Bioremediation of selenium-contaminated soil using earthworm Eisenia fetida: Effects of gut bacteria in feces on the soil microbiome

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.

Effect of microplastic pollution on the gut microbiome of anecic and endogeic earthworms

Microplastic (MP) pollution constitutes an emerging type of pollution threatening both aquatic and terrestrial ecosystems. The impact on aquatic ecosystems has been extensively studied, but the effect on terrestrial ecosystems and their inhabitants is mostly underexplored. In this study, we explored the effect of MP pollution on gut bacterial microbiome of endogeic (Aporrectodea caliginosa) and anecic (Lumbricus terrestris) earthworms. The experiments were performed in sandy soil with 0.2% of low-density polyethylene MPs (LDPE MPs). We observed that the endogeic earthworms had 100% survival, while anecic earthworms survived 25 days in the control (i.e. in absence of MPs) and 21 days in the treatment with LDPE MPs. The main driver of shifts in the diversity and composition of the bacterial communities in the gut of tested earthworms was the lifestyle of the worms, followed by the presence of MPs. The bacterial microbiome diversity was significantly different among the two types of earthworms, and the highest bacterial diversity was found in the gut of the endogeic earthworms. The effect of MPs on gut bacterial microbiome was clearly observed in the changes in the relative abundance of several phyla and families of the bacterial communities in both types of earthworms, although it was most evident in the anecic earthworms. The Actinobacteriota, Proteobacteria, and Firmicutes were the main groups enhanced in the MP treatments, suggesting enrichment of the bacterial communities with potential plastic degraders.

Mitigation effects and microbial mechanism of two ecological earthworms on the uptake of chlortetracycline and antibiotic resistance genes in lettuce

The contamination of greenhouse vegetable soils with antibiotics and antibiotic resistance genes (ARGs), caused by the application of livestock and poultry manure, is a prominent environmental problem. In this study, the effects of two ecological earthworms (endogeic Metaphire guillelmi and epigeic Eisenia fetida) on the accumulation and transfer of chlortetracycline (CTC) and ARGs in a soil-lettuce system were studied via pot experiments. The results revealed that earthworm application accelerated the removal of the CTC from the soil and lettuce roots and leaves, with the CTC content reducing by 11.7-22.8 %, 15.7-36.1 %, and 8.93-19.6 % compared with that of the control, respectively. Both earthworms significantly reduced the CTC uptake by lettuce roots from the soil (P < 0.05) but did not change the CTC transfer efficiency from the roots to leaves. The high-throughput quantitative PCR results showed that the relative abundance of ARGs in the soil and lettuce roots and leaves decreased by 22.4-27.0 %, 25.1-44.1 %, and 24.4-25.4 %, respectively, with the application of earthworms. Earthworm addition decreased the interspecific bacterial interactions and the relative abundance of mobile genetic elements (MGEs), which helped reduce the dissemination of ARGs. Furthermore, some indigenous soil antibiotic degraders (Pseudomonas, Flavobacterium, Sphingobium, and Microbacterium) were stimulated by the earthworms. The results of redundancy analysis indicated that the bacterial community composition, CTC residues, and MGEs were the main parameters affecting the distribution of ARGs, accounting for 91.1 % of the total distribution. In addition, the bacterial function prediction results showed that the addition of earthworms reduced the abundance of some pathogenic bacteria in the system. Overall, our findings imply that earthworm application can substantially reduce the accumulation and transmission risk of antibiotics and ARGs in soil-lettuce systems, providing a cost-effective soil bioremediation practice for addressing antibiotic and ARGs contamination to guarantee the safety of vegetables and human health.

A Comparative Study of the Synthesis and Characterization of Biogenic Selenium Nanoparticles by Two Contrasting Endophytic Selenobacteria

The present study examined the biosynthesis and characterization of selenium nanoparticles (SeNPs) using two contrasting endophytic selenobacteria, one Gram-positive (Bacillus sp. E5 identified as Bacillus paranthracis) and one Gram-negative (Enterobacter sp. EC5.2 identified as Enterobacter ludwigi), for further use as biofortifying agents and/or for other biotechnological purposes. We demonstrated that, upon regulating culture conditions and selenite exposure time, both strains were suitable "cell factories" for producing SeNPs (B-SeNPs from B. paranthracis and E-SeNPs from E. ludwigii) with different properties. Briefly, dynamic light scattering (DLS), transmission electron microscopy (TEM), and atomic force microscopy (AFM) studies revealed that intracellular E-SeNPs (56.23 ± 4.85 nm) were smaller in diameter than B-SeNPs (83.44 ± 2.90 nm) and that both formulations were located in the surrounding medium or bound to the cell wall. AFM images indicated the absence of relevant variations in bacterial volume and shape and revealed the existence of layers of peptidoglycan surrounding the bacterial cell wall under the conditions of biosynthesis, particularly in the case of B. paranthracis. Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR), energy-dispersive X-ray (EDS), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) showed that SeNPs were surrounded by the proteins, lipids, and polysaccharides of bacterial cells and that the numbers of the functional groups present in B-SeNPs were higher than in E-SeNPs. Thus, considering that these findings support the suitability of these two endophytic stains as potential biocatalysts to produce high-quality Se-based nanoparticles, our future efforts must be focused on the evaluation of their bioactivity, as well as on the determination of how the different features of each SeNP modulate their biological action and their stability.

Predicting the bioremediation potential of earthworms of different ecotypes through a multi-biomarker approach

Earthworms are attracting the attention of bioremediation research because of their short-term impact on pollutant fate. However, earthworm-assisted bioremediation largely depends on the earthworm sensitivity to target pollutants and its metabolic capacity to break down contaminants. The most studied species in soil bioremediation has been Eisenia fetida, which inhabits the soil surface feeding on decomposing organic residues. Therefore, its bioremediation potential may be limited to organic matter-rich topsoil. We compared the detoxification potential against organophosphate (OP) pesticides of three earthworm species representative of the main ecotypes: epigeic, anecic, and endogeic. Selected biomarkers of pesticide detoxification (esterases, cytochrome P450-dependent monooxygenase, and glutathione S-transferase) and oxidative homeostasis (total antioxidant capacity, glutathione levels, and glutathione reductase [GR] and catalase activities) were measured in the muscle wall and gastrointestinal tract of E. fetida (epigeic), Lumbricus terrestris (anecic) and Aporrectodea caliginosa (endogeic). Our results show that L. terrestris was the most suitable species to bioremediate OP-contaminated soil for the following reasons: 1) Gut carboxylesterase (CbE) activity of L. terrestris was higher than that of E. fetida, whereas muscle CbE activity was more sensitivity to OP inhibition than that of E. fetida, which means a high capacity to inactivate the toxic oxon metabolites of OPs. 2) Muscle and gut phosphotriesterase activities were significantly higher in L. terrestris than in the other species. 3) Enzymatic (catalase and GR) and molecular mechanisms of free radical inactivation (glutathione) were 3- to 4-fold higher in L. terrestris concerning E. fetida and A. caliginosa, which reveals a higher potential to keep the cellular oxidative homeostasis against reactive metabolites formed during OP metabolism. Together with biological and ecological traits, these toxicological traits suggest L. terrestris a better candidate for soil bioremediation than epigeic earthworms.

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.

Effects of glycosylation on the accumulation and transport of fipronil in earthworm (Eisenia fetida)

In this study, the differences in the accumulation of fipronil (F) and the glycosylated product glucose-fipronil (GTF) in Eisenia fetida within 48 h were investigated, and the reason for these differences was discussed. The accumulation of F and GTF in E. fetida and soil was determined by high-performance liquid chromatography (HPLC) after simple, rapid pretreatment; the mean recoveries of F and GTF were 84.79 ~ 95.83%, and the relative standard deviations were 3.39 ~ 9.21%, indicating that the methods could accurately detect the accumulation of F and GTF in E. fetida and soil. Results showed that the accumulation concentrations of F and GTF in E. fetida increased with exposure time; the concentrations of F in E. fetida were 3.1 ~ 6.2 times higher than those of GTF. In addition, the half-lives of GTF in soil (16.90 ~ 18.24 days) were significantly lower than those of F (24.75 ~ 26.65 days). After the addition of phlorizin, a hexose transport inhibitor, the accumulation of F in E. fetida did not change significantly, but the accumulation of GTF in E. fetida was significantly inhibited. The concentrations of GTF in E. fetida after adding phlorizin were 32.71 ~ 59.07% of those without phlorizin. Overall, our results indicated that the uptake and transport of F and GTF in E. fetida were significantly different; the uptake and transport of GTF was related to monosaccharide transporters, and glycosylation could reduce the bioaccumulation of fipronil to E. fetida and shorten the half-life of fipronil in soil, providing an important reference for the application of glucose-fipronil.

Microbial functional communities and the antibiotic resistome profile in a high-selenium ecosystem

Enshi City, in the Hubei Province of China, is known as the world capital of selenium with the most abundant selenium resource. An important selenium hyperaccumulator plant, Cardamine violifolia, was found to naturally grow in this high-selenium ecosystem. However, relatively little is known about the impact of the selenium levels on microbial community and functional shifts in C. violifolia rhizosphere. Here, we tested the hypothesis that underground microbial diversity and function vary along a selenium gradient, including antibiotic resistance genes (ARGs). Comprehensive metagenomic analyses, such as taxonomic investigation, functional detection, and ARG annotation, showed that selenium, mercury, cadmium, lead, arsenic, and available phosphorus and potassium were correlated with microbial diversity and function. Thaumarchaeota was exclusively dominant in the highest selenium concentration of mine outcrop, and Rhodanobacter and Nitrospira were predominant in the high-selenium ecosystem. The plant C. violifolia enriched a high concentration of selenium in the rhizosphere compared to those in the bulk soil, and it recruited Variovorax and Polaromonas in its rhizosphere. Microbial abundance showed a trend of increasing first and then decreasing from low to high selenium concentrations. Annotation of ARGs showed that the multidrug resistance genes adeF, mtrA, and poxtA, the aminoglycoside resistance gene rpsL, and the sulfonamide resistant gene sul2 were enriched in the high-selenium system. It was discovered that putative antibiotic resistant bacteria displayed obvious differences in the farmland and the soils with various selenium concentrations, indicating that a high-selenium ecosystem harbors the specific microbes with a higher capacity to enrich or resist selenium, toxic metals, or antibiotics. Taken together, these results reveal the effects of selenium concentration and the selenium hyperaccumulator plant C. violifolia on shaping the microbial functional community and ARGs. Metalloid selenium-inducible antibiotic resistance is worth paying attention to in future.