The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils

Multi-omics reveals different impact patterns of conventional and biodegradable microplastics on the crop rhizosphere in a biofertilizer environment

Microplastics (MPs) from the incomplete degradation of agricultural mulch can stress the effectiveness of biofertilizers and ultimately affect the rhizosphere environment of crops. Yet, the involved mechanisms are poorly known and robust empirical data is generally lacking. Here, conventional polyethylene (PE) MPs and poly(butylene adipate-co-butylene terephthalate) (PBAT) / poly(lactic acid) (PLA) biodegradable MPs (PBAT-PLA BioMPs) were investigated to assess their potential impact on the rhizosphere environment of Brassica parachinensis in the presence of Bacillus amyloliquefaciens biofertilizer. The results revealed that both MPs caused different levels of inhibited crop both above- and belowground crop biomass (up to 50.11% and 57.09%, respectively), as well as a significant decrease in plant height (up to 48.63% and 25.95%, respectively), along with an imbalance of microbial communities. Transcriptomic analyses showed that PE MPs mainly affected root's vitamin metabolism, whereas PBAT-PLA BioMPs mainly interfered with the lipid's enrichment. Metabolomic analyses further indicated that PE MPs interfered with amino acid synthesis that involved in crops' oxidative stress, and that PBAT-PLA BioMPs mainly affected the pathways associated with root growth. Additionally, PBAT-PLA BioMPs had a bigger ecological negative impact than did PE MPs, as evidenced by more pronounced alterations in root antioxidant abilities, a higher count of identified differential metabolites, more robust interrelationships among rhizosphere parameters, and a more intricate pattern of impacts on rhizosphere metrics. This study highlights the MPs' impact on crop rhizosphere in a biofertilizer environment from a rhizosphere multi-omics perspective, and has theoretical implications for scientific application of biofertilizers.

Ecologically different earthworm species are the driving force of microbial hotspots influencing Pb uptake by the leafy vegetable Brassica campestris

Food chain contamination by soil lead (Pb), beginning with Pb uptake by leafy vegetables, is a threat to food safety and poses a potential risk to human health. This study highlights the importance of two ecologically different earthworm species (the anecic species Amynthas aspergillum and the epigeic species Eisenia fetida) as the driving force of microbial hotspots to enhance Pb accumulation in the leafy vegetable Brassica campestris at different Pb contamination levels (0, 100, 500, and 1,000 mg·kg-1). The fingerprints of phospholipid fatty acids (PLFAs) were employed to reveal the microbial mechanism of Pb accumulation involving earthworm-plant interaction, as PLFAs provide a general profile of soil microbial biomass and community structure. The results showed that Gram-positive (G+) bacteria dominated the microbial community. At 0 mg·kg-1 Pb, the presence of earthworms significantly reduced the total PLFAs. The maximum total of PLFAs was found at 100 mg·kg-1 Pb with E. fetida inoculation. A significant shift in the bacterial community was observed in the treatments with E. fetida inoculation at 500 and 1,000 mg·kg-1 Pb, where the G+/G- bacteria ratio was significantly decreased compared to no earthworm inoculation. Principal component analysis (PCA) showed that E. fetida had a greater effect on soil microbial hotspots than A. aspergillum, thus having a greater effect on the Pb uptake by B. campestris. Redundancy analysis (RDA) showed that soil microbial biomass and structure explained 43.0% (R2 = 0.53) of the total variation in Pb uptake by B. campestris, compared to 9.51% of microbial activity. G- bacteria explained 23.2% of the total variation in the Pb uptake by B. campestris, significantly higher than the other microbes. The Mantel test showed that microbial properties significantly influenced Pb uptake by B. campestris under the driving force of earthworms. E. fetida inoculation was favorable for the G- bacterial community, whereas A. aspergillum inoculation was favorable for the fungal community. Both microbial communities facilitated the entry of Pb into the vegetable food chain system. This study delivers novel evidence and meaningful insights into how earthworms prime the microbial mechanism of Pb uptake by leafy vegetables by influencing soil microbial biomass and community composition. Comprehensive metagenomics analysis can be employed in future studies to identify the microbial strains promoting Pb migration and develop effective strategies to mitigate Pb contamination in food chains.

Change of tetracycline speciation and its impacts on tetracycline removal efficiency in vermicomposting with epigeic and endogeic earthworms

Tetracycline pollution is common in Chinese arable soils, and vermicomposting is an effective approach to accelerate tetracycline bioremediation. However, current studies mainly focus on the impacts of soil physicochemical properties, microbial degraders and responsive degradation/resistance genes on tetracycline degradation efficiencies, and limited information is known about tetracycline speciation in vermicomposting. This study explored the roles of epigeic E. fetida and endogeic A. robustus in altering tetracycline speciation and accelerating tetracycline degradation in a laterite soil. Both earthworms significantly affected tetracycline profiles in soils by decreasing exchangeable and bound tetracycline but increasing water soluble tetracycline, thereby facilitating tetracycline degradation efficiencies. Although earthworms increased soil cation exchange capacity and enhanced tetracycline adsorption on soil particles, the significantly elevated soil pH and dissolved organic carbon benefited faster tetracycline degradation, attributing to the consumption of soil organic matter and humus by earthworms. Different from endogeic A. robustus which promoted both abiotic and biotic degradation of tetracycline, epigeic E. foetida preferently accelerated abiotic tetracyline degradation. Our findings described the change of tetracycline speciation during vermicompsiting process, unraveled the mechanisms of different earthworm types in tetracycline speciation and metabolisms, and offered clues for effective vermiremediation application at tetracycline contaminated sites.

Earthworms enhance the bioremediation of tris(2-butoxyethyl) phosphate-contaminated soil by releasing degrading microbes

The escalating awareness of the environmental risks posed by organophosphorus flame retardants (OPFRs), e.g., tris(2-butoxyethyl) phosphate (TBOEP), necessitates the development of effective approaches to mitigate their adverse ecological effects. However, research on the remediation of OPFR-contaminated soil remains limited. In this study, a strategy is proposed to enhance the microbial remediation of TBOEP-contaminated soil through the introduction of exotic earthworms (Eisenia fetida). The presence of earthworms led to a substantial increase in the 28-d removal rates of TBOEP at concentrations of 0.05, 0.5, and 5 mg/kg, with improvements of 32.3 ± 2.0%, 33.2 ± 1.3%, and 33.0 ± 5.6% compared to rates in the absence of earthworms, respectively. The underlying mechanisms for this enhancement include the earthworm-mediated enrichment of TBOEP-degrading bacteria, particularly Rhodococcus, Flavobacterium, and Pseudomonas, and the transfer of Rhodococcus from the earthworm gut to the soil, resulting in an increased relative abundance within the soil. Concurrently, the earthworms stimulated soil peroxidase activity, facilitating the oxidative degradation of TBOEP. Furthermore, the rise in dissolved organic matter content following earthworm treatment fostered the growth of degrading bacteria in the soil. Rhodococcus emerged as a dominant contributor to soil TBOEP removal, consuming humic-like compounds in dissolved organic matter. This investigation underscores the significance of gut microbes and offers valuable insights for the application of earthworm-based remediation strategies in OPFR-contaminated soil.

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.

Change of the structure and assembly of bacterial and photosynthetic communities by the ecological engineering practices in Dianchi Lake

Cyanobacterial bloom challenges the aquatic ecosystem and ecological restoration is an effective approach for cyanobacterial bloom control, but the change of aquatic community after ecological restoration is still unclear. Dianchi Lake is an eutrophic lake with frequent cyanobacterial blooms in China, and recent ecological restoration projects in Caohai (north part) have a satisfactory performance. In this study, we collected 249 water samples at 23 sites from Dianchi Lake to explore the relationships between water physicochemical variables and aquatic microbial communities. Water physicochemical variables in Waihai (south part) intensively changed along time, whereas those in Caohai did not. Photoautotrophic communities were significantly divergent between Caohai and Waihai. Waihai had a lower diversity of photoautotrophic community, containing higher abundance of Cyanophyceae (89.9%) than Caohai (42.7%). Nutrient level and Cyanophyceae only exhibited strong correlations in Wahai (p < 0.05). Redundancy analysis and microbial ecological network suggested that microbial communities in Caohai had a higher stability. Deterministic process dominated the microbial assembly (50-80% for bacteria and >90% for photoautotrophs), and particularly in Caohai. Our results unraveled that the structure and assembly of bacterial and photoautotrophic communities significantly changed after ecological restoration, offering valuable suggestions that photosynthetic diversity should be focused for other ecological restoration projects.

Chemical fertilizer reduction combined with bio-organic fertilizers increases cauliflower yield via regulation of soil biochemical properties and bacterial communities in Northwest China

The continuous application of chemical fertilizers in vegetable cropping has led to deterioration of the soil environment and reduced yield and quality. The objective of this study was to evaluate the effect of combining chemical and bio-organic fertilizers on cauliflower yield, soil biochemical properties, and the bacterial community. Six treatments were established: no fertilizer (CK, control), chemical fertilizers (CF, conventional dosage for this region), balanced fertilization (BF, 30% reduction of chemical fertilizers), and balanced fertilization plus 3,000, 6,000, or 12,000 kg.ha-1 bio-organic fertilizer (Lvneng Ruiqi Biotechnology Co., Ltd., Gansu, China) (BF + OF1, BF + OF2, BF + OF3, respectively). A two-season field experiment with cauliflower was conducted under the different fertilizer treatments in irrigation districts along the Yellow River, Northwest China. The results indicate that the yield, soil organic matter, total potassium content, and enzyme activity under the bio-organic treatments were generally higher than those under the CF treatment. Compared with the CF treatment, the BF treatment increased soil organic matter content, enzyme activity and soil bacterial relative abundance. Moreover, the bacterial alpha-diversity were higher than those of conventional fertilization. The predominant phyla, including Proteobacteria, Actinobacteria, Gemmatimonadetes, and Chloroflexi, were the main contributors to the microbiome shift, as demonstrated by their remarkable enrichment in the soil under BF + OF2 and BF + OF3 treatments. Furthermore, Pearson correlation analyses show significant correlations among the soil organic matter, available P and K, electrical conductivity, and relative abundance of potentially beneficial microbial groups, such as the genera Massilia, Bacillus, Lysobacter, and Nitrosospira. Overall, this study suggests that balanced fertilization and the application of bio-organic fertilizers are essential to ensure soil fertility and long-term sustainable green productivity.

Concurrent anaerobic chromate bio-reduction and pentachlorophenol bio-degradation in a synthetic aquifer

Chromate [Cr(VI)] and pentachlorophenol (PCP) coexist widely in the environment and are highly toxic to public health. However, whether Cr(VI) bio-reduction is accompanied by PCP bio-degradation and how microbial communities can keep long-term stability to mediate these bioprocesses in aquifer remain elusive. Herein, we conducted a 365-day continuous column experiment, during which the concurrent removals of Cr(VI) and PCP were realized under anaerobic condition. This process allowed for complete Cr(VI) bio-reduction and PCP bio-degradation at an efficiency of 92.8 ± 4.2% using ethanol as a co-metabolic substrate. More specifically, Cr(VI) was reduced to insoluble chromium (III) and PCP was efficiently dechlorinated with chloride ion release. Collectively, Acinetobacter and Spirochaeta regulated Cr(VI) bio-reduction heterotrophically, while Pseudomonas mediated not only Cr(VI) bio-reduction but also PCP bio-dechlorination. The bio-dechlorinated products were further mineralized by Azospira and Longilinea. Genes encoding proteins for Cr(VI) bio-reduction (chrA and yieF) and PCP bio-degradation (pceA) were upregulated. Cytochrome c and intracellular nicotinamide adenine dinucleotide were involved in Cr(VI) and PCP detoxification by promoting electron transfer. Taken together, our findings provide a promising bioremediation strategy for concurrent removal of Cr(VI) and PCP in aquifers through bio-stimulation with supplementation of appropriate substrates.

Effects of biochar on the fate of conazole fungicides in soils and their bioavailability to earthworms and plants

The study showed novel findings about changes in the fate and bioavailability of conazole fungicides (CFs) after biochar (BC) addition to soil. Two contrasting soils (low- and high-sorbing of CF; L soils, H soils) were amended by three BCs (low-, moderate-, and high-sorbing of CF; L-BC, M-BC, H-BC) at 0.2% and 2% doses. Epoxiconazole (EPC) and tebuconazole (TBC) were then added to the soil-BC mixtures, and their degradation, bioaccumulation in earthworms (Eisenia andrei), and bioconcentration in lettuce (Lactuca sativa) were studied for three months. Also, stir bar sorptive extraction (SBSE) was performed to determine CF (bio)accessibility. The EPC and TBC degradation in the soil-BC mixtures followed usually the first-order decay kinetics. The BC addition prevalently decreased the pesticides degradation in the L soil mixtures but often increased it in the H soil mixtures. In general, EPC degraded less than TBC. BC type and dose roles in the pesticides degradation were unclear. The BC addition significantly reduced pesticide uptake to the earthworms in the L soil mixtures (by 37-96%) and in the H soil mixtures (by 6-89%) with 2% BC. The BC addition reduced pesticide uptake to the lettuce roots and leaves significantly-up to two orders of magnitude, and this reduction was strong in H soil mixtures at 2% of BC. The BC addition reduced the CF (bio)accessibility measured by SBSE in all L soil mixtures and some H soil mixtures with 2% BC. Although not significant, it also seems that the pesticide bioaccumulation, bioconcentration, and (bio)accessibility were decreasing according to the BC type (L-BC > M-BC > H-BC). The pesticide concentrations in the earthworms and lettuce correlated significantly to the SBSE results, which indicates this technique as a possible predictor of biotic uptake. Our results showed that the interactions were hard to predict in the complex soil-BC-pesticide system.

Impacts of earthworm casts on atrazine catabolism and bacterial community structure in laterite soil

Atrazine accumulation in agricultural soil is prone to cause serious environmental problems and pose risks to human health. Vermicomposting is an eco-friendly approach to accelerating atrazine biodegradation, but the roles of earthworm cast in the accelerated atrazine removal remains unclear. This work aimed to investigate the roles of earthworm cast in promoting atrazine degradation performance by comprehensively exploring the change in atrazine metabolites and bacterial communities. Our results showed that earthworm cast amendment significantly increased soil pH, organic matters, humic acid, fulvic acid and humin, and achieved a significantly higher atrazine removal efficiency. Earthworm cast addition also remarkably changed soil microbial communities by enriching potential soil atrazine degraders (Pseudomonadaceae, Streptomycetaceae, and Thermomonosporaceae) and introducing cast microbial degraders (Saccharimonadaceae). Particularly, earthworm casts increased the production of metabolites deethylatrazine and deisopropylatrazine, but not hydroxyatrazine. Some bacterial taxa (Gaiellaceaea and Micromonosporaceae) and humus (humic acid, fulvic acid and humin) were strongly correlated with atrazine metabolism into deisopropylatrazine and deethylatrazine, whereas hydroxyatrazine production was benefited by higher pH. Our findings verified the accelerated atrazine degradation with earthworm cast supplement, providing new insights into the influential factors on atrazine bioremediation in vermicomposting.

Combined bioaugmentation and biostimulation techniques in bioremediation of pentachlorophenol contaminated forest soil

Pentachlorophenol (PCP) is quite persistent in the environment and severely affects different ecosystems including forest soil. The main objective of this work was to study different bioremediation processes of artificially PCP (100 mg kg^-1) contaminated forest soil (Sc). In fact, we used bioaugmentation by adding two different bacterial consortia B1 and B2, biostimulation procedures by amendments based on forest compost (FC), municipal solid waste compost (MC), sewage sludge (SS), and phosphate, and their combined treatments. Soil physical and chemical properties, residual PCP, soil microbial biomass carbon, soil respiration and some enzymatic activities at zero time and after 30 d of incubation, were evaluated. A net reduction of PCP, 71% of the initial concentration, after 30 d-incubation occurred in the sample Sc+B1+FC, as the best performance among all treatments, due to natural attenuation, immobilization of PCP molecules in the forest soil through organic amendments, and the action of the exogenous microbial consortium B1. The single application of FC or B1 led to a depletion of PCP concentration of 52% and 41%, respectively. Soil microbial biomass carbon decreased in PCP contaminated soil but it increased when organic amendment also in combination with microbial consortia was carried out as bioremediation action. Soil respiration underwent no changes in contaminated soil and increased under FC based bioremediation treatment. These results demonstrate that the combined treatments of biostimulation and bioaugmentation might be a promising process for remediation of PCP contaminated soil.

Evolution of the earthworm (Eisenia fetida) microbial community in vitro and in vivo under tetracycline stress

Bioremediation of contaminated soil has received increasing attention, and the effects of antibiotic residues on the soil ecological environment are a current research hotspot. Earthworms are the first choice of soil organisms to indicate the degree of soil pollution, and their detoxification mechanism after antibiotic stress must be further explored. Taking Eisenia fetida as the research object, an antibiotic (tetracycline) stress test was carried out in sterile artificial soil. The stress concentrations were set at 0, 0.3, 3, 30, 300 and 600 mg/kg. The ECO method was used to cultivate microbes in earthworms and soil. The carbon source utilization intensity algorithm developed by our team was used for data statistics, and a factor analysis model was constructed to explore the succession process of microbes of earthworms in vivo and in vitro under tetracycline stress. The results showed that there were four processes in the evolution of microbes under short-term tetracycline stress: at 1-3 days, the microbes in worms played a leading role; at 4-5 days, the microbes in the worms and the soil microbes jointly resisted TET stress; after 6-8 days of stress, the microbes in worms still played the main role, but their role was weakened; and after 9-10 days, soil microbes played a leading role, and tolerant microbes appeared. Under long-term stress, the microbes of earthworms in vivo and in vitro were obvious different, and there may be no regulatory relationship. And the factor analysis model is suitable for the analyse of the changes in microbial communities in vivo and in vitro under TET stress. The research results provide a reference method and model basis for the bioremediation of antibiotic-contaminated soil and the study of earthworm detoxification mechanisms, and help agricultural development.

Vermiremediation of engine oil contaminated soil employing indigenous earthworms, Drawida modesta and Lampito mauritii

Engine oil consists of hazardous substances that adversely affect the environment and soil quality. Bioremediation (employing organisms) is an appropriate technique to mitigate engine oil pollution. In the present study, the earthworm species, Drawida modesta (epigeic) and Lampito mauritii (anecic) were used to restore the soil polluted with polycyclic aromatic hydrocarbons (PAHs) and total petroleum hydrocarbons (TPHs) from used engine oil. Four treatments were set up in addition to positive and negative controls. A maximum of 68.6% PAHs and 34.3% TPHs removal in the treatment with soil (1 kg), cow dung (50 g), used engine oil (7.5 mL) and earthworms was recorded after 60 days. Undoubtedly, earthworms effectively removed PAHs and TPHs from the oil-contaminated soil. PAHs were more strongly accumulated in D. modesta (16.25 mg kg^-1) than in L. mauritii (13.25 mg kg^-1). Further, histological analysis revealed the epidermal surface irregularity, cellular disintegration, and cellular debris in earthworms. The pH (6.3%), electrical conductivity (12.7%), and total organic carbon (35.4%) were significantly (at P < 0.05) decreased after 60 days; while, total nitrogen (62%), total potassium (76.2%), and total phosphorus (19.2%) were substantially increased at the end of the experiment. The seed germination assay with fenugreek indicates that germination percentage (95%), and germination index (179), were dramatically increased in earthworm inoculated treatments when compared to the negative control (without earthworms). The results reveal that there is a great scope for utilizing the earthworms, D. modesta and L. mauritii for the bioremediation of soils contaminated with PAHs and TPHs.

Bacterial Succession during Vermicomposting of Silver Wattle (Acacia dealbata Link)

Vermicomposting is the process of organic waste degradation through interactions between earthworms and microbes. A variety of organic wastes can be vermicomposted, producing a nutrient-rich final product that can be used as a soil biofertilizer. Giving the prolific invasive nature of the Australian silver wattle Acacia dealbata Link in Europe, it is important to find alternatives for its sustainable use. However, optimization of vermicomposting needs further comprehension of the fundamental microbial processes. Here, we characterized bacterial succession during the vermicomposting of silver wattle during 56 days using the earthworm species Eisenia andrei. We observed significant differences in α- and β-diversity between fresh silver wattle (day 0) and days 14 and 28, while the bacterial community seemed more stable between days 28 and 56. Accordingly, during the first 28 days, a higher number of taxa experienced significant changes in relative abundance. A microbiome core composed of 10 amplicon sequence variants was identified during the vermicomposting of silver wattle (days 14 to 56). Finally, predicted functional profiles of genes involved in cellulose metabolism, nitrification, and salicylic acid also changed significantly during vermicomposting. This study, hence, provides detailed insights of the bacterial succession occurring during vermicomposting of the silver wattle and the characteristics of its final product as a sustainable plant biofertilizer.

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.

Earthworms accelerated the degradation of the highly toxic acetochlor S-enantiomer by stimulating soil microbiota in repeatedly treated soils

This study investigated the effects of earthworms on the enantioselective degradation of chloroacetamide herbicide acetochlor with soil microorganisms in repeatedly treated soils. The S-enantiomer degraded more slowly and exerted stronger inhibition on soil microbial functions than the R-enantiomer in single soil system. A synergistic effect was observed between soil microorganisms and earthworms that accelerated the degradation of both the enantiomers, particularly the highly toxic S-enantiomer, which resulted in the preferential degradation of S-enantiomer in soil-earthworm system. Earthworms stimulated five potential indigenous degraders (i.e. Lysobacter, Kaistobacter, Flavobacterium, Arenimonas, and Aquicell), induced two new potential degraders (i.e. Aeromonas and Algoriphagus), and also significantly strengthened the correlations among these seven dominant potential degraders and other microorganisms. Notably, the relative abundances of Flavobacterium and Aeromonas in soil treated with earthworms for S-enantiomer were higher than those for R-enantiomer. Furthermore, earthworms significantly stimulated overall soil microbial activity and improved three microbial metabolic pathways, and xenobiotics biodegradation and metabolism, signal transduction, cell motility, particularly for the S-enantiomer treatment with earthworms, which alleviated the strong inhibition of S-enantiomer on microbial community functions. This study confirmed that earthworms accelerated the degradation of the highly toxic acetochlor S-enantiomer in soil, providing a potential approach in chloroacetamide herbicide-polluted soil remediation.

Accelerated atrazine degradation and altered metabolic pathways in goat manure assisted soil bioremediation

The intensive and long-term use of atrazine in agriculture has resulted in serious environmental pollution and consequently endangered ecosystem and human health. Soil microorganisms play an important role in atrazine degradation. However, their degradation efficiencies are relatively low due to their slow growth and low abundance, and manure amendment as a practice to improve soil nutrients and microbial activities can solve these problems. This study investigated the roles of goat manure in atrazine degradation performance, metabolites and bacterial community structure. Our results showed that atrazine degradation efficiencies in un-amended soils were 26.9-35.7% and increased to 60.9-84.3% in goat manure amended treatments. Hydroxyatrazine pathway was not significantly altered, whereas deethylatrazine and deisopropylatrazine pathways were remarkably enhanced in treatments amended with manure by encouraging the N-dealkylation of atrazine side chains. In addition, goat manure significantly increased soil pH and contents of organic matters and humus, explaining the change of atrazine metabolic pathway. Nocardioides, Sphingomonas and Massilia were positively correlated with atrazine degradation efficiency and three metabolites, suggesting their preference in atrazine contaminated soils and potential roles in atrazine degradation. Our findings suggested that goat manure acts as both bacterial inoculum and nutrients to improve soil microenvironment, and its amendment is a potential practice in accelerating atrazine degradation at contaminated sites, offering an efficient, cheap, and eco-friendly strategy for herbicide polluted soil remediation.

Removal of chlortetracycline and antibiotic resistance genes in soil by earthworms (epigeic Eisenia fetida and endogeic Metaphire guillelmi)

The impacts of two ecological earthworms on the removal of chlortetracycline (CTC, 0.5 and 15 mg kg^-1) and antibiotic resistance genes (ARGs) in soil were explored through the soil column experiments. The findings showed that earthworm could significantly accelerate the degradation of CTC and its metabolites (ECTC) in soil (P < 0.05), with epigeic Eisenia fetida promoting degradation rapidly and endogeic Metaphire guillelmi exhibiting a slightly better elimination effect. Earthworms alleviated the abundances of tetR, tetD, tetPB, tetG, tetA, sul1, TnpA, ttgB and intI1 in soil, with the total relative abundances of ARGs decreasing by 35.0-44.2% in earthworm treatments at the 28th day of cultivation. High throughput sequencing results displayed that the structure of soil bacteria community was modified apparently with earthworm added, and some possible CTC degraders, Aeromonas, Flavobacterium and Luteolibacter, were promoted by two kinds of earthworms. Redundancy analysis demonstrated that the reduction of CTC residues, Actinobacteria, Acidobacteria and Gemmatimonadetes owing to earthworm stimulation was responsible for the removal of ARGs and intI1 in soil. Additionally, intI1 declined obviously in earthworm treatments, which could weaken the risk of horizontal transmission of ARGs. Therefore, earthworm could restore the CTC-contaminated soil via enhancing the removal of CTC, its metabolites and ARGs.

Conazole fungicides epoxiconazole and tebuconazole in biochar amended soils: Degradation and bioaccumulation in earthworms

Biochar usage in agriculture becomes increasingly important for the improvement of soil properties. However, from the perspective of pesticides, biochar can influence exposure to pesticides of both target and non-target organisms and also pesticides' fate in soil. Our study investigated degradation and bioaccumulation (in the Eisenia andrei earthworm) of two conazole fungicides, epoxiconazole and tebuconazole, added to high- and low-sorbing soils (by means of fungicides' sorption measured beforehand) amended with low-, moderate- and high-sorbing biochars at 0.2% and 2% doses. We aimed to investigate the effects of contrasting soil and biochar properties, different doses of biochar in soil-biochar mixtures, and different compounds on the degradation and bioaccumulation. We also wanted to explore if the beforehand determined sorption of fungicides on individual soils and biochars is manifested somehow in their degradation and/or bioaccumulation in soil-biochar mixtures. The biochars' presence in the soils promoted the degradation of fungicides with a clear effect of dose and soil, but less clear effect of biochar or compound. The bioaccumulation factors were higher in low-sorbing soil variants and also decreased with increasing biochar dose. For low-sorbing soil variants, the bioaccumulation was also influenced by the type of biochar corresponding to its sorbing potential and the possible effect on the bioavailability of the fungicides. Our results show that mixing of biochars with soils changes the fate and bioaccumulation of the conazole fungicides. However, the sorption results from original materials are not straightforwardly manifested in the more complex soil-biota system.

Effects of two ecological earthworm species on tetracycline degradation performance, pathway and bacterial community structure in laterite soil

This study explored the change of tetracycline degradation efficiency, metabolic pathway, soil physiochemical properties and degraders in vermiremediation by two earthworm species of epigeic Eisenia fetida and endogeic Amynthas robustus. We found a significant acceleration of tetracycline degradation in both earthworm treatments, and 4-epitetracycline dehydration pathway was remarkably enhanced only by vermiremediation. Tetracycline degraders from soils, earthworm intestines and casts were different. Ralstonia and Sphingomonas were potential tetracycline degraders in soils and metabolized tetracycline through direct dehydration pathway. Degraders in earthworm casts (Comamonas, Acinetobacter and Stenotrophomonas) and intestines (Pseudomonas and Arthrobacter) dehydrated 4-epitetracycline into 4-epianhydrotetracycline. More bacterial lineages resisting tetracycline were found in earthworm treatments, indicating the adaptation of soil and intestinal flora under tetracycline pressure. Earthworm amendment primarily enhanced tetracycline degradation by neutralizing soil pH and consuming organic matters, stimulating both direct dehydration and epimerization-dehydration pathways. Our findings proved that vermicomposting with earthworms is effective to alter soil microenvironment and accelerate tetracycline degradation, behaving as a potential approach in soil remediation at tetracycline contaminated sites.

Ecological improvement of antimony and cadmium contaminated soil by earthworm Eisenia fetida: Soil enzyme and microorganism diversity

Vermiremediation on improvement of antimony (Sb) and cadmium (Cd) contaminated soil was less reported. In this study, earthworm Eisenia fetida was exposed into soil spiked with Sb and Cd and their mixture for 30 days, and then we measured multiple soil enzyme activities and bacteria communities via enzymatic reaction and high-throughput sequencing of 16 S rRNA genes. The results showed that Sb and Cd at high treatment levels inhibited the activities of urease, neutral phosphatase and protease significantly, but earthworm could promote the activities of urease and neutral phosphatase by 17.75%-121.91% and 1.46%-118.97%, respectively. However, earthworms inhibited catalase and had no effect on protease. The Geometric Mean Index suggested that earthworms led to a higher soil biochemistry function. According to a taxonomic analysis, bacterial community structure predominantly consisted of phylum Proteobacteria, Actinobacteria, Firmicutes, etc. and class Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, etc.; furthermore, Pielou index and Shannon index (Alpha diversity in the habitat) indicated that bacteria diversity and evenness increased in the presence of earthworms. The heating map revealed that earthworms made genus Sphingomonas, Flavobacterium, etc. and species Sphingomonas jaspsi, Conexibacter, etc. dominate. Overall, earthworm is a suitable remediation species to improve the ecological function of heavy metal polluted soil. However, the specific mechanism and causal relationship of how earthworm to control enzyme activity and bacteria community remained to be explored.

Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus

Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.

Different acetonitrile degraders and degrading genes between anaerobic ammonium oxidation and sequencing batch reactor as revealed by stable isotope probing and magnetic-nanoparticle mediated isolation

Microbial degraders play crucial roles in wastewater treatment processes, but their use is limited as most microbes are yet unculturable. Stable isotope probing (SIP) is a cultivation-independent technique identifying functional-yet-uncultivable microbes in ambient environment, but is unsatisfactory for substrates with low assimilation rate owing to the low isotope incorporation into DNA. In this study, we used acetonitrile as the target low-assimilation chemical in many wastewater treatment plants and attempted to identify the active acetonitrile degraders in the activated sludge, via DNA-SIP and magnetic-nanoparticle mediated isolation (MMI) which is another cultivation-independent approach without the requirement of substrate labeling. The two approaches identified different active acetonitrile degraders in a 3-day short-term anaerobic ammonium oxidation (ANAMMOX). MMI enriched significantly more acetonitrile-degraders than SIP, showing the advantages in identifying the active degraders for low-assimilation substrates. Sequencing batch reactor (SBR, 30-day degradation) helped in more incorporation of ¹⁵N-labeled acetonitrile into the active degraders, thus the same acetonitrile-degraders and acetonitrile-degrading genes were identified by SIP and MMI. Different acetonitrile degraders between ANAMMOX and SBR were attributed to the distinct hydrological conditions. Our study for the first time explored the succession of acetonitrile-degraders in wastewater and identified the active acetonitrile-degraders which could be further enriched for enhancing acetonitrile degradation performance. These findings provide new insights into the acetonitrile metabolic process in wastewater treatment plants and offer suggestive conclusions for selecting appropriate treatment strategy in wastewater management.

Tri-n-butyl phosphate induced earthworm intestinal damage by influencing nutrient absorption and energy homeostasis of intestinal epithelial cells

Tri-n-butyl phosphate (TnBP) is a typical alkyl organophosphate ester that has been used for decades in various products. However, toxicity on terrestrial organisms induced by TnBP has been rarely reported though soil is a predominant sink for hydrophobic organic compounds. The objective of this study was to investigate the TnBP-induced intestinal toxicity mechanism on earthworm Eisenia fetida as well as the potential role of gut bacteria on host's health. TnBP was found to have high bioconcentrations in earthworm intestinal tract. Digestive tract degradation and digestive enzyme activities disruption associated with nutrients absorption were noticed. Using multi-omics approaches, detailed intestinal toxic mechanism of earthworms under TnBP exposure was provided. Tight junctions between small intestinal epithelial cells and osmotic equilibrium were destroyed under 10 mg/kg TnBP, leading to nutrient absorption disturbance. To satisfy the excessive energy requirements induced by TnBP, amino acids gluconeogenesis and protein degradation were detected. Moreover, TnBP significantly decreased the diversity of gut microbiota and changed their structure and function involved in hosts' health and nutrients supply. Overall, this study provides insight into the molecular mechanism of intestinal toxicity by which earthworms respond to TnBP exposure and offer important information for risk assessment of organophosphate esters on soil ecosystems.

Earthworm Eisenia andrei modulates oxidative stress in bean plants Vicia faba irrigated with treated wastewater

With respect to reducing the pressure on freshwater resources, treated wastewater (TWW) irrigation represents a sustainable alternative in agriculture. Due to their low quality and variable composition, TWW could entail harmful consequences for living organisms in terrestrial ecosystems. This study aims to evaluate how earthworm (Eisenia andrei) can modulate oxidative stress in bean plants (Vicia faba) that are irrigated over a course of 60 days with two doses of TWW (50 and 100%) in addition to a control condition (0%) irrigated with distilled water. This is achieved by measuring glutathione-S-transferase (GST) activity and malondialdehyde accumulation (MDA) in plants. Furthermore, catalase (CAT), GST, MDA, and acetylcholinesterase (AChE) activities of the earthworms are also assessed. Our results show that growth and physiological parameters are modified when applying TWW irrigation. Moreover, oxidative stress apprehended by GST activity and MDA accumulation is exacerbated in V. faba plants after exposure to increased TWW doses. Similarly, TWW irrigation enhances oxidative stress parameters in earthworms with a crucial decrease in AChE activity. In addition, the presence of earthworms increases growth and physiological parameters; it also results in a significant reduction in GST activity and MDA rate in V. faba plants. Our results provide new insights into the impact of TWW irrigation on soil organisms and the importance of earthworms in the reduction of oxidative stress in plants.

Sub-Lethal Effects of Pesticides on the DNA of Soil Organisms as Early Ecotoxicological Biomarkers

This review describes the researches performed in the last years to assess the impact of pesticide sub-lethal doses on soil microorganisms and non-target organisms in agricultural soil ecosystems. The overview was developed through the careful description and a critical analysis of three methodologies based on culture-independent approaches involving DNA extraction and sequencing (denaturing gradient gel electrophoresis, DGGE; next-generation sequencing, NGS) to characterize the microbial population and DNA damage assessment (comet assay) to determine the effect on soil invertebrates. The examination of the related published articles showed a continuous improvement of the possibility to detect the detrimental effect of the pesticides on soil microorganisms and non-target organisms at sub-lethal doses, i.e., doses which have no lethal effect on the organisms. Considering the overall critical discussion on microbial soil monitoring in the function of pesticide treatments, we can confirm the usefulness of PCR-DGGE as a screening technique to assess the genetic diversity of microbial communities. Nowadays, DGGE remains a preliminary technique to highlight rapidly the main differences in microbial community composition, which is able to give further information if coupled with culture-dependent microbiological approaches, while thorough assessments must be gained by high-throughput techniques such as NGS. The comet assay represents an elective technique for assessing genotoxicity in environmental biomonitoring, being mature after decades of implementation and widely used worldwide for its direct, simple, and affordable implementation. Nonetheless, in order to promote the consistency and reliability of results, regulatory bodies should provide guidelines on the optimal use of this tool, strongly indicating the most reliable indicators of DNA damage. This review may help the European Regulation Authority in deriving new ecotoxicological endpoints to be included in the Registration Procedure of new pesticides.

Characteristics of Soil Moisture and Evaporation under the Activities of Earthworms in Typical Anthrosols in China

Earthworms have an important influence on the terrestrial ecological environment. This study assesses the effect of different earthworm densities on soil water content (SWC) and evaporation in a laboratory experiment. Four earthworm densities (0 no-earthworm, control [C]; 207 earthworms m−2, low density [LDE]; 345 earthworms m−2, medium density [MDE]; and 690 earthworms m−2, high density [HDE]) are tested in soil columns. Results show that cumulative evaporation occurs in the decreasing order of densities: C (98.6 mm) > LDE (115.8 mm) > MDE (118.4 mm) > HDE (124.6 mm). Compared with the control, earthworm activity decreases cumulative soil evaporation by 5.0–20.9%, increases soil temperature to 0.46 °C–0.63 °C at 8:00, and decreases soil temperature to 0.21 °C–0.52 °C at 14:00 on the soil surface. Temperature fluctuations reduce with increasing earthworm densities. A negative correlation is found between cumulative soil evaporation and earthworm density (R2 = 0.969, p < 0.001). Earthworms significantly (p < 0.05) decrease the surface SWC loss (0–20 cm) soil layer but increase the subsoil SWC loss (60–100 cm) by adjusting the soil temperature and reducing soil water evaporation. Earthworm activities (burrows, casts…) improve the soil water holding ability by adjusting soil temperature and reducing soil water evaporation. Thus, the population quantity of earthworms may provide valuable ecosystem services in soil water and heat cycles to save water resources and realize sustainable agricultural development.

Assessment of earthworm activity on Cu, Cd, Pb and Zn bioavailability in contaminated soils using biota to soil accumulation factor and DTPA extraction

The study aims to investigate effect of earthworm activity on metal bioavailability in soils using their BSAF-metals. Based on a microcosmic laboratory experiment, epigeic species Amynthas corticis (A. corticis) and endogeic species Amynthas robustus (A. robustus) were cultured in two types of soils contaminated by Cd, Zn, Pb and Cu for 120 days. Earthworm characteristics (i.e. numbers, biomass and BSAF), soil properties (i.e. pH, organic C and N contents along with their components such as mineralization and microbial masses) and DTPA extracted metals in soil were determined. After the incubation, the biomass and survival numbers of both earthworm species decreased significantly (P < 0.05). The accumulation of Cd, Zn and Pb in earthworm tissues and BSAF-metals were earthworm species dependent. According to two-way ANOVA, BSAF-Pb clearly showed the effect of different species of earthworms while BSAF-Cu indicated an interactive effect of earthworms and soil type. Earthworms changed soil properties significantly, especially for mineralized C (C_min), dissolved N (N_dis) and pH (P < 0.05). Earthworm activity increase DTPA extracted Zn and Cu, and the effect of A. robustus were stronger than for A. corticis. Redundancy analysis (RDA) showed that BSAF-Cu and BSAF-Pb contributed for respectively 51.9% and 51.7% of soil properties and DTPA metal changes, indicating that the effects of BSAF-Cu and BSAF-Pb on soil properties and on metal bioavailability in soil were similar. BSAF-Cu, indicating the interactive effect of earthworms and soil, accounted for 38.5% and 45.1% of soil properties and soil metal bioavailability changes. BSAF-Pb, representing the effect of earthworm species, accounted for 13.3% and 6.6% of soil property and soil metal bioavailability variations. Stepwise regression indicated that earthworm might change soil properties through their activities and interactions with soil, and hence increase heavy metal bioavailability. It suggested that BSAF is an important indicator for evaluating the effect of earthworm activity on soil metal bioavailability and designing remediation strategies.

Soil Microbiome Response to Contamination with Bisphenol A, Bisphenol F and Bisphenol S

The choice of the study objective was affected by numerous controversies and concerns around bisphenol F (BPF) and bisphenol S (BPS)—analogues of bisphenol A (BPA). The study focused on the determination and comparison of the scale of the BPA, BPF, and BPS impact on the soil microbiome and its enzymatic activity. The following parameters were determined in soil uncontaminated and contaminated with BPA, BPF, and BPS: the count of eleven groups of microorganisms, colony development (CD) index, microorganism ecophysiological diversity (EP) index, genetic diversity of bacteria and activity of dehydrogenases (Deh), urease (Ure), catalase (Cat), acid phosphatase (Pac), alkaline phosphatase (Pal), arylsulphatase (Aryl) and β-glucosidase (Glu). Bisphenols A, S and F significantly disrupted the soil homeostasis. BPF is regarded as the most toxic, followed by BPS and BPA. BPF and BPS reduced the abundance of Proteobacteria and Acidobacteria and increased that of Actinobacteria. Unique types of bacteria were identified as well as the characteristics of each bisphenol: Lysobacter, Steroidobacter, Variovorax, Mycoplana, for BPA, Caldilinea, Arthrobacter, Cellulosimicrobium and Promicromonospora for BPF and Dactylosporangium Geodermatophilus, Sphingopyxis for BPS. Considering the strength of a negative impact of bisphenols on the soil biochemical activity, they can be arranged as follows: BPS > BPF > BPA. Urease and arylsulphatase proved to be the most susceptible and dehydrogenases the least susceptible to bisphenols pressure, regardless of the study duration.

Earthworms offset straw-induced increase of greenhouse gas emission in upland rice production

Increasing water scarcity and rapid socio-economic development are driving farmers in Asia to transform traditionally flooded rice cropping systems into non-flooded crop production. The management of earthworms in non-flooded rice fields appears to be a promising strategy to support residue recycling and mitigate greenhouse gas (GHG) emissions triggered by residue amendment. We conducted a field experiment on non-flooded rainfed rice fields, with and without residue amendment. In-situ mesocosms were inoculated with endogeic earthworms (Metaphire sp.), with either low (ET1: 150 individuals m^-2), or high density (ET2: 450 individuals m^-2), and a control (ET0: no earthworms). We measured GHG emissions (methane (CH₄); nitrous oxide (N₂O); carbon dioxide (CO₂)) twice a week during the cropping season with static chambers. Effects of earthworms on yield and root growth were additionally assessed. Earthworms offset the enormous increase of CH₄ emissions induced by straw amendment (from 4.6 ± 5 to 75.3 ± 46 kg CH₄-C ha^-1 in ET0). Earthworm activity significantly reduced CH₄ release, particularly at ET2, by more than one-third (to 22 ± 15 kg CH₄-C ha^-1). In contrast, earthworm inoculation did not affect N₂O emission. Straw amendment more than doubled the global warming potential (GWP). Earthworms reduced GWP by 39% at low (ET1) and 55% at high densities (ET2). Earthworm activity reduced root mass density under conditions of straw amendment but did not affect yield. Earthworms can significantly reduce detrimental effects of rice crop residue amendment on GHG release under upland rice production. Organic carbon (C) might be preserved in earthworm casts and thereby limit C availability for CH₄ production. At the same time, earthworm activity might increase methanotrophic CH₄ consumption, due to improved soil aeration or less root exudates. Consequently, earthworms have a strong potential for regulating ecosystem functions related to rice straw decomposition, nutrient allocation and thus GHG reduction.

Response of soil bacterial and fungal community structure succession to earthworm addition for bioremediation of metolachlor

Synergistic biodegradation of earthworms and soil microorganisms plays a key role in the removal of organic pollutants in soil, yet microbially mediated processes remain unclear, especially regarding the succession of soil microbial interactions. Herein, soil biochemical evaluation, microbial community characterization, and interaction network construction were combined to understand the mechanisms dominating microbial community succession during synergistic bioremediation of metolachlor-polluted soils. The results of the network analysis indicated that metolachlor could render more complex relations but weaker connection strength among soil microorganisms. The addition of earthworms significantly alleviated the stress of metolachlor on soil microbial interactions and resulted in the restoration of interactions to a great extent. Additionally, the soil physicochemical properties, enzyme activities, and microbial community changed greatly with the addition of metolachlor and earthworms. Some soil microorganisms became significantly correlated with soil properties, metolachlor concentrations, and enzyme activities. These results, dominated by the succession of soil microbial communities, provide a new perspective for assessing the remediation effect of contaminated soil by organic pollutants.

Assembly of root-associated microbiomes of typical rice cultivars in response to lindane pollution

Organochlorine pesticides have been extensively used for many years to prevent insect diseases of rice (Oryza sativa L.), but little is known about their residual impacts on the underground micro-ecology in anaerobic environment. In this glasshouse study, we characterized the lindane effects on the assembly of root-associated microbiomes of commonly used indica, japonica and hybrid rice cultivars, and their feedback in turn, in modifying lindane anaerobic dissipation during 60 days' rice production. The results showed that rice growth inhibited the anaerobic dissipation of lindane, but was not affected apparently by lindane at initial spiked concentration of 4.62 and 18.54 mg kg^-1 soil. Suppressed removal of lindane in rice planted treatments as compared with that in unplanted control was likely due to inhibited reductive dechlorination induced by a comprehensive effect of radial O₂ secretion of rice root and co-occurring Fe(III) reduction that consumed electron competitively in rice rhizosphere. However, the hybrid cultivar exhibited a less suppression than the conventional cultivars in high polluted soils. Bacteria was more sensitively responded to lindane pollution than fungal taxa, and Actinobacteria, Chloroflexi, Verrucomicrobia and Proteobacteria were the main different phyla between hybrid and conventional cultivars, with a more stable community structure exhibited in the hybrid rice under lindane stress. Our study highlights the assembly and variation of root-associated microbiomes in responses of lindane pollution, and suggests that hybrid rice cultivar might be most competent for cultivation in paddy fields polluted by lindane and other organochlorine pesticides, especially in the area with high residual levels.

Enhanced remediation of bispyribac sodium by wheat (Triticum aestivum) and a bispyribac sodium degrading bacterial consortium (BDAM)

The use of plant-bacterial association is a promising approach for the enhanced remediation of pesticides. Generally, both rhizo- and endosphere bacteria assist their host plants to survive in the contaminated environment. In this work, we have studied the individual and combined effects of wheat (Triticum aestivum) and a previously optimized bispyribac sodium (BS) degrading bacterial consortium (BDAM) on the degradation of BS and plant biomass production. Results showed that the bacterial strains of the BDAM have successfully survived in the plant rhizo-as well as endosphere and enhanced degradation of BS and plant biomass. In soil spiked with 2 mg/kg and 5 mg/kg of BS and was planted and inoculated with BDAM (P_I) showed 100% degradation of BS both in rhizosphere soil and endosphere of the plant. However, during the same period (45 days) the degradation of BS was 96 and 90%, and 93 and 84% in inoculated but un-planted (I_UP) and planted but un-inoculated (P_UI) soils spiked with 2 and 5 mg/kg, respectively. Liquid chromatography-mass spectrometry (LC-MS) analysis of the treated samples showed novel degradation products of BS. Based on the results, we concluded that plant-bacterial association is an efficient tool for enhanced remediation of BS contaminated soil and herbicide free crop production.

Nitrate addition promotes the nitrogen cycling processes under the co-contaminated tetrabromobisphenol A and copper condition in river sediment

Tetrabromobisphenol A (TBBPA) and copper (Cu) are the main pollutants at e-waste recycling sites and the effects of their biotoxicity on microorganisms have drawn extensive attention. Nitrate-based bioremediation has been applied to organic pollutant-contaminated sediments since nitrate is a favorable electron acceptor for microbes. However, the effects of TBBPA and Cu on nitrogen (N)-cycling microorganisms and bioremediation in co-contaminated sediments remain unclear. Thus, our study examined the effects of TBBPA and Cu with/without nitrate addition on the TBBPA biodegradation efficiencies, microbial activities, and N functional genes. It was found the biodegradation efficiencies of TBBPA were improved by the nitrate addition from 34.7% to 59.3% and from 22.6% to 42.8% in the TBBPA and TBBPA-Cu contaminated groups, respectively. The inhibitions of the catalase activity increased with the nitrate addition because of the anaerobic respiration of the microorganisms. In addition, the potential denitrification rate exhibited an increasing trend from 6.46 to 8.23 mg-N kg^-1 dry sediment day^-1 during the period of 15-90 days after adding nitrate to the co-contaminated group, whereas the potential nitrification rate exhibited an opposite trend and decreased from 4.47 to 3.19 mg-N kg^-1 dry sediment day^-1. The denitrification gene abundances of the N-cycling genes were 10⁷-10⁸ orders of magnitude higher and significantly increased in the nitrate addition groups. The amoA gene abundances were lower than the denitrification gene abundances and were 10⁵-10⁶ orders of magnitude in the same groups. Moreover, the interaction types of the pollutants on the gene abundances were changed from synergistic to antagonistic as nitrate addition. Our study emphasized the gap of knowledge on nitrate addition affecting N-cycling microbes in the combined pollutants exposure sediments, and will be helpful for further bioremediation in different contaminated scenarios.

Stimulation of earthworms (Eisenia fetida) on soil microbial communities to promote metolachlor degradation

Degradation of metolachlor in surface soil is extremely important to its potential mobility and overall persistence. In this study, the effects of earthworms (Eisenia fetida) on the degradation of metolachlor at two concentration levels (5 and 20 mg kg^-1) in soil were investigated via the column experiment. The degradation kinetics of metolachlor indicate that addition of earthworms enhances metolachlor degradation significantly (P < 0.05), with the enhanced degradation rate of 30% and 63% in the low and high concentration treatments at the 15th day, respectively. Fungi rather than bacteria are primarily responsible for metolachlor degradation in soil, and earthworms stimulate metolachlor degradation mainly by stimulating the metolachlor-degrading functional microorganisms and improving fungal community structure. Earthworms prefer to promote the possible fungal degraders like order Sordariales, Microascales, Hypocreales and Mortierellales and the possible bacteria genus Rubritalea and strengthen the relationships between these primary fungi. Two metabolites metolachlor oxanilic (MOXA) and moetolachlor ethanesulfonic acid (MESA) are detected in soil and earthworms in the high concentration treatments. Earthworms stimulate the formation of MOXA and yet inhibit the formation of MESA in soil. Another metabolite metolachlor-2-hydroxy (M2H) is also detected in earthworms, which is reported firstly. The study provides an important information for the remediation of metolachlor-polluted soil.

Changes in atrazine speciation and the degradation pathway in red soil during the vermiremediation process

Atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) is a triazine herbicide intensively used in agricultural production and is often detected in different environmental matrices at concentrations above the permitted limit. This study investigated the influence of two earthworm species (epigeic Eisenia foetida and endogeic Amynthas robustus) on atrazine speciation and the degradation pathway. Our results revealed that both earthworms significantly accelerated atrazine degradation in a 28-day vermiremediation, and the residual atrazine declined from 4.23 ± 0.21 mg/kg in bulk soils to 0.51 ± 0.29 mg/kg (E. foetida) and 0.43 ± 0.19 mg/kg (A. robustus). By consuming organic matter (from 40.37 ± 1.14 to 36.31 ± 1.55 and 34.59 ± 1.13 g/kg for E. foetida and A. robustus) and neutralizing the soil pH (from 5.37 ± 0.27 to 6.36 ± 0.11 and 6.61 ± 0.30 for E. foetida and A. robustus), both earthworms reduced humus-fixed atrazine and increased the available atrazine. The percentage of available atrazine increased from 8.80 ± 0.21% in bulk soil to 10.30 ± 0.29% and 16.42 ± 0.18% in the vermiremediation treatments. Both earthworms promoted the hydroxyatrazine pathway by consuming soil organic matter and encouraged the deethylatrazine/deisopropylatrazine pathway by neutralizing the soil pH. Our findings unravel a new mechanism of vermiremediation by improving the soil physical-chemical properties and altering the atrazine degradation pathway, providing new insights into the influential factors on atrazine bioremediation in red soil.

Monitoring the Activated Sludge Activities Affected by Industrial Toxins via an Early-Warning System Based on the Relative Oxygen Uptake Rate (ROUR) Index

Shock load from industrial wastewater is known to harm the microbial activities of the activated sludge in wastewater treatment plants (WWTPs) and disturb their performance. This study developed a system monitoring the activated sludge activities based on the relative oxygen uptake rate (ROUR) and explored the influential factors with wastewater and the activated sludge samples collected from a typical WWTP in the Taihu Lake of southern Jiangsu province, China. The ROUR was affected by the concentration of toxic substances, mixed liquid suspended solids (MLSS), hydraulic retention time (HRT) and pH. Higher toxin contents significantly decreased the ROUR and the EC50 value of Zn2+, Ni2+, Cr(VI), Cu2+, and Cd2+ was 13.40, 15.54, 97.56, 12.01, and 14.65 mg/L, respectively. The ROUR declined with the increasing HRT and MLSS above 2000 mg/L had buffering capacities for the impacts of toxic substances to some extent. The ROUR remained stable within a broad range pH (6–10), covering most of the operational pH in WWTPs and behaving as an appropriate indicator for monitoring the shock load. A toxicity model assessing and predicting the ROUR was developed and fitted well with experimental data. Coupling the ROUR monitoring system and toxicity model, an online early-warning system was assembled and successfully used for predicting the toxicity of different potential toxic metals. This study provides a new universal toxicity model and an online early-warning system for monitoring the shock load from industrial wastewater, which is useful for improving the performance of WWTPs.

Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum

Pentachlorophenol (PCP) is a highly toxic pesticide that was first introduced in the 1930s. The alphaproteobacterium Sphingobium chlorophenolicum, which was isolated from PCP-contaminated sediment, has assembled a metabolic pathway capable of completely degrading PCP. This pathway produces four toxic intermediates, including a chlorinated benzoquinone that is a potent alkylating agent and three chlorinated hydroquinones that react with O2 to produce reactive oxygen species (ROS). RNA-seq analysis revealed that PCP causes a global stress response that resembles responses to proton motive force uncoupling and membrane disruption, while surprisingly, little of the response resembles the responses expected to be produced by the PCP degradation intermediates. Tn-seq was used to identify genes important for fitness in the presence of PCP. By comparing the genes that are important for fitness in wild-type S. chlorophenolicum and a non-PCP-degrading mutant, we identified genes that are important only when the PCP degradation intermediates are produced. These include genes encoding two enzymes that are likely to be involved in protection against ROS. In addition to these enzymes, the endogenous levels of other enzymes that protect cells from oxidative stress appear to mitigate the toxic effects of the chlorinated benzoquinone and hydroquinone metabolites of PCP. The combination of RNA-seq and Tn-seq results identify important mechanisms for defense against the toxicity of PCP. IMPORTANCE Phenolic compounds such as pentachlorophenol (PCP), triclosan, and 2,4-dichlorophenoxyacetic acid (2,4-D) represent a common class of anthropogenic biocides. Despite the novelty of these compounds, many can be degraded by microbes isolated from contaminated sites. However, degradation of this class of chemicals often generates toxic intermediates, which may contribute to their recalcitrance to biodegradation. We have addressed the stresses associated with degradation of PCP by Sphingobium chlorophenolicum by examining the transcriptional response after PCP exposure and identifying genes necessary for growth during both exposure to and degradation of PCP. This work identifies some of the mechanisms that protect cells from this toxic compound and facilitate its degradation. This information could be used to engineer strains capable of improved biodegradation of PCP or similar phenolic pollutants.

Rhizospheric effects on atrazine speciation and degradation in laterite soils of Pennisetum alopecuroides (L.) Spreng

Atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) is a worldwide-used herbicide and often detected in agricultural soils and groundwater at concentrations above the permitted limit, because of its high mobility, persistence, and massive application. This study applied pot experiments to investigate the atrazine contents and speciation during the phytoremediation process by Pennisetum alopecuroides (L.) Spreng. in laterite soils. From the change of the total atrazine and bioavailable atrazine measured by diffusive gradients in thin film (DGT), P. alopecuroides significantly improved atrazine degradation efficiency from 15.22 to 51.46%, attributing to the increasing bioavailable atrazine in rhizosphere. Only a small amount of atrazine was taken up by P. alopecuroides root and the acropetal translocation from roots to shoots was limited. The atrazine speciation was significantly different between rhizosphere and non-rhizosphere, attributing to the declining pH and organic matters in rhizosphere. The relationship between pH and soil-bound/humus-fixed atrazine illustrated the pH-dependant release of the atrazine from soils and the competition between humus adsorption and uptake by P. alopecuroides. The present study reveals the important roles of soil pH and organic matters in atrazine speciation and availability in laterite soils, and provides new insights in the rhizospheric effects on effective phytoremediation of atrazine.

Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil

Vermicomposting is an effective and environmentally friendly approach for eliminating soil organic contamination. Atrazine is one of the most commonly applied triazinic herbicides and frequently detected in agricultural soils. This study investigated the roles and mechanisms of two earthworm species (epigeic Eisenia foetida and endogeic Amynthas robustus) in microbial degradation of atrazine. Both earthworms accelerated atrazine degradation performance from 39.0% in sterile soils to 94.9%-95.7%, via neutralizing soil pH, consuming soil humus, altering bacterial community structure, enriching indigenous atrazine degraders and excreting the intestinal atrazine-degrading bacteria. Rhodoplanes and Kaistobacter were identified as soil indigenous degraders for atrazine mineralization and stimulated by both earthworm species. A. robustus excreted the intestinal Cupriavidus and Pseudomonas, whereas Flavobacterium was released by E. foetida. This study provides a comprehensive understanding of the distinct effects of two earthworm species on soil microbial community and atrazine degradation, offering technical supports to apply vermicomposting in effective soil bioremediation.

Hyphospheric impacts of earthworms and arbuscular mycorrhizal fungus on soil bacterial community to promote oxytetracycline degradation

A two-compartment microcosm was used to investigate the role of arbuscular mycorrhizal fungus (AMF) hyphae and earthworm in altering soil microbial community and OTC degradation. Treatments comprised OTC-contaminated hyphal compartments with or without AMF hyphae and with or without earthworms. Results indicated both AMF hyphae and earthworms accelerated OTC degradation; two degradation products were identified as 4-epi-oxytetracycline (EOTC) and 2-acetyl-2-decarboxamido-oxytetracycline (ADOTC). Q-PCR results indicated that both earthworms and AMF hyphae increased 16s rDNA gene, enhancing OTC degradation consequently. Illumina sequencing of the 16S rRNA genes showed that AMF hyphae and earthworm altered bacterial community. Earthworms stimulated the growth of class Anaerolineae, family Flavobacteriaceae, Genus Pseudomonas, reducing OTC residues. AMF hyphae significantly increased the abundance of family Pirellulaceae, genus Glycomyces, and Nonomuraea which had a negative correlation with EOTC, accelerating OTC degradation. When used together, AMF hyphae and earthworms enhanced OTC degradation by stimulating class Anaerolineae and family Flavobacteriaceae.

Advanced technologies for the remediation of pesticide-contaminated soils

The occurrence of pesticides in soil has become a highly significant environmental problem, which has been increased by the vast use of pesticides worldwide and the absence of remediation technologies that have been tested at full-scale. The aim of this review is to give an overview on technologies really studied and/or developed during the last years for remediation of soils contaminated by pesticides. Depending on the nature of the decontamination process, these techniques have been included into three categories: containment-immobilization, separation or destruction. The review includes some considerations about the status of emerging technologies as well as their advantages, limitations, and pesticides treated. In most cases, emerging technologies, such as those based on oxidation-reduction or bioremediation, may be incorporated into existing technologies to improve their performance or overcome limitations. Research and development actions are still needed for emerging technologies to bring them for full-scale implementation.

Earthworms (Eisenia fetida) demonstrate potential for use in soil bioremediation by increasing the degradation rates of heavy crude oil hydrocarbons

Crude oil contamination widely impacts soil as a result of release during oil and gas exploration and production activities. The success of bioremediation methods to meet remediation goals often depends on the composition of the crude oil, the soil, and microbial community. Earthworms may enhance bioremediation by mixing and aerating the soil, and exposing soil microorganisms to conditions in the earthworm gut that lead to increased activity. In this study, the common composting earthworm Eisenia fetida was tested for utility to improve remediation of oil-impacted soil. E. fetida survival in soil contaminated with two distinct crude oils was tested in an artificial (lab-mixed) sandy loam soil, and survival compared to that in the clean soil. Crude oil with a high fraction of light-weight hydrocarbons was more toxic to earthworms than the crude oil with a high proportion of heavy polyaromatic and aliphatic hydrocarbons. The heavier crude oil was added to soil to create a 30,000mg/kg crude oil impacted soil, and degradation in the presence of added earthworms and feed, feed alone, or no additions was monitored over time and compared. Earthworm feed was spread on top to test effectiveness of no mixing. TPH degradation rate for the earthworm treatments was ~90mg/day slowing by 200days to ~20mg/day, producing two phases of degradation. With feed alone, the rate was ~40mg/day, with signs of slowing after 500days. Both treatments reached the same end point concentrations, and exhibited faster degradation of aliphatic hydrocarbons <C21, but all fractions, including aromatics >C21, decreased. During these experiments, soils were moderately toxic during the first three months, then earthworms survived well, were active and reproduced with petroleum hydrocarbons present. This study demonstrated that earthworms accelerate bioremediation of crude oil in soils, including the degradation of the heaviest polyaromatic fractions.

Toxicological effects of dimethomorph on soil enzymatic activity and soil earthworm (Eisenia fetida)

The objective of this study was to evaluate the toxicity of the fungicide dimethomorph to soil microbial activity and the earthworm Eisenia fetida. Multiple biomarkers, namely, four soil enzymes (urease, dehydrogenase, invertase, and acid phosphatase), four earthworm biochemical indices (dismutase, catalase, cellulase, and malondialdehyde), and the transcriptional levels of both target genes (dismutase and catalase) were measured at 1, 10, and 100 mg kg^-1 after 1, 7, 21, and 28 days. The degradation rate of dimethomorph in soil was also determined, and the results indicated that most parameters did not differ from the controls at 1 and 10 mg kg^-1 dimethomorph by the last exposure time (28 d). However, high concentrations (100 mg kg^-1) of dimethomorph had varying effects on soil enzymatic activity and earthworms. These effects gradually decreased with prolonged exposure times. Positive correlations (R² > 0.57) between the target gene expression levels and antioxidant enzyme activities were observed in this study. We also found that earthworms have improved soil microbial activity and accelerated the degradation of dimethomorph. Overall, higher concentrations of dimethomorph might pose an ecological hazard to soil environments in the short term.

Determination of pentachlorophenol by anodic electrochemiluminescence of Ru(bpy)32+ based on nitrogen-doped graphene quantum dots as co-reactant

A novel ultrasensitive Ru(bpy)₃²⁺-based anodic ECL sensor using NGQDs as co-reactant was developed for PCP detection.

Variations in the bacterial community compositions at different sites in the tomb of Emperor Yang of the Sui Dynasty

To fully understand the bacterial processes in tomb environments, it is necessary to investigate the details of the bacterial communities present under such oligotrophic conditions. Here, high-throughput sequencing based on partial 16S rRNA gene sequences was used to fully evaluate the bacterial communities at different sites in the tomb of Emperor Yang of the Sui Dynasty. We also aimed to identify the soil factors that were significant related to bacterial diversity and community composition. The results showed the presence of a broad taxonomic diversity that included nine major phyla. Actinobacteria, Firmicutes and Proteobacteria dominated the bacterial profiles in all tomb soil samples. However, significant differences between deposited soils (DS) and covering soils (CSA, CSB and CSC) were revealed by chemistry-based principal component analysis (PCA), the number of OTUs, and the Chao 1 and Shannon indexes. At the family level, hierarchically clustered heatmap and LefSe analyses showed differences in the bacterial community compositions at different sampling sites. Notably, CSA contained significant populations of Nocardioidaceae, Pseudonocardiaceae and Streptomycetaceae, which are often reported to be associated with biodeterioration in cave environments. Further, the most abundant group (>10%) in all soil samples was Streptococcaceae, whose abundance decreased from 34.66% to 13.43% with increasing soil depth. The results of redundancy analysis (RDA) and the Monte Carlo permutation test indicated that soil pH and Cu and Mn levels were significantly related to the bacterial communities in this tomb. This research offers new insight into bacterial communities in cave environments and also provides important information for the protection of this historically important tomb.

High-throughput pyrosequencing analysis of bacteria relevant to cometabolic and metabolic degradation of ibuprofen in horizontal subsurface flow constructed wetlands

The potential toxicity of pharmaceutical residues including ibuprofen on the aquatic vertebrates and invertebrates has attracted growing attention to the pharmaceutical pollution control using constructed wetlands, but there lacks of an insight into the relevant microbial degradation mechanisms. This study investigated the bacteria associated with the cometabolic and metabolic degradation of ibuprofen in a horizontal subsurface flow constructed wetland system by high-throughput pyrosequencing analysis. The ibuprofen degradation dynamics, bacterial diversity and evenness, and bacterial community structure in a planted bed with Typha angustifolia and an unplanted bed (control) were compared. The results showed that the plants promoted the microbial degradation of ibuprofen, especially at the downstream zones of wetland. However, at the upstream one-third zone of wetland, the presence of plants did not significantly enhance ibuprofen degradation, probably due to the much greater contribution of cometabolic behaviors of certain non-ibuprofen-degrading microorganisms than that of the plants. By analyzing bacterial characteristics, we found that: (1) The aerobic species of family Flavobacteriaceae, family Methylococcaceae and genus Methylocystis, and the anaerobic species of family Spirochaetaceae and genus Clostridium_sensu_stricto were the most possible bacteria relevant to the cometabolic degradation of ibuprofen; (2) The family Rhodocyclaceae and the genus Ignavibacterium closely related to the plants appeared to be associated with the metabolic degradation of ibuprofen.

Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation

Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.