contaminated seleniferous soil with two traditional chemical amendments. The results indicated that earthworms and DS strain decreased DGT-extractable Cd by 25.52 - 41.53% and reduced Cd accumulation in lettuce leaves by 20.83 - 37.50% compared with control through converting the exchangeable Cd (EX-Cd) into residual Cd (RE-Cd) fractions. Overall, earthworms and DS strain were more effective in Cd immobilization, growth and quality promotion, oxidative stress alleviation, Cd accumulation and bioaccessibility reduction in the soil-lettuce-human continuum than biochar and lime. Moreover, all amendments induced the antagonism between Se and Cd through increasing bioavailable Se/Cd molar ratios in soil. However, all the Cd concentrations in lettuce exceeded the maximum permissible limit of Cd for leaf vegetables, indicating that soil amendment alone could not ensure food safety. This study confirmed that biological amendments were superior to chemical amendments in the remediation of Cd-contaminated seleniferous soil.

Comparative Study on Bacterial Population Dynamics of Foregut, Midgut, and Hindgut Content of Perionyx excavatus (Perrier) Isolated from Eco-friendly, Non-hazardous Vermicompost

The ideal condition of earthworm gut promotes growth and multiplication of beneficial soil microorganisms eliminating pathogens and converts organic wastes into nutrients rich compost. The present study has been carried out to determine the population dynamics of earthworm gut bacteria and to find out relative abundance of different functional bacterial groups in the foregut, midgut, and hindgut of earthworm Perionyx excavatus. To assess bacterial diversity, a viable plate count method was adopted. In the different gut region of earthworm, aerobic heterotrophic, amylolytic, Bacillus, Gram-negative, proteolytic, fat hydrolyzing, nitrate-reducing, nitrifying, asymbiotic nitrogen-fixing, Azotobacter, and phosphate solubilizing bacterial populations ranged from 22.2 to 241.6 × 10⁶, 8.0 to 171.60 × 10⁶, 1.83 to 2.79 × 10⁶, 10.68 to 23.04 × 10⁴, 3.70 to 5.52 × 10⁴, 59.60 to 208.40 × 10⁴, 1.86 to 7.34 × 10⁴, 10.94 to 19.78 × 10⁴, 0.80 to 3.42 × 10⁴, 7.83 to 13.70 × 10⁴, 1.31 to 2.67 × 10⁴ cfu/ml gut suspension, respectively. The results of the one-way ANOVA revealed that the bacterial load of most of the bacterial groups was significantly higher (p < 0.05) in the hindgut region, followed by midgut and foregut. Only the density of the proteolytic group was significantly higher (p < 0.05) in the midgut region followed by foregut and hindgut. Starch hydrolyzing bacteria constitute the largest group of bacteria in the gut content. From principal component analysis, two components were extracted with the eigenvalues of 8.485 and 1.132. Agglomerative hierarchical cluster analysis revealed that the bacterial populations were clustered into four different groups. Quantitative variation among bacterial groups in earthworm's gut seems to determine the soil health and composting efficiency; from this point of view, the present study will provide a better understanding about different functional bacterial groups of earthworm's guts and might be helpful in sustainable agriculture and waste management.

Length- and polymer-dependent ecotoxicities of microfibers to the earthworm Eisenia andrei

Microfibers are widespread environmental pollutants introduced to the soil environment because of the increasing use of plastic polymers. However, research on the soil ecotoxicity of microfibers is limited, especially when compared to research on their aquatic toxicity. This study investigated the effects of sub-chronic microfiber exposure on the earthworm Eisenia andrei. We compared the effects of three types of microfibers: short lyocell microfibers (231 ± 126 μm long), short polypropylene microfibers (191 ± 107 μm long), and long polypropylene microfibers (891 ± 141 μm long). After exposure for 21 days, earthworm survival, coelomocyte viability, cast microbial viability, and gut microbial viability were assessed, and a histopathological examination of the digestive tract and reproductive tissues was conducted. In addition, long polypropylene microfibers egested by the earthworms were collected to explore the possibility of earthworm-driven biofragmentation. Results indicated that high exposure concentration (1000 mg/kg dry soil) negatively affected earthworm coelomocytes and intestinal tissue, gut, and cast microbiomes. Although all three microfiber types reduced earthworm survival, the short polypropylene microfibers were more toxic to the earthworms than the long polypropylene microfibers or short lyocell microfibers, which indicated that size-dependent soil ecotoxicity was induced. PP microfibers were found to more negatively affect cast microbial activity and intestinal tissue than lyocell microfibers, indicating polymer-dependent soil ecotoxicity potential against earthworm species. This study provides evidence that synthesized microfibers cause cytotoxicity and decrease gut microbiome viability in earthworms, and that they can be biofragmented by earthworms.

Earthworm inoculation and straw return decrease the phosphorus adsorption capacity of soils in the Loess region, China

Loess Plateau is important for maize production in China. Therefore, a good understanding of soil phosphorus (P) behavior in the Loess region is crucial for optimizing fertilization in its agriculture systems. To date, research on factors influencing P adsorption/desorption has mainly focused on fertilization. Widespread application of straw return and increasing soil fauna in agricultural croplands inevitably affect soil P behavior either directly or indirectly in this area. However, less attention has been focused on these effects and their interactions. Here, a field plot experiment was performed based on a completely randomized design to investigate the response of P adsorption-desorption characteristics to the presence/absence of earthworms and straw return. Treatments included: (1) control without earthworms and straw (E0S0); (2) treatment with only earthworms (E1S0); (3) treatment with only straw (E0S1); (4) treatment with both earthworms and straw. The Langmuir model was superior to the Freundlich model in interpreting the P adsorption data and allowed better evaluation of the maximum P adsorption values. The maximal P adsorption, P adsorption affinity constant, and maximum buffer capacity in the earthworm and straw treatments were 2.4-8.3%, 8.3-13.9%, and 2.2-26.3% lower than those in E0S0. The readily desorbable P, standard P requirement, and degree of P saturation increased by 15.6-44.3%, 13.1-23.1%, and 4.4-16.5%, respectively, in earthworm and straw treatments. Additionally, earthworm inoculation and straw return treatments significantly increased total soil P, Olsen P, soil organic carbon, free Fe₂O₃, and CaCO₃ contents and specific surface area of the soil. Redundancy analysis showed that soil organic carbon explained most (14.7%) of the total variation in P adsorption and desorption. These results show that combining earthworm inoculation with straw return can effectively reduce soil P adsorption capacity, increase its P desorption capacity, and thus, increase its available P content. These results provide a scientific basis for improving the utilization efficiency of soil P.

Insights into the mechanisms of organic pollutant toxicity to earthworms: Advances and perspectives

Earthworms play positive ecological roles in soil formation, structure, and fertility, environmental protection, and terrestrial food chains. For this review, we searched the Web of Science database for articles published from 2011 to 2021 using the keywords "toxic" and "earthworm" and retrieved 632 publications. From the perspective of bibliometric analysis, we conducted a co-occurrence network analysis using the keywords "toxic" and "earthworm" to identify the most and least reported topics. "Eisenia fetida," "bioaccumulation," "heavy metals," "oxidative stress," and "pesticides" were the most common terms, and "microbial community," "bacteria," "PFOS," "bioaugmentation," "potentially toxic elements," "celomic fluid," "neurotoxicity," "joint toxicity," "apoptosis," and "nanoparticles" were uncommon terms. Additionally, in this review we highlight the main routes of organic pollutant entry into soil, and discuss the adverse effects on the soil ecosystem. We then systematically review the mechanisms underlying organic pollutant toxicity to earthworms, including oxidative stress, energy and lipid metabolism disturbances, neurological toxicity, intestinal inflammation and injury, gut microbiota dysbiosis, and reproductive toxicity. We conclude by discussing future research perspectives, focusing on environmentally relevant concentrations and conditions, novel data processing approaches, technologies, and detoxification and mitigation methods. This review has implications for soil management in the context of environmental pollution.

Deciphering waste bound nitrogen by employing psychrophillic Aporrectodea caliginosa and priming of coprolites by associated heterotrophic nitrifiers under high altitude Himalayas

Himalayan ecosystem is characterized by its fragile climate with rich repositories of biodiversity. Waste collection and disposal are becoming increasingly difficult due to topographical variations. Aporrectodea caligenosa, a versatile psychrophillic soil dweller, is a useful biocatalyst with potent bio-augmented capability for waste treatment at low temperatures. Microcosm experiments were conducted to elucidate the comprehensive nature of biogenic nitrogen transformation to NH₄⁺ and NO₃⁻ produced by coupling of earthworm-microbes. Higher biogenic recovery of NH₄⁺-N from coprolites of garden soil (47.73 ± 1.16%) and Himalayan goat manure (86.32 ± 0.92%) with an increment of 14.12 and 47.21% respectively over their respective control (without earthworms) with a linear decline beyond 4th week of incubation was reported. NO₃^–-N recovery progressively sustained in garden soil and goat manure coprolites during entire incubation with highest 81.81 ± 0.45 and 87.20 ± 1.08 µg-N g⁻¹dry weight recorded in 6th and 5th week of incubation respectively and peak increments as 38.58 and 53.71% relative to respective control (without earthworms). Declined NH₄⁺–N in coprolites at low temperature (15.0 ± 2.0 °C) evidenced increased nitrification rates by taking over the process by abundant nitrifying microbes. Steady de-nitrification with progressive incubation on an average was 16.95 ± 0.46 ng-N g⁻¹ per week and 21.08 ± 0.87 ng-N g⁻¹ per week compared to 14.03 ± 0.58 ng-N g⁻¹ per week and 4.50 ± 0.31 ng-N g⁻¹ per week in respective control treatments. Simultaneous heterotrophic nitrification and aerobic denitrification (SHNAD) was found to be a prominent bioprocess at low temperature that resulted in high and stable total nitrogen and nitrate accumulation from garden soil and goat manure with relative recovery efficiency of 11.12%, 14.97% and 14.20%; 19.34%. A. caligenosa shows promising prospects for mass applicability in biogenic N removal from manure of Himalayan goat.

Quantitative relationship between earthworms' sensitivity to organic pollutants and the contaminants' degradation in soil: A meta-analysis

Using earthworms to remove soil organic pollutants is a common bioremediation method. However, it remains challenging to evaluate and predict their effect on removing soil organic pollutants based on earthworm toxicology and pollutant degradation rates. Peer-reviewed journal articles on ecotoxicology and bioremediation from the years 1974-2020 (cutoff date September 2020) were selected for meta-analysis to quantify the effect size of earthworms on organic pollutant degradation. The meta-analysis shows that the average effect size of earthworms on organic pollutant degradation is 128.5% (p < 0.05). Soils with high soil organic matter or clay textures are more conducive to earthworm-mediated removal of organic pollutants. Structural equation modeling reveals that earthworms' sensitivity to contaminant exposure may be a greater limiting factor on pollutant degradation than environmental factors. In addition, the quantitative relationship existed between LC50 and the pollutants' degradation that an elevated LC50 threshold resulted in at least 1.5 times increase in the pollutants' degradation size. This correlation was dually confirmed via meta-analysis and the validation trial. The results of this study contribute to a more profound understanding of the potential to use earthworms to mitigate organic pollution in soils and develop earthworm-based soil remediation techniques on a global scale.

Carbendazim shapes microbiome and enhances resistome in the earthworm gut

BACKGROUND

It is worrisome that several pollutants can enhance the abundance of antibiotic resistance genes (ARGs) in the environment, including agricultural fungicides. As an important bioindicator for environmental risk assessment, earthworm is still a neglected focus that the effects of the fungicide carbendazim (CBD) residues on the gut microbiome and resistome are largely unknown. In this study, Eisenia fetida was selected to investigate the effects of CBD in the soil-earthworm systems using shotgun metagenomics and qPCR methods.

RESULTS

CBD could significantly perturb bacterial community and enrich specific bacteria mainly belonging to the phylum Actinobacteria. More importantly, CBD could serve as a co-selective agent to elevate the abundance and diversity of ARGs, particularly for some specific types (e.g., multidrug, glycopeptide, tetracycline, and rifamycin resistance genes) in the earthworm gut. Additionally, host tracking analysis suggested that ARGs were mainly carried in some genera of the phyla Actinobacteria and Proteobacteria. Meanwhile, the level of ARGs was positively relevant to the abundance of mobile genetic elements (MGEs) and some representative co-occurrence patterns of ARGs and MGEs (e.g., cmx-transposase and sul1-integrase) were further found on the metagenome-assembled contigs in the CBD treatments.

CONCLUSIONS

It can be concluded that the enhancement effect of CBD on the resistome in the earthworm gut may be attributed to its stress on the gut microbiome and facilitation on the ARGs dissemination mediated by MGEs, which may provide a novel insight into the neglected ecotoxicological risk of the widely used agrochemicals on the gut resistome of earthworm dwelling in soil. Video abstract.

Effects of Three Pesticides on the Earthworm Lumbricus terrestris Gut Microbiota

Earthworms play a vital role in the terrestrial ecosystem functioning and maintenance of soil fertility. However, many pesticides, for example, imidacloprid, benomyl, and metribuzin that are world-widely used in agriculture, may be potentially dangerous to earthworms. At the same time, standard tests for pesticides acute and chronic toxicity do not reflect all aspects of their negative impact and might not be enough sensitive for effective assessment. In this paper, we studied the effects of non-lethal concentrations of imidacloprid, benomyl, and metribuzin on the gut bacterial community of Lumbricus terrestris using high-throughput sequencing approach. We found that pesticides reduced the total bacterial diversity in the earthworm's gut even at the recommended application rate. Under the applied pesticides, the structure of the gut prokaryotic community underwent changes in the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Planctomyces, Verrucomicrobia, and Cyanobacteria, as well as the genera Haliangium, Gaiella, Paenisporosarcina, Oryzihumus, Candidatus Udaeobacter, and Aquisphaera. Moreover, the pesticides affected the abundance of Verminephrobacter-the earthworms' nephridia specific symbionts. In general, the negative impact of pesticides on bacterial biodiversity was significant even under pesticides content, which was much lower than their acute and chronic toxicity values for the earthworms. These results highlighted the fact that the earthworm's gut microbial community is highly sensitive to soil contamination with pesticides. Therefore, such examination should be considered in the pesticide risk assessment protocols.

Extractable additives in microplastics: A hidden threat to soil fauna

Microplastics (MPs) have become an emerging threat for organisms. However, the toxicity mechanisms on biota, especially soil biota remain largely unclear. This study distinguished the effects of five types of MPs and their extractable additives on a typical soil oligochaete Enchytraeus crypticus using a traditional ecotoxicological approach combined with gut microbiota analysis. A variety of inorganic and organic compounds were screened in extractable solutions. Both MPs and their extractable additives decreased the growth and survival rates of the worms and shifted the gut microbiota, and the effects were type-specific. The differences between the effects of MPs and their extractable additives on traditional ecotoxicological parameters were insignificant, suggesting that extractable additives were the main toxicity pathways on soil fauna. The type-specific effects of MPs were attributed to the varied chemical compositions of extractable additives, and the compounds responsible for the shift of gut microbiota were further identified. The distinguishable effects on gut microbiota between MPs and their extractable additives together with the significant regressions between gut microbiota and traditional ecotoxicological parameters confirmed that gut microbiota could be a more sensitive indicator of organism's health conditions. Combined, the study provided an important insight into the toxicity mechanisms of MPs on soil fauna and extractable additives of MPs may be a hidden threat.

Hemicellulolytic bacteria in the anterior intestine of the earthworm Eisenia fetida (Sav.)

Tropical agriculture produces large amounts of lignocellulosic residues that can potentially be used as a natural source of value-added products. The complexity of lignocellulose makes industrial-scale processing difficult. New processing techniques must be developed to improve the yield and avoid this valuable resource going to waste. Hemicelluloses comprise a variety of polysaccharides with different backbone compositions and decorations (such as methylations and acetylations), and form part of an intricate framework that confers structural stability to the plant cell wall. Organisms that are able to degrade these biopolymers include earthworms (Eisenia fetida), which can rapidly decompose a wide variety of lignocellulosic substrates. This ability probably derives from enzymes and symbiotic microorganisms in the earthworm gut. In this work, two substrates with similar C/N ratios but different hemicellulose content were selected. Palm fibre and coffee husk have relatively high (28%) and low (5%) hemicellulose contents, respectively. A vermicomposting mixture was prepared for the earthworms to feed on by mixing a hemicellulose substrate with organic market waste. Xylanase activity was determined in earthworm gut and used as a selection criterion for the isolation of hemicellulose-degrading bacteria. Xylanase activity was similar for both substrates, even though their physicochemical properties principally pH and electrical conductivity, as shown by the MANOVA analysis) were different for the total duration of the experiment (120 days). Xylanolytic strains isolated from earthworm gut were identified by sequence analysis of the 16S rRNA gene. Our results indicate that the four Actinobacteria, two Proteobacteria, and one Firmicutes isolated are active participants of the xylanolytic degradation by microbiota in the intestine of E. fetida. Most bacteria were more active at pH 7 and 28 °C, and those with higher activities are reported as being facultatively anaerobic, coinciding with the microenvironment reported for the earthworm gut. Each strain had a different degradative capacity.

Responses of earthworm Metaphire vulgaris gut microbiota to arsenic and nanoplastics contamination

The growing contamination of arsenic and plastics has severely effects on the soil fauna health, including shifts of gut microbiota community. A few studies have focused on effects of microplastics and metal(loid) in soil and fauna gut microbiome. However, the environmental effect of nanoplastics and arsenic on the earthworm gut microbiota, especially on arsenic biotransformation in the gut, remain largely unknown. Here, a microcosm study was performed to explore the effects of nanoplastics and arsenic on the microbiota characteristics in earthworm Metaphire vulgaris gut using Illumina high throughput sequencing, and to investigate changes in the gut microbiota-mediated arsenic biotransformation genes (ABGs) by using high-throughput quantitative PCR. Our results demonstrated that the concentration of arsenic in the earthworm body tissues after exposure to arsenic and nanoplastics was significantly lower from that with arsenic alone exposure. Moreover, the clearly different bacterial community was observed in the soil compared with the earthworm gut, which was dominated by Proteobacteria, Actinobacteria, and Firmicutes at phylum level. Arsenic exposure significantly disturbed bacterial community structure in the earthworm gut, but exposure to nanoplastics did not induce gut microbiota changes. More interestingly, nanoplastics can relieve adverse effect of arsenic on the gut microbiota possibly by adsorbing arsenic. In addition, a total of 16 ABGs were detected, and predominant genes involved in arsenic reduction and transport process were observed in the earthworm guts. In short, this study provides a new picture of the effects of nanoplastics and arsenic on the gut microbiota and arsenic biotransformation in soil fauna gut.

Mechanistic insights into primary biotransformation of diethyl phthalate in earthworm and significant SOD inhibitory effect of esterolytic products

Phthalic acid esters (PAEs) are used as plasticizer or modifier in artificially-manufactured products. Though the rapid biotransformation of phthalates in microbes and plants have been well documented, it is less studied yet in terrestrial animals, e.g. earthworm. In this study, the major biotransformation of diethyl phthalate (DEP) in Eisenia fetida was illustrated using in vitro incubation of earthworm crude enzymes. DEP could be substantially biotransformed into phthalate monoester (MEP) and a small amount of phthalic acid (PA) through esterolysis, which was verified to be driven by endogenous carboxylesterase. Despite the inferior contribution, the oxidation of DEP might also occur under the initiated electron transfer by NADPH coenzyme. The dominant metabolite MEP showed a higher inhibition of superoxide dismutase (SOD) activity than DEP with EC₅₀ of 0.0082 ± 0.0016 mmol/L, so the higher ecological risks of MEP would be marked. The inhibition effect of PA was validated to be even stronger than MEP though it was slightly generated. The direct binding interaction with SOD was proved to be an important molecular event for regulation of SOD activity. Besides the static quenching mechanism, the caused conformational changes including despiralization of α-helix and spatial reorientation of tryptophan were spectrally believed to affect binding and underlie inhibition efficiency of SOD activity.

Exposure to fomesafen alters the gut microbiota and the physiology of the earthworm Pheretima guillelmi

The application of herbicide fomesafen plays a crucial role in ensuring global soybean productivity in modern agriculture, but it results in both adverse effects on soil ecosystems and phytotoxicity to succeeding crops. Soil pollution due to herbicides has raised much concern worldwide. However, there has been little investigations concerning their effects on soil fauna, especially on the gut microbial communities of earthworms. In this study, the soil endogeic earthworm Pheretima guillelmi was incubated for 20 days in natural and fomesafen-polluted soils to investigate the effects of the herbicide on gut bacterial microbiota and the earthworm's physiological indices, including energy resource (protein) and antioxidant enzyme (superoxide dismutase, SOD) of earthworms in the soil ecosystem. A significantly different and smaller microbial community was presented in the earthworm's gut compared with the cast and the surrounding soil, with exposure to fomesafen further reducing the bacterial diversity and altering the gut community composition. This was observed as significant changes in the relative abundance of the phyla Actinobacteria, Firmicutes, and Proteobacteria as well as the genera Bacillus, Microvirga, Blastococcus, Nocardioides, and Gaiella. Moreover, exposure to fomesafen reduced earthworms' energy resources and activated the antioxidant system, with both effects being significantly correlated with the gut microbial diversity. These findings unravel the fact that exposure to the herbicide fomesafen may affect non-target soil fauna via changes in their microbiota and physiological indices, thereby contributing new knowledge regarding the adverse impacts of fomesafen on the terrestrial ecosystem.

Incubation trial indicated the earthworm intestinal bacteria as promising biodigestor for mitigating tetracycline resistance risk in anthropogenic disturbed forest soil

The continuous input of antibiotics due to frequent anthropogenic activities have increased the dissemination risk of antibiotic resistance genes (ARGs) in forest soil. As soil engineers, it remains unclear whether earthworm intestinal microbial communities might play a role in controlling the ARG proliferation in forest soil. This study collected forest soil in the Yangtze River Delta, China, and its resident Metaphire guillelmi to investigate the interaction between tetracycline (50 μg kg^-1) and the bacteria in worm gut and soil. Metagenome sequencing analysis indicated that the abundance of the total ARGs in both the soil (S2) and the worm gut (E2) was 1.3 (p < 0.001) and 1.2 (p < 0.001) times higher than the soil (S1) and (E1) without tetracycline exposure; and under tetracycline stress, the relative abundance of 36 and 20 bacterial genera in forest soil and worm gut were significantly increased respectively. However, the ARGs/ARB abundance decreased in the soil with the worm addition than that without, which may be related to the fact that earthworm intestinal bacteria harbored more tetracycline-degrading genes, i.e. dehydrogenase genes adh, ETFDH, and gpr, etc. Structural equation model analysis indicated that bacteria in worm intestinal has stronger ability to degrade tetracycline than in soil, and the main dissipate way was dehydrogenation. Together, the results contributed to understanding the promising role of worm intestinal bacteria in controlling the ARG risk caused by antibiotic disturbed forest soil.

Influence of Tubificidae Limnodrilus and electron acceptors on the environmental fate of BDE-47 in sediments by (14)C-labelling

2,2',4,4'-tetrabromodiphenyl ether (BDE-47) was difficult to degrade in sediments. In this study, the environmental behavior of BDE-47 with/without the effect of benthos (Tubificidae Limnodrilus) and electron acceptors in sediments was investigated using C-14 tracer. Generally, extractable residues of BDE-47 were dominant in sediment and posed high environment risk. The amount of non-extractable residues (NERs) accounted for 39.0% of initial radioactivity in oxic sediments was significantly higher than those in anoxic sediments (17.6%). Most of NERs were localized in the humin fraction and presented as sequestrated forms. Under oxic conditions, the present of Limnodrilus significantly increased the proportion of NERs in sediment. Limnodrilus accumulated 34.2% of initial radioactivity. Under anoxic conditions, the addition of iron (Ⅲ) [Fe(III)], sulfate and nitrate reduced the environmental risk of BDE-47 with the increase of NERs formation, while manganese (IV) [Mn(IV)] addition had no effect on the formation of NERs. The present of Limnodrilus and electron acceptors promoted the production of metabolites. Meanwhile, BDE-47 changed the microbial community structure of sediments. These findings indicated that the environmental behavior and risk of BDE-47 was affected by benthos and electron acceptors, and the high proportion of sequestrated NERs posed high bioactivity and toxic threat to ecological environment.

Isolation of Rhodococcus equi from the gastrointestinal contents of earthworms (family Megascolecidae)

Rhodococcus equi was isolated from the gastrointestinal contents of earthworms (family Megascolecidae) and their surrounding soil collected from pastures of two horse-breeding farms in Aomori Prefecture, outdoor pig pens, forest in Towada campus, orange groves and forest where wild boars (Sus scrofa) are established in Tanabe, Wakayama Prefecture. The number of R. equi in the lower gastrointestinal contents of 23 earthworms collected from our campus was significantly larger than that of the upper gastrointestinal content. The mean numbers of R. equi from the gastrointestinal contents of earthworms collected from the various places were 2·3-fold to 39·7-fold more than those of the surrounding soil samples. In all, 1771 isolates from the earthworms and 489 isolates from the soil samples were tested for the presence of vapA and vapB genes using polymerase chain reaction. At the horse-breeding farm N, 9 of the 109 isolates (8·3%) from the earthworms and 7 of the 106 isolates (6·6%) from the soil samples were positive for the vapA gene. At the University's forest, one of the 250 isolates (0·4%) from the gastrointestinal contents of the earthworm was positive for the vapB gene. These results revealed that R. equi can be found in significant quantities in the gastrointestinal contents of earthworms, suggesting that they act as an accumulator of R. equi in the soil environment and as a source or reservoir of animal infection.

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.

Trophic level drives the host microbiome of soil invertebrates at a continental scale

BACKGROUND

Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China.

RESULTS

Different soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web.

CONCLUSIONS

Our findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates. Video abstract.