New insights into the responses of soil microorganisms to polycyclic aromatic hydrocarbon stress by combining enzyme activity and sequencing analysis with metabolomics

"Active carbon" is more advantageous to the bacterial community in the rice rhizosphere than "stable carbon"

Carbon materials are commonly used for soil carbon sequestration and fertilization, which can also affect crop growth by manipulating the rhizosphere bacterial community. However, the comparison of the differences between active carbon (e.g., organic fertilizers) and stable carbon (e.g., biochar) on rhizosphere microdomains is still unclear. Hence, a trial was implemented to explore the influence of control (CK, no fertilizer; NPK, chemical fertilizer), organic fertilizer (CF-O, organic fertilizer; CF-BO, biochar-based organic fertilizer) and biochar material (CF-B, perishable garbage biochar; CF-PMB, pig manure biochar) on the diversity, composition, and interaction of rice rhizosphere bacterial community through 16 S rRNA gene high-throughput sequencing. Our results demonstrate that organic fertilizer increases bacterial alpha-diversity compared to no-carbon supply treatment to the extend, whereas biochar has the opposite effect. The rhizosphere bacterial community composition showed pronounced variations among the various fertilization treatments. The relative abundance in Firmicutes decreased with organic fertilizer application, whereas that in Chloroflexi and Actinobacteria decreased with biochar application. Bacterial network analysis demonstrate that organic fertilizer enhances the complexity and key taxa of bacterial interactions, while biochar exhibits an opposing trend. The findings of our study indicate that organic fertilizer may contribute to a positive and advantageous impact on bacterial diversity and interaction in rice rhizosphere, whereas the influence of biochar is not as favorable and constructive. This study lays the foundation for elucidating the fate of the rhizosphere bacterial community following different carbon material inputs in the context of sustainable agricultural development.

Metal nanoparticles and pesticides under global climate change: Assessing the combined effects of multiple abiotic stressors on soil microbial ecosystems

The soil is a vital resource that hosts many microorganisms crucial in biogeochemical cycles and ecosystem health. However, human activities such as the use of metal nanoparticles (MNPs), pesticides and the impacts of global climate change (GCCh) can significantly affect soil microbial communities (SMC). For many years, pesticides and, more recently, nanoparticles have contributed to sustainable agriculture to ensure continuous food production to sustain the significant growth of the world population and, therefore, the demand for food. Pesticides have a recognized pest control capacity. On the other hand, nanoparticles have demonstrated a high ability to improve water and nutrient retention, promote plant growth, and control pests. However, it has been reported that their accumulation in agricultural soils can also adversely affect the environment and soil microbial health. In addition, climate change, with its variations in temperature and extreme water conditions, can lead to drought and increased soil salinity, modifying both soil conditions and the composition and function of microbial communities. Abiotic stressors can interact and synergistically or additively affect soil microorganisms, significantly impacting soil functioning and the capacity to provide ecosystem services. Therefore, this work reviewed the current scientific literature to understand how multiple stressors interact and affect the SMC. In addition, the importance of molecular tools such as metagenomics, metatranscriptomics, proteomics, or metabolomics in the study of the responses of SMC to exposure to multiple abiotic stressors was examined. Future research directions were also proposed, focusing on exploring the complex interactions between stressors and their long-term effects and developing strategies for sustainable soil management. These efforts will contribute to the preservation of soil health and the promotion of sustainable agricultural practices.

Large-scale soil application of hydrochar: Reducing its polycyclic aromatic hydrocarbon content and toxicity by heating

The beneficial roles of hydrochar in carbon sequestration and soil improvement are widely accepted. Despite few available reports regarding polycyclic aromatic hydrocarbons (PAHs) generated during preparation, their potential negative impacts on ecosystems remain a concern. A heating treatment method was employed in this study for rapidly removing PAHs and reducing the toxicity of corn stover-based hydrochar (CHC). The result showed total PAHs content (∑PAH) decreased and then sharply increased within the temperature range from 150 °C to 400 °C. The ∑PAH and related toxicity in CHC decreased by more than 80% under 200 °C heating temperature, compared with those in the untreated sample, representing the lowest microbial toxicity. Benzo(a)pyrene produced a significant influence on the ecological toxicity of the hydrochar among the 16 types of PAHs. The impact of thermal treatment on the composition, content, and toxicity of PAHs was significantly influenced by the adsorption, migration, and desorption of PAHs within hydrochar pores, as well as the disintegration and aggregation of large molecular polymers. The combination of hydrochar with carbonized waste heat and exhaust gas collection could be a promising method to efficiently and affordably reduce hydrochar ecological toxicity.

Optimizing carbon sources regulation in the biochemical treatment systems for coal chemical wastewater: Aromatic compounds biodegradation and microbial response strategies

The complex composition of coal chemical wastewater (CCW), marked by numerous highly toxic aromatic compounds, induces the destabilization of the biochemical treatment system, leading to suboptimal treatment efficacy. In this study, a biochemical treatment system was established to efficiently degrade aromatic compounds by quantitatively regulating the dosage of co-metabolized substrates (specifically, the chemical oxygen demand (COD) Glucose: COD Sodium acetate = 3:1, 1:3, and 1:1). The findings demonstrated that the system achieved optimal performance under the condition that the ratio of COD Glucose to COD Sodium acetate was 3:1. When the co-metabolized substrate was added to the system at an optimal ratio, examination of pollutant removal and cumulative effects revealed that the removal efficiencies for COD and total organic carbon (TOC) reached 94.61 % and 86.40 %, respectively. The removal rates of benzene series, nitrogen heterocyclic compounds, polycyclic aromatic hydrocarbons, and phenols were 100 %, 100 %, 63.58 %, and 94.12 %, respectively. Research on the physiological response of microbial cells showed that, under optimal ratio regulation, co-metabolic substrates led to a substantial rise in microbial extracellular polymeric substances (EPS) secretion, particularly extracellular proteins. When the system reached the end of its operation, the contents of loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS) for proteins in the optimal group were 7.12 mg/g-SS and 152.28 mg/g-SS, respectively. Meanwhile, the ratio of α-Helix / (β-Sheet + Random coil) and the proportion of intermolecular interaction forces were also increased in the optimal group. At system completion, the ratio of α-Helix / (β-Sheet + Random coil) reached 0.717 (LB-EPS) and 0.618 (TB-EPS), respectively. Additionally, the proportion of intermolecular interaction forces reached 74.83 % (LB-EPS) and 55.03 % (TB-EPS). An in-depth analysis of the metabolic regulation of microorganisms indicated that the introduction of optimal ratios of co-metabolic substrates contributed to a noteworthy upregulation in the expression of Catechol 2,3-dioxygenase (C23O) and Dehydrogenase (DHA). The expression levels of C23O and DHA were measured at 0.029 U/mg Pro·g MLSS and 75.25 mg TF·(g MLSS·h)-1 (peak value), respectively. Correspondingly, enrichment of aromatic compound-degrading bacteria, including Thauera, Saccharimonadales, and Candidatus_Competibacter, occurred, along with the upregulation of associated functional genes such as Catechol 1,2-dioxygenase, Catechol 2,3-dioxygenase, Protocatechuate 3,4-dioxygenase, and Protocatechuate 4,5-dioxygenase. Considering the intricate system of multiple coexisting aromatic compounds in real CCW, this study not only obtained an optimal ratio for carbon source addition but also enhanced the efficient utilization of carbon sources and improved the capability of the system to effectively degrade aromatic compounds. Additionally, this paper established a theoretical foundation for metabolic regulation and harmless treatment within the biochemical treatment of intricate systems, exemplified by real CCW.

Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems

Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.

Metabolomics perspectives of the ecotoxicological risks of polycyclic aromatic hydrocarbons: A scoping review

Polycyclic Aromatic Hydrocarbons (PAHs) represent persistent environmental pollutants ubiquitously distributed in the environment. Their presence alongside various other contaminants gives rise to intricate interactions, culminating in profound deleterious consequences. The combination effects of different PAH mixtures on biota remains a relatively unexplored domain. Recent studies have harnessed the exceptional sensitivity of metabolomic techniques to unveil the significant ecotoxicological perils of PAH pollution confronting both human populations and ecosystems. This article furnishes a comprehensive overview of current literature focused on the metabolic repercussions stemming from exposure to complex mixtures of PAHs or PAH-pollution sources using metabolomics approaches. These insights are obtained through a wide range of models, including in vitro assessments, animal studies, investigations on human subjects, botanical specimens, and soil environments. The findings underscore that PAH mixtures induce cellular stress responses and systemic effects, leading to metabolic dysregulations in amino acids, carbohydrates, lipids, and other key metabolites (e.g., organic acids, purines), with specific variations observed based on the organism and PAH compounds involved. Additionally, the ecological consequences of PAH pollutants on plant and soil microbial responses are emphasized, revealing significant changes in stress-related metabolites and nutrient cycling in soil ecosystems. The complex interplay of various PAHs and their metabolic effects on several models, as elucidated through metabolomics, highlight the urgency of further research and the need for comprehensive strategies to mitigate the risks posed by these widespread environmental pollutants.

The Combination of Buchloe dactyloides Engelm and Biochar Promotes the Remediation of Soil Contaminated with Polycyclic Aromatic Hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) cause serious stress to biological health and the soil environment as persistent pollutants. Despite the wide use of biochar in promoting soil improvement, the mechanism of biochar removing soil PAHs through rhizosphere effect in the process of phytoremediation remain uncertain. In this study, the regulation of soil niche and microbial degradation strategies under plants and biochar were explored by analyzing the effects of plants and biochar on microbial community composition, soil metabolism and enzyme activity in the process of PAH degradation. The combination of plants and biochar significantly increased the removal of phenanthrene (6.10%), pyrene (11.50%), benzo[a]pyrene (106.02%) and PAHs (27.10%) when compared with natural attenuation, and significantly increased the removal of benzo[a]pyrene (34.51%) and PAHs (5.96%) when compared with phytoremediation. Compared with phytoremediation, the combination of plants and biochar significantly increased soil nutrient availability, enhanced soil enzyme activity (urease and catalase), improved soil microbial carbon metabolism and amino acid metabolism, thereby benefiting microbial resistance to PAH stress. In addition, the activity of soil enzymes (dehydrogenase, polyphenol oxidase and laccase) and the expression of genes involved in the degradation and microorganisms (streptomyces, curvularia, mortierella and acremonium) were up-regulated through the combined action of plants and biochar. In view of the aforementioned results, the combined application of plants and biochar can enhance the degradation of PAHs and alleviate the stress of PAH on soil microorganisms.

The dissipation of organophosphate esters mediated by ryegrass root exudate oxalic acid in soil: Analysis of enzymes activities, microorganism

Complex rhizoremediation is the main mechanism of phytoremediation in organic-contaminated soil. Low molecular weight organic acids (LMWOAs) in root exudates have been shown to increase the bioavailability of contaminants and are essential for promoting the dissipation of contaminants. The effects of root exudates on the dissipation of organophosphate esters (OPEs) in soil are unclear. Consequently, we studied the combined effects of root exudates, soil enzymes and microorganisms on OPEs (tri (1-chloro-2-propyl) phosphate (TCPP) and triphenyl phosphate (TPP)) dissipation through pot experiments. Oxalic acid (OA) was confirmed to be the main component of LMWOAs in root exudates of ryegrass. The existence of OA increased the dissipation rate of OPEs by 6.04%-25.50%. Catalase and dehydrogenase activities were firstly activated and then inhibited in soil. While, urease activity was activated and alkaline phosphatase activity was inhibited during the exposure period. More bacteria enrichment (e.g., Sphingomonas, Pseudomonas, Flavisolibacter, Pontibacter, Methylophilus and Massilia) improved the biodegradation of OPEs. In addition, the transformation paths of OPEs hydrolysis and methylation under the action of root exudates were observed. This study provided theoretical insights into reducing the pollution risk of OPEs in the soil.

Combined effects of azoxystrobin and oxytetracycline on rhizosphere microbiota of Arabidopsis thaliana

The rhizosphere is one of the key determinants of plant health and productivity. Mixtures of pesticides are commonly used in intensified agriculture. However, the combined mechanisms underlying their impacts on soil microbiota remain unknown. The present study revealed that the rhizosphere microbiota was more sensitive to azoxystrobin and oxytetracycline, two commonly used pesticides, than was the microbiota present in bulk soil. Moreover, the rhizosphere microbiota enhanced network complexity and stability and increased carbohydrate metabolism and xenobiotic biodegradation as well as the expression of metabolic genes involved in defence against pesticide stress. Co-exposure to azoxystrobin and oxytetracycline had antagonistic effects on Arabidopsis thaliana growth and soil microbial variation by recruiting organic-degrading bacteria and regulating ABC transporters to reduce pesticide uptake. Our study explored the composition and function of soil microorganisms through amplicon sequencing and metagenomic approaches, providing comprehensive insights into the synergistic effect of plants and rhizosphere microbiota on pesticides and contributing to our understanding of the ecological risks associated with pesticide use.

Effects of biochar pyrolysis temperature on uranium immobilization in soil remediation: Revealed by 16S rDNA and metabolomic analyses

Uranium-stressed soil caused by nuclear industry development and energy acquisition have attracted extensive attentions for a long time. This study investigated the effects of biochar application with different pyrolysis temperatures (300 ℃, 500 ℃ and 700 ℃) on remediation of uranium-stressed soil. The results showed that higher pyrolysis temperature (700 ℃) was benefit for ryegrass growing and caused a lower uranium accumulation in plants. At the same time, uranium immobilization was more effective at higher biochar pyrolysis temperature. Careful investigations indicated that activities of soil urease and sucrase were promoted, and bacterial diversity was strengthened in C700 group, which may contribute to uranium immobilization. The biochar application could activate metabolic of lipids and amino acids, organic acids and derivatives, and organic oxygen compounds. Nicotinate and nicotinamide metabolism, and Benzoxazinoid biosynthesis were unique metabolic pathways in the C700 group, which could enhance the uranium tolerance from different perspectives. Based on these results, we recommend to use biochar with 700 °C pyrolysis temperature when processing remediation of uranium-stressed soil. This study will facilitate the implementation of biochar screening and provide theoretical helps for remediation of uranium-stressed soil.

Identification of an efficient phenanthrene-degrading Pseudarthrobacter sp. L1SW and characterization of its metabolites and catabolic pathway

Phenanthrene, a typical chemical of polycyclic aromatic hydrocarbons (PAHs) pollutants, severely threatens health of wild life and human being. Microbial degradation is effective and environment-friendly for PAH removal, while the phenanthrene-degrading mechanism in Gram-positive bacteria is unclear. In this work, one Gram-positive strain of plant growth-promoting rhizobacteria (PGPR), Pseudarthrobacter sp. L1SW, was isolated and identified with high phenanthrene-degrading efficiency and great stress tolerance. It degraded 96.3% of 500 mg/L phenanthrene in 72 h and kept stable degradation performance with heavy metals (65 mg/L of Zn2+, 5.56 mg/L of Ni2+, and 5.20 mg/L of Cr3+) and surfactant (10 CMC of Tween 80). Strain L1SW degraded phenanthrene mainly through phthalic acid pathway, generating intermediate metabolites including cis-3,4-dihydrophenanthrene-3,4-diol, 1-hydroxy-2-naphthoic acid, and phthalic acid. A novel metabolite (m/z 419.0939) was successfully separated and identified as an end-product of phenanthrene, suggesting a unique metabolic pathway. With the whole genome sequence alignment and comparative genomic analysis, 19 putative genes associated with phenanthrene metabolism in strain L1SW were identified to be distributed in three gene clusters and induced by phenanthrene and its metabolites. These findings advance the phenanthrene-degrading study in Gram-positive bacteria and promote the practical use of PGPR strains in the bioremediation of PAH-contaminated environments.

Adaptation strategies and functional transitions of microbial community in pyrene-contaminated soils promoted by lead with Pseudomonas veronii and its extracellular polymeric substances

Pyrene was designated as a remediation target in this study, and low contamination of lead (Pb) was set to induce heavy metal stress. Pseudomonas veronii and its extracellular polymeric substances (EPSs) were chosen for biofortification, with the aim of elucidating the structural, metabolic, and functional responses of soil microbial communities. Community analysis of soil microorganisms using high-throughput sequencing showed that the co-addition of P. veronii and EPSs resulted in an increase in relative abundance of phyla associated with pyrene degradation, and formed a symbiotic system dominated by Firmicutes and Proteobacteria, which involved in pyrene metabolism. Co-occurrence network analysis revealed that the module containing P. veronii was the only one exhibiting a positive correlation between bacterial abundance and pyrene removal, indicating the potential of bioaugmentation in enriching functional taxa. Biofortification also enhanced the abundance of functional gene linked to EPS production (biofilm formation-Pseudomonas aeruginosa) and pyrene degradation. Furthermore, 17 potential functional bacteria were screened out using random forest algorithm. Lead contamination further promoted the growth of Proteobacteria, intensified cooperative associations among bacteria, and increased the abundance of bacteria with positive correlation with pyrene degradation. The results offer novel perspectives on alterations in microbial communities resulting from the synergistic impact of heavy metal stress and biofortification.

Characteristics of bacterial community and extracellular enzymes in response to atrazine application in black soil

The ecological functioning of black soil largely depends on the activities of various groups of microorganisms. However, little is known about how atrazine, a widely used herbicide with known harmful effects on the environment, influences the microbial ecology of black soil, and the extracellular enzymes related to the carbon, nitrogen and phosphorus cycles. Here, we evaluated the change in extracellular enzymes and bacterial community characteristics in black soil after exposure to various concentrations of atrazine. Low concentrations of applied atrazine (10 - 20 mg kg-1) were almost completely degraded after 120 days. At high concentrations (80 - 100 mg kg-1), about 95% of the applied atrazine was degraded over the same period. Additionally, linear fitting of data indicated that the total enzymatic activity index (TEI) and bacterial α-diversity index were negatively correlated with atrazine applied concentration. The atrazine had a greater effect on bacterial beta diversity after 120 days, which differentiated species clusters treated with low and high atrazine concentrations. Soil bacterial community structure and function were affected by atrazine, especially at high atrazine concentrations (80 - 100 mg kg-1). Key microorganisms such as Sphingomonas and Nocardioides were identified as biomarkers for atrazine dissipation. Functional prediction indicated that most metabolic pathways might be involved in atrazine dissipation. Overall, the findings enhance our understanding of the factors driving atrazine degradation in black soil and supports the use of biomarkers as indicators of atrazine dissipation.

Biosurfactants-based mixed polycyclic aromatic hydrocarbon degradation: From microbial community structure toward non-targeted metabolomic profile determination

Biosurfactants-based bioremediation is considered an efficient technology to eliminate environmental pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the precise role of rhamnolipids or lipopeptide-biosurfactants in mixed PAH dissipation, shaping microbial community structure, and influencing metabolomic profile remained unclear. In this study, results showed that the maximum PAH degradation was achieved in lipopeptide-assisted treatment (SPS), where the pyrene and phenanthrene were substantially degraded up to 74.28 % and 63.05 % respectively, as compared to rhamnolipids (SPR) and un-aided biosurfactants (SP). Furthermore, the high throughput sequencing analysis revealed a significant change in the PAH-degrading microbial community, with Proteobacteria being the predominant phylum (>98 %) followed by Bacteroidota and Firmicutes in all the treatments. Moreover, Pseudomonas and Pannonibacter were found as highly potent bacterial genera for mixed PAH degradation in SPR, SPS, and SP treatments, nevertheless, the abundance of the genus Pseudomonas was significantly enhanced (>97 %) in SPR treatment groups. On the other hand, the non-targeted metabolomic profile through UHPLC-MS/MS exhibited a remarkable change in the metabolites of amino acids, carbohydrates, and lipid metabolisms by the input of rhamnolipids or lipopeptide-biosurfactants whereas, the maximum intensities of metabolites (more than two-fold) were observed in SPR treatment. The findings of this study suggested that the aforementioned biosurfactants can play an indispensable role in mixed PAH degradation as well as seek to offer new insights into shifts in PAH-degrading microbial communities and their metabolic function, which can guide the development of more efficient and targeted strategies for complete removal of organic pollutants such as PAH from the contaminated environment.

Effects of Polycyclic Aromatic Hydrocarbons on the Composition of the Soil Bacterial Communities in the Tidal Flat Wetlands of the Yellow River Delta of China

Polycyclic aromatic hydrocarbons (PAHs) are pervasive organic pollutants in coastal ecosystems, especially in tidal flat wetlands. However, the mechanisms through which PAHs impact the soil bacterial communities of wetlands featuring a simple vegetation structure in the Yellow River Delta (China) remain largely unclear. In this study, we examined soil samples from two sites featuring a single vegetation type (Suaeda salsa) in the Yellow River Delta. Specifically, we investigated the impacts of PAHs on the diversity and composition of soil bacteria communities through high-throughput 16 S rRNA sequencing. PAHs significantly increased the soil organic carbon content but decreased the total phosphorus content (p = 0.02). PAH contamination notably reduced soil bacterial community α diversity (Shannon index) and β diversity. Furthermore, PAHs significantly altered the relative abundance of bacterial phyla, classes, and genera (p < 0.05). Specifically, PAHs increased the relative abundance of the bacterial phyla Acidobacteriota and Gemmatimonadota (p < 0.05), while decreasing the relative abundance of Bacteroidota, Desulfobacterota, and Firmicutes compared to the control wetland (p < 0.05). Moreover, PAHs and certain soil properties [total nitrogen (TN), soil organic carbon (SOC), total phosphorus (TP), and total salt (TS)] were identified as key parameters affecting the community of soil bacteria, with the abundance of specific bacteria being both negatively and positively affected by PAHs, SOC, and TN. In summary, our findings could facilitate the identification of existing environmental problems and offer insights for improving the protection and management of tidal flat wetland ecosystems in the Yellow River Delta of China.

Influence of cultivation duration on microbial taxa aggregation in Panax ginseng soils across ecological niches

Introduction

Microbial communities are crucial for plant health and productivity. However, the influence of cultivation age on the ecological processes in assembling plant microbiomes at various ecological niches remains unclear.

Methods

We selected 12 samples from ginseng farmlands with different cultivation years (N4: 4 years old, N6: 6 years old). We used soil physicochemical properties, enzyme activities, and high-throughput sequencing (16S rDNA and ITS) to examine the rhizoplane (RP), rhizosphere (RS), and bulk soil (BS).

Results

Our results indicated that cultivation years significantly affect the soil microbiome's diversity and community composition across different ecological niches. The BS microbiome experienced the largest effect, while the RS experienced the smallest. N6 showed a greater impact than N4. This effect was more pronounced on the fungal communities than the bacterial communities of various ecological niches and can be closely related to the soil's physicochemical properties. In N4 soils, we observed an upward trend in both the number of ASVs (amplicon sequence variations) and the diversity of soil microbial taxa across various ecological niches. In N4RP, the bacteria Sphingomonas, known for degrading toxic soil compounds, was present. All ecological niches in N4 showed significant enrichment of Tetracladium fungi, positively associated with crop yield (N4RP at 6.41%, N4RS at 11.31%, and N4BS at 3.45%). In N6 soils, we noted a stark decline in fungal diversity within the BS, with a 57.5% reduction in ASVs. Moreover, Sphingomonas was abundantly present in N6RS and N6BS soils. The relative abundance of the pathogen-inhibiting fungus Exophiala in N6RP and N6RS reached 34.18% and 13.71%, respectively, marking increases of 4.9-fold and 7.7-fold. Additionally, another pathogeninhibiting fungus, Humicola, showed significant enrichment in N6BS, with a 7.5-fold increase. The phenolic acid-producing fungus Pseudogymnoascus in N6RP, N6RS, and N6BS showed increases of 2.41-fold, 2.55-fold, and 4.32-fold, respectively. We hypothesize that functional genes related to the metabolism of terpenoids and polyketides, as well as signaling molecules and interactions, regulate soil microbial taxa in ginseng from different cultivation years.

Discussion

In conclusion, our study enhances understanding of plant-microbe interactions and aids the sustainable development of medicinal plants, particularly by addressing ginseng succession disorder.

Long-term effects of oil contamination on soil quality and metabolic function

Widespread soil contamination with oil and the toxicity of petroleum hydrocarbons to soil biota make it extremely important to study microbial responses to oil stress. Soil metabolites reflect the main metabolic pathways in the soil microbial community. The examination of changes in the soil metabolic profile and metabolic function is essential for a better understanding of the nature of the pollution and restoration of the disturbed soils. The present study aimed to assess the long-term effect of oil on the ecological state of the soil, evaluate quantitative and qualitative differences in metabolite composition between soil contaminated with oil and non-contaminated soil, and reveal biologically active metabolites that are related to oil contamination and can be used for contamination assessment. A long-term field experiment was conducted to examine the effects of various oil concentrations on the biochemical properties and metabolic profile of the soil. Podzolic soil contaminated with oil demonstrated the long-term inhibition of soil biological activity and vegetation. Oil affected the metabolic activity of soil fungi increasing the production of toxic metabolites. A metabolomic approach was employed to determine soil metabolites. The metabolite profile was found to vary greatly between oil-contaminated and non-contaminated soils. Carbohydrates had the largest number of metabolites negatively affected by oil, while the content of organic acids, phenolic compounds, and terpenoids was mainly increased in oil-contaminated soil. The evaluation of the long-term impact of oil on microbial metabolism can make a valuable contribution to the assessment of soil quality and the activity of soil microorganisms being under stress from oil pollution. The results contribute to a further understanding of the role of microorganisms in the ecological functions of contaminated soil, which can be useful in the development of rehabilitation strategies for disturbed sites.

Spatial distribution, source identification and flux estimation of polycyclic aromatic hydrocarbons and organochlorine pesticides in basins of the Eastern Indian Ocean

Although polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs) have been recorded worldwide, information on their presence in the Eastern Indian Ocean (EIO), especially south of 10°S, remains limited. We investigated the distribution and depositional fluxes of PAHs and OCPs, and the major sources and ecological risks of PAHs in EIO surface sediments from the Central Indian Ocean (CIOB) and Wharton Basin (WB). The concentration of Σ18 PAHs and ∑10 OCPs had an average value (± SD) of 138.4 ± 52.34 and 0.8 ± 0.20 ng g-1, respectively. PAHs may mainly affected by traffic emission and biomass and wood combustion. Persistent organic pollutant accumulation rate (PAR) and depositional flux (DF) values showed that abundant PAHs might lost during top-down transport. The low trans- chordane (CHL)/cis-CHL ratio and PAR of OCPs may indicated few OCPs were inputted into the EIO recently. The results of binary isotope mixing modeling indicate the predominance of marine organic matter (MOM) in total organic carbon (TOC) of sediments. Fluoranthene (Flour) and pyrene (Py) might have potential biological effects in the EIO. The study provided background values for PAHs and OCPs in the Indian Ocean, and preliminarily revealed the fate of POPs in the open oceans.

Regulation methods and enhanced mechanism on the efficient degradation of aromatics in biochemical treatment system of coal chemical wastewater

In order to address the problems of poor treatment effect of coal chemical wastewater (CCW) biochemical treatment system resulting in non-compliance with effluent standards and unstable operation, a combination regulation method of co-substrate metabolism and predominant flora enhancement was constructed, and the performance and mechanism of enhanced degradation of aromatics in CCW was also investigated in this study. The results showed that when the influent concentration of chemical oxygen demand (COD) and aromatics was less than 600 mg/L and 180 mg/L respectively, there was no significant effect of the combined regulation method on the enhanced treatment of aromatics, the removal rate of total organic carbon (TOC) in the system could all more than 73%; while when the influent concentration of COD increased to 800 mg/L and the aromatics concentration increased to more than 240 mg/L, the ordinary activated sludge system had collapsed. Compared with the regulation method of co-substrate metabolism alone, the combination regulation method increased the removal rate of TOC by 21%. The analysis of antioxidant enzyme activity showed that under the combination regulation method, the antioxidant enzyme activity of microorganisms was higher and their resistance to adverse environments was stronger. EPS and dehydrogenase analysis indicated that the combination regulation method was more conducive to microbial degradation of aromatics. Meanwhile, the analysis of microbial community structure showed that the aromatics degradation bacteria genera Rhodococcus, Luteococcus, etc. were enriched under the combination regulation method. The study provides a theoretical basis and technical guidance for solving the problems of unstable operation of CCW biochemical treatment systems and non-compliance with effluent standards.

Effects of single and combined contamination of total petroleum hydrocarbons and heavy metals on soil microecosystems: Insights into bacterial diversity, assembly, and ecological function

Deciphering the impact of single and combined contamination of total petroleum hydrocarbons (TPH) and heavy metals on soil microecosystems is essential for the remediation of contaminated habitats, yet it remains incompletely understood. In this study, we employed high-throughput sequencing to investigate the impact of single TPH contamination, single metal contamination, and their co-contamination on soil microbial diversity, assembly mechanisms, composition, ecological function, and resistome. Our results revealed that contamination led to a reduction in alpha diversity, with single contamination displaying lower diversity compared to co-contamination, depending on the concentration of pollutants. Community beta diversity was primarily driven by turnover rather than nestedness, and narrower ecological niches were detected under pollution conditions. The neutral community model suggested that homogenizing dispersal played a significant role in the community assembly process under single TPH or co-contamination, while homogeneous selection dominated under heavy metals pollution. Procrustes analysis demonstrated a correlation between community composition and functional divergence, while Mantel tests linked this divergence to concentrations of Cr, Cr6+, Pb, and TPH. Interestingly, soils co-polluted with TPH and heavy metals exhibited similar genera, community functions, and resistomes as soils contaminated with only metals, highlighting the significant impact of heavy metals. Ecological functions related to carbon (C), nitrogen (N), and sulfur (S) cycles were enhanced under TPH pollution but impaired under heavy metals stress. These findings enhance our understanding of soil microecosystems subjected to TPH, heavy metals, and their co-contamination, and carry significant implications for environmental microecology and pollutant risk assessment.

Research progress and prospect of glomalin-related soil protein in the remediation of slightly contaminated soil

Soil pollution caused by organic pollutants and potentially toxic elements poses a serious threat to sustainable agricultural development, global food security and human health. Therefore, strategies for reducing soil pollution are urgently required. Arbuscular mycorrhizal fungi (AMF)-assisted phytoremediation is widely recognized for its ability to remediate slightly-contaminated soil. Glomalin-related soil protein (GRSP) production by AMF is considered a vital mechanism of AMF-assisted phytoremediation. GRSP is widespread in soils and may contribute to the remediation of slightly contaminated soils. GRSP facilitates stabilization of pollutants in soils by interacting with pollutants owing to its abundant functional groups, recalcitrance, and long turnover time. It also enhances soil bioremediation and phytoremediation by stimulating soil microbial activity, improving soil structure, and providing nutrients for plants. However, research on GRSP is still in its early stages, and studies on contaminated soil remediation are limited. The effectiveness of GRSP in situ remediation remains to be proved. This review summarizes current knowledge regarding the GRSP distribution and its contribution to the remediation of slightly contaminated soils. Additionally, we present strategies to increase the GRSP content in contaminated soils, as well as prospects for future studies on the use of GRSP in contaminated soil remediation. This study focuses on recent developments that aim to improve awareness of the role of GRSP in soil remediation and relevant future directions.

Mechanism of synergistic remediation of soil phenanthrene contamination in paddy fields by rice-crab coculture and bioaugmentation with Pseudomonas sp

Polycyclic aromatic hydrocarbons (PAHs) are persistent and harmful pollutants with high priority concern in agricultural fields. This work constructed a rice-crab coculture and bioaugmentation (RCM) system to remediate phenanthrene (a model PAH) contamination in rice fields. The results showed that RCM had a higher remediation performance of phenanthrene in rice paddy compared with rice cultivation alone, microbial addition alone, and crab-rice coculture, reaching a remediation efficiency of 88.92 % in 42 d. The concentration of phenanthrene in the rice plants decreased to 6.58 mg/kg, and its bioconcentration effect was efficiently inhibited in the RCM system. In addition, some low molecular weight organic acids of rice root increased by 12.87 %∼73.87 %, and some amino acids increased by 140 %∼1150 % in RCM. Bioturbation of crabs improves soil aeration structure and microbial migration, and adding Pseudomonas promoted the proliferation of some plant growth-promoting rhizobacteria (PGPRs), which facilitated the degradation of phenanthrene. This coupling rice-crab coculture with bioaugmentation had favorable effects on soil enzyme activity, microbial community structure, and PAH degradation genes in paddy fields, enhancing the removal of and resistance to PAH contamination in paddy fields and providing new strategies for achieving a balance between production and remediation in contaminated paddy fields.

Traditional and new proposals for environmental microbial indicators-a review

The continuous increment in world population coupled with the greatest natural resource consumption and waste generation has an enormous impact on the environment. To date, using biological indicators (bioindicators) to evaluate the biological quality of natural environments is very common. Nonetheless, selecting those suitable for each ecosystem or contaminant is one of the most important issues for environmental sciences. Bacteria and helminths are mainly related to fecal contamination, while antibiotic-resistant bacteria, fungi, viruses, and microalgae are organisms used to determine deteriorated ecosystems by diverse contaminants. Nowadays, each bioindicator is used as a specific agent of different contaminant types, but detecting and quantifying these bioindicator microorganisms can be performed from simple microscopy and culture methods up to a complex procedure based on omic sciences. Developing new techniques based on the metabolism and physiological responses of traditional bioindicators is shown in a fast environmental sensitivity analysis. Therefore, the present review focuses on analyzing different bioindicators to facilitate developing suitable monitoring environmental systems according to different pollutant agents. The traditional and new methods proposed to detect and quantify different bioindicators are also discussed. Their vital role is considered in implementing efficient ecosystem bioprospection, restoration, and conservation strategies directed to natural resource management.

Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation

As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.

Regulatory mechanisms of submerged macrophyte on bacterial community recovery in decabromodiphenyl ether contaminated sediment: Microbiological and metabolomic perspectives

Polybrominated diphenyl ether contamination in sediments poses serious threats to human health and ecological safety. Despite the broad application of submerged macrophytes for remediating pollutants, their regulatory influence on bacterial communities in contaminated sediments remains unclear. Herein, we analyzed the effects of decabromodiphenyl ether (BDE-209) and Hydrilla verticillata on sediment bacterial community and function using 16S rRNA gene sequencing and sediment metabolomics. Results showed that BDE-209 significantly inhibited sediment bacterial diversity and metabolic functions. It also enhanced bacterial interactions and altered both the bacterial community and metabolite composition. Uridine and inosine were critical metabolites that positively co-occurred with bacterial taxa inhibited by BDE-209. Notably, planting H. verticillata effectively alleviated the adverse impacts of BDE-209 by reducing its residuals, increasing the total organic carbon, and modifying metabolic profiles. Such mitigation was evidenced by enhancing bacterial diversity, restoring metabolic functions, and attenuating bacterial interactions. However, mitigation effectiveness depended on treatment time. Additionally, propionic acid, palmitic acid, and palmitoleic acid may facilitate the restoration of phylum Proteobacteria and class Planctomycetacia in H. verticillata planted sediment. Together, these findings improve understanding of BDE-209's impacts on aquatic ecosystems and provide valuable insights for ecological restoration using submerged macrophytes.

Exposure to three herbicide mixtures influenced maize root-associated microbial community structure, function and the network complexity

Herbicide mixtures are a new and effective agricultural strategy for managing suppress weed resistance and have been widely used in controlling weeding growth in maize fields. However, the potential ecotoxicological impact of these mixtures on the microbial community structure and function within various root-associated niches, remains inadequately understood. Here, the effects of nicosulfuron, mesotrione and atrazine on soil enzyme activity and microbial community structure and function were investigated when applied alone and in combination. The findings indicated that herbicide mixtures exhibit a prolonged half-life compared to single herbicides. Ecological niches are the major factor influencing the structure and functions of the microbial community, with the rhizosphere exhibiting a more intensive response to herbicide stress. Herbicides significantly inhibited the activities of soil functional enzymes, including dehydrogenase, urease and sucrose in the short-term. Single herbicide did not drastically influence the alpha or beta diversity of the soil bacterial community, but herbicide mixtures significantly increased the richness of the fungal community. Meanwhile, the key functional microbial populations, such as Pseudomonas and Enterobacteriaceae, were significantly altered by herbicide stress. Both individual and combined use of the three herbicides reduced the complexity and stability of the bacterial network but increased the interspecific cooperations of fungal community in the rhizosphere. Moreover, by quantification of residual herbicide concentrations in the soil, we showed that the degradation period of the herbicide mixture was longer than that of single herbicides. Herbicide mixtures increased the contents of NO3--N and NH4+-N in the soil in the short-term. Overall, our study provided a comprehensive insight into the response of maize root-associated microbial communities to herbicide mixtures and facilitated the assessment of the ecological risks posed by herbicide mixtures to the agricultural environment from an agricultural sustainability perspective.

Unveiling the novel role of ryegrass rhizospheric metabolites in benzo[a]pyrene biodegradation

Rhizoremediation is a promising remediation technology for the removal of soil persistent organic pollutants (POPs), especially benzo[a]pyrene (BaP). However, our understanding of the associations among rhizospheric soil metabolites, functional microorganisms, and POPs degradation in different plant growth stages is limited. We combined stable-isotope probing (SIP), high-throughput sequencing, and metabolomics to analyze changes in rhizospheric soil metabolites, functional microbes, and BaP biodegradation in the early growth stages (tillering, jointing) and later stage (booting) of ryegrass. Microbial community structures differed significantly among growth stages. Metabolisms such as benzenoids and carboxylic acids tended to be enriched in the early growth stage, while lipids and organic heterocyclic compounds dominated in the later stage. From SIP, eight BaP-degrading microbes were identified, and most of which such as Ilumatobacter and Singulisphaera were first linked with BaP biodegradation. Notably, the relationship between the differential metabolites and BaP degradation efficiency further suggested that BaP-degrading microbes might metabolize BaP directly to produce benzenoid metabolites (3-hydroxybenzo[a]pyrene), or utilize benzenoids (phyllodulcin) to stimulate the co-metabolism of BaP in early growth stage; some lipids and organic acids, e.g. 1-aminocyclopropane-1-carboxylic acid, might provide nutrients for the degraders to promote BaP metabolism in later stage. Accordingly, we determined that certain rhizospheric metabolites might regulate the rhizospheric microbial communities at different growth stages, and shift the composition and diversity of BaP-degrading bacteria, thereby enhancing in situ BaP degradation. Our study sheds light on POPs rhizoremediation mechanisms in petroleum-contaminated soils.

Restoration of soils contaminated with PAHs by the mixture of zeolite composites mixed with exogenous organic matter and mineral salts

The major cause of soil degradation (contamination, erosion, compaction) is closely linked to agriculture, i.e., unsustainable agriculture practices, which are reflected in the depletion of the soil organic carbon pool, loss in soil biodiversity, and reduction of C sink capacity in soils. Therefore, the agricultural practice of applying carbon-rich materials into the soil is an attractive solution for climate change mitigation and soil ecosystem sustainability. The paper aimed to evaluate the effectiveness of the addition of organic-mineral mixtures to the mineral salts (NPK), including the exogenous organic matter (lignite) mixed with zeolite-carbon (NaX-C) or zeolite-vermiculite (NaX-Ver) composites in the restoration of soils contaminated with PAHs. The addition of zeolite composites to fertilizer resulted in a significant reduction in soil PAH levels and a corresponding reduction in plant tissue content, without compromising yields, compared to the control and separate application of NPK. A Significant correlation between PAHs and pHH2O, pHKCl, EC and dehydrogenase activity (DhA) was found in soils. The addition of zeolite composites with lignite significantly reduced the content of PAHs in straws, especially following the application of NaX-C. However, in the case of grains, the highest percentage reduction in comparison to NPK was observed for the highest dose of NaX-Ver.

Microplastics drive microbial assembly, their interactions, and metagenomic functions in two soils with distinct pH and heavy metal availability

Microplastics (MPs) have emerged as widely existing global environmental concerns in terrestrial ecosystems. However, the mechanisms that how MPs are affecting soil microbes and their metagenomic functioning is currently uncertain. Herein, we investigated the response mechanisms of bacterial and fungal communities as well as the metagenomic functions to the addition of MPs in two soils with distinct pH and heavy metals. In this study, the acidic soil (Xintong) and the neutral soil (Huanshan) contaminated by heavy metals were incubated with Polyvinyl Chloride (PVC) MPs at ratios of 2.5% and 5% on 60 and 120 days. We aimed to evaluate the responding, assembly, and interactions of the metagenomic taxonomy and function. Results showed that only in the acidic soil, PVC MPs significantly increased soil pH and decreased CaCl₂-extractable heavy metals, and also reduced bacterial alpha diversity and interaction networks. The relative proportions of Proteobacteria and Bacteroidota in bacteria, and Mortierellomycota in fungi, were increased, but Chloroflexi and Acidobacteriota in bacteria, Ascomycota and Basidiomycota in fungi, were significantly decreased by PVC MPs. Metagenomic functions related to C cycling were repressed but the nutrient cycles were enriched with PVC MPs. In conclusion, our study suggests that the addition of PVC MPs could shift soil microbial community and metagenomic functioning, as well as increasing soil pH and reduced heavy metal availability.

Effects of atrazine on microbial metabolic limitations in black soils: Evidence from enzyme stoichiometry

Long-term input of agricultural chemicals such as pesticides into the soil can increase soil pollution, thereby affecting the productivity and quality of black soil. Triazine herbicide atrazine has been shown to have long-lasting residual effects in black soil. The atrazine residues affected soil biochemical properties, further leading to microbial metabolism restriction. It is necessary to explore the strategies to mitigate the limitations on microbial metabolism in atrazine-contaminated soils. Here, we evaluated the effect of the atrazine on microbial nutrient acquisition strategies as indicated by extracellular enzyme stoichiometry (EES) in four black soils. Atrazine degradation in soil followed the first-order kinetics model across various concentrations ranging from 10 to 100 mg kg^-1. We found that the atrazine was negatively correlated with the EES for C-, N-, and P-acquisition. Vector lengths and angles decreased and increased significantly with an increase of atrazine concentration in tested black soils except for Lishu soils. Moreover, the vector angles were >45° for tested four black soils, indicating that atrazine residue had the greatest P-limitation on soil microorganisms. Interestingly, microbial C- and P-limitations with different atrazine concentrations showed a strong linear relationship, especially in Qiqihar and Nongan soils. Atrazine treatment significantly negatively affected microbial metabolic limitation. Soil properties and EES interaction explained up to 88.2% for microbial C-/P-limitation. In conclusion, this study confirms the EES as a useful method in evaluating the effects of pesticides on microbial metabolic limitations.

The characteristics and metabolic potentials of the soil bacterial community of two typical military demolition ranges in China

The response mechanism of soil microbiota in military polluted sites can effectively indicate the biotoxicity of ammunition. In this study, two military demolition ranges polluted soils of grenades and bullet were collected. According to high-throughput sequencing, after grenade explosion, the dominant bacteria in Site 1 (S1) are Proteobacteria (97.29 %) and Actinobacteria (1.05 %). The dominant bacterium in Site 2 (S2) is Proteobacteria (32.95 %), followed by Actinobacteria (31.17 %). After the military exercise, the soil bacterial diversity index declined significantly, and the bacterial communities interacted more closely. The indigenous bacteria in S1 were influenced more compared to those in S2. According to the environmental factor analysis, the bacteria composition can easily be influenced by heavy metals and organic pollutants, including Cu, Pb, Cr and Trinitrotoluene (TNT). About 269 metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were detected in bacterial communities, including nutrition metabolism (C, 4.09 %; N, 1.14 %; S, 0.82 %), external pollutant metabolism (2.52 %) and heavy metal detoxication (2.12 %), respectively. The explosion of ammunition changes the basic metabolism of indigenous bacteria, and heavy metal stress inhibits the TNT degradation ability of bacterial communities. The pollution degree and community structure influence the metal detoxication strategy at the contaminated sites together. Heavy metal ions in S1 are mainly discharged through membrane transporters, while heavy metal ions in S2 are mainly degraded through lipid metabolism and biosynthesis of secondary metabolites. The results obtained in this study can provide deep insight into the response mechanism of the soil bacterial community in military demolition ranges with composite pollutions of heavy metals and organic substances. CAPSULE: Heavy metal stress changed the composition, interaction and metabolism of indigenous communities in military demolition ranges, especially the TNT degradation process.

Increased daily temperature fluctuations exacerbate the toxicity of phenanthrene in Enchytraeus albidus (Enchytraeidae)

Temperature variability in soils is expected to increase due to the more frequent occurrence of heat waves, putting species under thermal stress. In addition, organic pollutants such as polycyclic aromatic hydrocarbons (PAHs) are released into the environment due to anthropogenic activities. Both stressors negatively impact terrestrial organisms and may interact with each other. Here, we subjected the soil living enchytraeid, Enchytraeus albidus, to combined exposure to phenanthrene (PHE; 0, 10, 20, 40, and 80 mg kg^-1 dry soil) and a range of temperature treatments (constant temperature (CT): 10, 15 and 20 °C; different mean temperature with the same daily temperature fluctuation (DTF-5): 10 ± 5, 15 ± 5 and 20 ± 5 °C; daily temperature fluctuation with the same mean, but different amplitudes (DTF-A): 20, 20 ± 2, 20 ± 5 and 20 ± 7 °C). We measured internal PHE concentration in adults and found that an increase in mean temperature significantly increased the internal PHE concentration. The production of juveniles was measured using a standardized test. We found a synergistic interaction between the temperature amplitude (DTF-A treatments) and PHE on the reproduction of E. albidus. The EC₅₀ of reproduction decreased with increasing amplitude. These results show that the negative effects of PHE on E. albidus can be magnified if stressful temperatures are reached (although briefly) during diurnal fluctuations of soil temperature. Our results highlight the importance and inclusion of extreme thermal events in the risk assessment of pollutants.

Salt stress-induced changes in soil metabolites promote cadmium transport into wheat tissues

Soil salinity is known to improve cadmium (Cd) mobility, especially in arid soils. However, the mechanisms involved in how salt stress-associated metabolic profiles participate in mediating Cd transport in the soil-plant system remain poorly understood. This study was designed to investigate the effects of salinity-induced changes in soil metabolites on Cd bioavailability. Sodium salts in different combinations according to molar ratio (NaCl:Na₂SO₄=1:1; NaCl:Na₂SO₄:NaHCO₃=1:2:1; NaCl:Na₂SO₄:NaHCO₃:Na₂CO₃=1:9:9:1; NaCl:Na₂SO₄:NaHCO₃:Na₂CO₃=1:1:1:1) were applied to the Cd-contaminated soils, which increased soil Cd availability by 22.36% and the Cd content in wheat grains by 36.61%, compared to the control. Salt stress resulted in soil metabolic reprogramming, which might explain the decreased growth of wheat plants and increased Cd transport from the soil into wheat tissues. For example, down-regulation of starch and sucrose metabolism reduced the production of sugars, which adversely affected growth; up-regulation of fatty acid metabolism allowed wheat plants to maintain a normal intracellular environment under saline conditions; up-regulation of the tricarboxylic acid (TCA) cycle was triggered, causing an increase in organic acid synthesis and the accumulation of organic acids, which facilitated the migration of soil Cd into wheat tissues. In summary, salt stress can facilitate Cd transport into wheat tissues by the direct effect of salt-based ions and the combined effect of altered soil physicochemical properties and soil metabolic profiles in Cd-contaminated soils.

Contrasting response strategies of microbial functional traits to polycyclic aromatic hydrocarbons contamination under aerobic and anaerobic conditions

PAHs (Polycyclic aromatic hydrocarbons) are widely distributed in soil ecosystems, but our knowledge regarding the impacts of PAHs effects on soil microbial functional traits is limited. In this study, we evaluated the response and regulating strategies of microbial functional traits that are associated with the typical C, N, P, S cycling processes in a pristine soil under aerobic and anaerobic conditions after the addition of PAHs. Results revealed that indigenous microorganisms had strong degradation potential and adaptability to PAHs especially under aerobic conditions, while anaerobic conditions favored the degradation of high molecular weight PAHs. PAHs exhibited contrasting effects on soil microbial functional traits under different aeration conditions. It would probably change microbial carbon source utilization preference, stimulate inorganic P solubilization and strengthen the functional interactions between soil microorganisms under aerobic conditions, while might cause the increase of H₂S and CH₄ emissions under anaerobic conditions. This research provides an effective theoretical support for the ecological risk assessment of soil PAHs pollution.

Revealing the key species for pyrene degradation in Vallisneria natans rhizosphere sediment via triple chamber rhizome-box experiments

To identify key species associated with pyrene degradation in Vallisneria natans (V.natans) rhizosphere sediment, this work investigated the temporal and spatial changes in the rhizosphere microbial community and the relationship between the changes and the pyrene degradation process through a three-compartment rhizome-box experiment under pyrene stress. The degradation kinetics of pyrene showed that the order of degradation rate was rhizosphere > near-rhizosphere > non-rhizosphere. The difference in the pyrene degradation behavior in the sediments corresponded to the change in the proportions of dominant phyla (Firmicutes and Proteobacteria) and genera (g_Massilia f_Comamonadaceae, g_Sphingomonas). The symbiosis networks and hierarchical clustering analysis indicated that the more important phyla related to the pyrene degradation in the rhizosphere was Proteobacteria, while g_Sphigomonas, f_Comamonadaceae, and especially g_Massilia were the core genera. Among them, f_Comamonadaceae was the genus most affected by rhizosphere effects. These findings strengthened our understanding of the PAHs-degradation microorganisms in V.natans rhizosphere and are of great significance for enhancing phytoremediation on PAHs-contaminated sediment.

New insights into the effects of antibiotics and copper on microbial community diversity and carbon source utilization

Residual antibiotics (ABs) and heavy metals (HMs) are continuously released from soil, reflecting their intensive use and contamination of water and soil, posing an environmental problem of great concern. Relatively few studies exist of the functional diversity of soil microorganisms under the combined action of ABs and HMs. To address this deficiency, BIOLOG ECO microplates and the Integrated Biological Responses version 2 (IBRv2) method were used to comprehensively explore the effects of single and combined actions of copper (Cu) and enrofloxacin (ENR), oxytetracycline (OTC), and sulfadimidine (SM2) on the soil microbial community. The results showed that the high concentration (0.80 mmol/kg) compound group had a significant effect on average well color development (AWCD) and OTC showed a dose-response relationship. The results of IBRv2 analysis showed that the single treatment group of ENR or SM2 had a significant effect on soil microbial communities, and the IBRv2 of E1 was 5.432. Microbes under ENR, SM2, and Cu stress had more types of available carbon sources, and all treatment groups were significantly more enriched with microorganisms having D-mannitol and L-asparagine as carbon sources. This study confirms that the combined effects of ABs and HMs can inhibit or promote the function of soil microbial communities. In addition, this paper will provide new insights into IBRv2 as an effective method to evaluate the impacts of contaminants on soil health.

Non-targeted metabolomics and 16s rDNA reveal the impact of uranium stress on rhizosphere and non-rhizosphere soil of ryegrass

As a radioactive heavy metal element with a long half-life, uranium causes environmental pollution when it enters the surrounding soil. This study analyzed the changes about soil enzyme activity, non-targeted metabolomics, microbial community structure and function microbial community structure and function to assess the differences in the effects of uranium stress on rhizosphere and non-rhizosphere soil. Results showed that uranium stress significantly inhibited the activities of urease and sucrase in rhizosphere and non-rhizosphere, which had less effect on rhizosphere. Compare to the non-rhizosphere soil, the uranium stress induced the production of gibberellin A1, to promoted several metabolic pathways, such as nitrogen and PTS (Phosphotransferase system) metabolic in rhizosphere soil. The species and abundance of Aspergillus, Acidobacter, and Synechococcus in both rhizosphere and non-rhizosphere soil were decreased by uranium stress. However, the microorganisms in rhizosphere soil were less inhibited according to the soil metabolism and microbial network map analysis. Furthermore, the Chujaibacter in rhizosphere soil under uranium stress was found significantly positively correlated with lipid and organic oxygen compounds. Overall, the results indicated that ryegrass roots significantly alleviated the effects of uranium stress on soil microbial activity and population abundances, thus playing a protective role. The study also provided a theoretical basis for in-depth understanding of the biological effects, prevention and control mechanisms of uranium-contaminated soil.

Effects of co-modified biochar immobilized laccase on remediation and bacterial community of PAHs-contaminated soil

Considering the stability and economy of immobilized enzymes, this study prepared co-modified biochar immobilized laccase product named Fe₃O₄@NaBC@GA@LC via orthogonal experimental design and explored its possibility of remediating polycyclic aromatic hydrocarbons (PAHs) contaminated soil in steel plants. Compared with the free laccase treatment, the relative activity of Fe₃O₄@NaBC@GA@LC remained 60 % after 50 days of incubation at room temperature. The relative activity of Fe₃O₄@NaBC@GA@LC could still retain nearly 80 % after five reuses. In the process of simulating the PAHs-contaminated site treatment experiment in Hangzhou Iron and steel plant, immobilized laccase exhibited efficient adsorption and degradation performances and even the removal rate of 5-ring PAHs reached more than 90 % in 40 days, resulting in improving urease activity and dehydrogenase in the soil and promoted the growth of a PAH degrading bacteria (Massilia). Our results further explained the efficient degradation effects of Fe₃O₄@NaBC@GA@LC on PAHs, which make it a promising candidate for PAHs-contaminated soil remediation.

Green manure increases peanut production by shaping the rhizosphere bacterial community and regulating soil metabolites under continuous peanut production systems

BACKGROUND

Green manure (GM) is a crop commonly grown during fallow periods, which has been applied in agriculture as a strategy to regulate nutrient cycling, improve organic matter, and enhance soil microbial biodiversity, but to date, few studies have examined the effects of GM treatments on rhizosphere soil bacterial community and soil metabolites from continuous cropping peanut field.

RESULTS

In this study, we found that the abundances of several functionally significant bacterial groups containing Actinobacteria, Acidobacteria, and genus Sphingomonas, which are associated with nitrogen cycling, were dramatically increased in GM-applied soils. Consistent with the bacterial community results, metabolomics analysis revealed a strong perturbation of nitrogen- or carbon-related metabolisms in GM-applied soils. The substantially up-regulated beneficial metabolites including sucrose, adenine, lysophosphatidylcholine (LPC), malic acid, and betaines in GM-applied soils may contribute to overcome continuous cropping obstacle. In contrast to peanut continuous cropping, planting winter wheat and oilseed rape in winter fallow period under continuous spring peanut production systems evidently improved the soil quality, concomitantly with raised peanut pod yield by 32.93% and 25.20%, in the 2020 season, respectively.

CONCLUSIONS

GMs application is an effective strategy to overcome continuous cropping obstacle under continuous peanut production systems by improving nutrient cycling, soil metabolites, and rhizobacterial properties.

Bio-organic fertilizers improve Dendrocalamus farinosus growth by remolding the soil microbiome and metabolome

Organic and microbial fertilizers have potential advantages over inorganic fertilizers in improving soil fertility and crop yield without harmful side-effects. However, the effects of these bio-organic fertilizers on the soil microbiome and metabolome remain largely unknown, especially in the context of bamboo cultivation. In this study, we cultivated Dendrocalamus farinosus (D. farinosus) plants under five different fertilization conditions: organic fertilizer (OF), Bacillus amyloliquefaciens bio-fertilizer (Ba), Bacillus mucilaginosus Krassilnikov bio-fertilizer (BmK), organic fertilizer plus Bacillus amyloliquefaciens bio-fertilizer (OFBa), and organic fertilizer plus Bacillus mucilaginosus Krassilnikov bio-fertilizer (OFBmK). We conducted 16S rRNA sequencing and liquid chromatography/mass spectrometry (LC-MS) to evaluate the soil bacterial composition and soil metabolic activity in the different treatment groups. The results demonstrate that all the fertilization conditions altered the soil bacterial community composition. Moreover, the combination of organic and microbial fertilizers (i.e., in the OFBa and OFBmK groups) significantly affected the relative abundance of soil bacterial species; the largest number of dominant microbial communities were found in the OFBa group, which were strongly correlated with each other. Additionally, non-targeted metabolomics revealed that the levels of soil lipids and lipid-like molecules, and organic acids and their derivatives, were greatly altered under all treatment conditions. The levels of galactitol, guanine, and deoxycytidine were also markedly decreased in the OFBa and OFBmK groups. Moreover, we constructed a regulatory network to delineated the relationships between bamboo phenotype, soil enzymatic activity, soil differential metabolites, and dominant microbial. The network revealed that bio-organic fertilizers promoted bamboo growth by modifying the soil microbiome and metabolome. Accordingly, we concluded that the use of organic fertilizers, microbial fertilizers, or their combination regulated bacterial composition and soil metabolic processes. These findings provide new insights into how D. farinosus-bacterial interactions are affected by different fertilization regiments, which are directly applicable to the agricultural cultivation of bamboo.

Bioaugmentation enhance the bioremediation of marine crude oil pollution: Microbial communities and metabolic pathways

Bioaugmentation is an effective strategy used to speed up the bioremediation of marine oil spills. In the present study, a highly efficient petroleum degrading bacterium (Pseudomonas aeruginosa ZS1) was applied to the bioremediation of simulated crude oil pollution in different sampling sites in the South China Sea. The metabolic pathways of ZS1 to degrade crude oil, the temporal dynamics of the microbial community response to crude oil contamination, and the biofortification process were investigated. The results showed that the abundance and diversity of the microbial community decreased sharply after the occurrence of crude oil contamination. The best degradation rate of crude oil, which was achieved in the samples from the sampling site N3 after the addition of ZS1 bacteria, was 50.94% at 50 days. C13 alkanes were totally oxidized by ZS1 in the 50 days. The degradation rate of solid n-alkanes (C18-C20) was about 70%. Based on the whole genome sequencing and the metabolites analysis of ZS1, we found that ZS1 degraded n-alkanes through the terminal oxidation pathway and aromatic compounds through the catechol pathway. This study provides data support for further research on biodegradation pathways of crude oil and contributes to the subsequent development of more reasonable bioremediation strategies.

Assessment of biological community in riparian zone contaminated by PAHs: Linking source apportionment to biodiversity

Riparian zone, an important land-water interface, plays an essential role in maintaining the ecological health of rivers, whereas the effects of Polycyclic aromatic hydrocarbons (PAHs) on the health of biological communities in riparian groundwater remain undetermined. To understand the responses of multiple communities to environmental variables, the distribution and ecosystem risk of 16 PAHs have been investigated in the Beiluo River, China. The distribution of multiple communities in riparian groundwater was investigated by environmental DNA metabarcoding, including 16S rRNA, 18S rRNA, and COI gene sequencing for bacteria, microbial eukaryotes (including algae, fungi, and protozoa), and metazoan, respectively, followed by correlation analysis between multiple communities and PAH contamination levels. The concentration of PAHs in the Beiluo River ranged largely from 35.32 to 728.59 ng/L. Here, the Shannon's diversity index of bacteria (Firmicutes) decreased possibly due to the occurrence of Pyrene, which mainly derives from coal and biomass combustion. Furthermore, the reduced richness of fungi (Ascomycota, Basidiomycota) and algae (Chlorophyta, Chrysophyceae) can be attributed to the presence of medium molecular weight (MMW) PAHs (Pyrene, Benz(a)anthracene, Chrysene), and low molecular weight (LMW) PAHs (Naphthalene, Fluorene, Phenanthrene). The richness and Shannon's diversity index of metazoan (Arthropoda) were promoted owing to MMW PAHs (Chrysene, Fluoranthene) generated from coal and biomass combustion and traffic emission. The ecological risk of PAHs in the groundwater environment of the Beiluo River was characterized as low to medium, where LMW and MMW PAHs posed higher risk than the high molecular weight (HMW) compounds. Overall, this study provides insights into the structures of riparian multi-biological communities altered by PAHs.

Effects of Comamonas testosteroni on dissipation of polycyclic aromatic hydrocarbons and the response of endogenous bacteria for soil bioremediation

Bioremediation is a promising method of treating polycyclic aromatic hydrocarbons (PAHs) in contaminated soil; however, the understanding of the efficiency and the way of microbial inoculants work in complex soil environments is limited. Comamonas testosteroni (Ct) strains could efficiently degrade PAHs, especially naphthalene (Nap) and phenanthrene (Phe). This study aimed to explore the functional role of Ct in soil indigenous microorganisms and analyze the effect of Ct addition on PAHs concentration in PAH-contaminated soil. The results showed that inoculation with Ct degraded naphthalene (Nap), phenanthrene (Phe), and benzo [α] pyrene (BaP) significantly; the degradation rates were 63.38%, 81.18%, and 37.98% on day 25, respectively, suggesting that the low molecular weights of Nap and Phe were more easily degraded by microorganisms than those of BaP. We speculated that BaP and Phe might be converted into Nap for further degradation, which is the main reason for the low degradation rate of Nap detected after 10-25 days. Network analysis showed that inoculation with Ct significantly increased bacteria community abundance closely related to PAHs. Structural equation models confirmed that Steroidobacter, as functional bacteria, could affect the degradation of Nap and BaP. Inoculated Ct effectively enhanced the synergy among indigenous bacteria to degrade PAHs. This finding will help understand the function of inoculated Ct strains in PAH-contaminated soil at the laboratory level.

Uniqueness and Dependence of Bacterial Communities on Microplastics: Comparison with Water, Sediment, and Soil

Revealing the dependence and uniqueness of microbial communities on microplastics could help us better understand the assembly of the microplastic microbial community in river ecosystems. In this study, we investigated the composition and ecological functions of the bacterial community on microplastics from the Three Gorges Reservoir area compared with those in water, sediment, and soil at species-level via full-length 16S rRNA gene sequencing. The results showed that the full-length 16S rRNA sequencing provided more detail and accurate taxa resolution of the bacterial community in microplastics (100%), water (99.90%), sediment (99.95%), and soil (100%). Betaproteobacteriales were the most abundant bacteria in microplastics (14.1%), water (32.3%), sediments (27.2%), and soil (21.0%). Unexpectedly, oligotrophic SAR11 clade was the third abundant bacteria (8.51%) and dominated the ecological functions of the bacterial community in water, but it was less observed on microplastics, with a relative abundance of 2.73×10^-5. However, four opportunistic pathogens identified at the species level were selectively enriched on microplastics. Stenotrophomonas maltophilia was the main opportunistic pathogen on microplastics (0.29%). Sediment rather than soil and water may be contributed mostly to pathogens on microplastics. Moreover, some bacteria species with the biodegradation function of microplastics were enriched on microplastics, such as bacteria Rhodobacter sp., and endemic bacteria Luteimonas sp. The distinct bacteria composition on microplastics enhanced several ecological functions, such as xenobiotics biodegradation, which allows screening the bacteria with the biodegradation function of microplastics through long-term exposure.

Pollution pressure and soil depth drive prokaryotic microbial assemblage and co-occurrence patterns in an organic polluted site

Organic polluted sites have become a global concern of soil contamination, yet little is known about microbial vertical distribution and community assembly in organic polluted sites. Here, high-throughput sequencing technology was employed to investigate prokaryotic microbial diversity and community assembly along soil profile in an abandoned chemical organic contaminated site. Results showed that there was no significant difference (P > 0.05) observed in microbial alpha diversity among different soil layers, whereas the structure of microbial communities presented significantly different (P < 0.05) in the superficial layer (0-0.5 m) compared with intermediate (1-1.5 m) and bottom (2.5-3 m) layers. Soil prokaryotic microbial community evolved to possess the potential of degrading organic pollutants under long-term organic pollution stress. A relatively homogeneous environment created by the organic polluted site mainly induced the ecological process of homogeneous selection driving community assembly, while dispersal limitation gained importance with the increase of soil depth. Organic contaminants were identified as the key driver of destabilizing co-occurrence networks, while the frequent cooperative behaviors among species could combat organic pollution stress and sustain prokaryotic community stability. Collectively, pollution pressure and soil depth jointly affected prokaryotic microbial assemblage and co-occurrence that underpinned the spatial scaling patterns of organic contaminated sites microbiota.

Influence of bacterial community diversity, functionality, and soil factors on polycyclic aromatic hydrocarbons under various vegetation types in mangrove wetlands

Polycyclic aromatic hydrocarbons (PAHs) are prevalent organic pollutants in coastal ecosystems, particularly in mangrove wetlands. However, it is still largely unclear how PAHs affect the soil bacterial community under various vegetation types in the Greater Bay Area. Here, we selected soil samples from four sites with different vegetation types (native mangrove forest dominated by Kandelia candel, invasive mangrove forest dominated by Sonneratia apetala, unvegetated mudflat, and riverine runoff outlet) in the Qi'ao and Futian Nature Reserves. We investigated the effects of PAHs on soil bacterial community composition and diversity, function, and co-occurrence via 16S rRNA high-throughput sequencing. PAHs obviously reduced soil bacterial community diversity and richness. Based on PICRUSt 2, PAHs demonstrated positive influences on PAHs degradation metabolism related bacterial genes. Meanwhile, we predicted that riverine runoff outlets can potentially degrade PAHs, may donate to sustain healthy mangrove ecosystem. Also, PAHs and total nitrogen (TN) were crucial factors driving the soil bacterial community in Qi'ao sites, whereas in the Futian sites, PAHs and SOC were more important. PAHs, SOC and TN showed negative effects on specific bacteria abundance. Subsequently, environmental factors and PAHs levels influenced the soil bacterial ecological functions community. Co-occurrence network analysis revealed non-random assembly patterns of the bacterial communities. SBR1031 and A4b were the keystone genera and played a crucial role whgich played an irreplaceable role in PAHs degradation in Qi'ao and Futian sites. PAHs inhibited specific microbial activity and metabolism in native mangrove forest, while affects positively to bacterial community in riverine runoff outlet which might profoundly affect the whole soil quality under various vegetation types. Overall, this study might identify existing health problems and provide insights for enhancing protection and utilization management for mangrove ecosystem in the Greater Bay Area.

Environmental behavior of the chiral fungicide epoxiconazole in earthworm-soil system: Enantioselective enrichment, degradation kinetics, chiral metabolite identification, and biotransformation mechanism

The environmental impact of the chiral fungicide epoxiconazole and its chiral transformation products (TPs) on non-target organisms and the environment has become a significant concern due to its widespread use in agricultural practice. Enantioselectivity studies of parent contaminants cannot adequately assess the complexity of its chiral TPs in the environment. This study aimed to investigate the environmental behavior of epoxiconazole in an earthworm-soil system. 2S,3R-(-)-epoxiconazole was preferentially enriched in earthworms during the accumulation phase (p < 0.05), but no enantioselectivity was observed during the elimination phase. One methoxylated and four hydroxylated chiral TPs were identified in soil, earthworm, and excrement. The epoxy ring hydroxylated TP and methoxylated TP of epoxiconazole were discovered for the first time in the environment. The chemically specific enantioselectivity with enantiomer fraction (EF) > 0.8 was observed for the TPs in different matrices. The CYP450 monooxygenase of earthworm was significant activated. In vitro enzyme metabolism experiments (earthworm microsomes and recombinant CYP450 enzymes CYP2A6, CYP 2C9, and CYP 3A4) were carried out to further explain the biotransformation mechanism of epoxiconazole in earthworm. This study provides new evidence of enantiomeric biotransformation of chiral fungicide epoxiconazole in the earthworm-soil system and could provide valuable insights into their environmental risk assessment.

Evaluation of the ecological impacts of short- and long-chain perfluoroalkyl acids on constructed wetland systems: Perfluorobutyric acid and perfluorooctanoic acid

Perfluoroalkyl substances (PFASs) contamination of aquatic system has attracted widespread attention in recent years. From both plant and microbial perspectives, the ecological risk of CWs by comparing PFASs with different chain lengths have not been fully understood. In this study, the influences of perfluorobutyric acid (PFBA) and perfluorooctanoic acid (PFOA) as typical of short- and long-chains on the ecological effect of CWs have been specifically studied. The results showed that plants produced oxidative stress response and the activities of superoxide dismutase (SOD) and peroxidase (POD) in leaves were stimulated by 17.23-28.13% and 10.49-14.17% upon 10 mg/L PFBA and PFOA exposure. Under the high level of PFBA and PFOA stress, the chlorophyll content was reduced by 15.20-39.40% and lipid peroxidation was observed in leaves with the accumulation of malondialdehyde (MDA) at 1.20-1.22 times of the control. Dehydrogenase (DHA) exhibited the most sensitivity in the presence of PFBA and PFOA with an inhibition ratio of over 90%. The biotoxicity of PFOA was higher than that of PFBA in terms of the inhibition degree of several substrate enzymes. The information of Illumina Miseq sequencing indicated that the diversity and structure of microbial community in CWs were significantly altered by PFBA and PFOA addition and led to an enrichment of more PFASs-tolerant bacteria.

Maize and peanut intercropping improves the nitrogen accumulation and yield per plant of maize by promoting the secretion of flavonoids and abundance of Bradyrhizobium in rhizosphere

Belowground interactions mediated by root exudates are critical for the productivity and efficiency of intercropping systems. Herein, we investigated the process of microbial community assembly in maize, peanuts, and shared rhizosphere soil as well as their regulatory mechanisms on root exudates under different planting patterns by combining metabolomic and metagenomic analyses. The results showed that the yield of intercropped maize increased significantly by 21.05% (2020) and 52.81% (2021), while the yield of intercropped peanut significantly decreased by 39.51% (2020) and 32.58% (2021). The nitrogen accumulation was significantly higher in the roots of the intercropped maize than in those of sole maize at 120 days after sowing, it increased by 129.16% (2020) and 151.93% (2021), respectively. The stems and leaves of intercropped peanut significantly decreased by 5.13 and 22.23% (2020) and 14.45 and 24.54% (2021), respectively. The root interaction had a significant effect on the content of ammonium nitrogen (NH₄ ⁺-N) as well as the activities of urease (UE), nitrate reductase (NR), protease (Pro), and dehydrogenase (DHO) in the rhizosphere soil. A combined network analysis showed that the content of NH₄ ⁺-N as well as the enzyme activities of UE, NR and Pro increased in the rhizosphere soil, resulting in cyanidin 3-sambubioside 5-glucoside and cyanidin 3-O-(6-Op-coumaroyl) glucoside-5-O-glucoside; shisonin were significantly up-regulated in the shared soil of intercropped maize and peanut, reshaped the bacterial community composition, and increased the relative abundance of Bradyrhizobium. These results indicate that interspecific root interactions improved the soil microenvironment, regulated the absorption and utilization of nitrogen nutrients, and provided a theoretical basis for high yield and sustainable development in the intercropping of maize and peanut.

Integrating high-throughput sequencing and metabolomics to investigate the stereoselective responses of soil microorganisms to chiral fungicide cis-epoxiconazole

The use of the chiral triazole fungicide cis-epoxiconazole in agricultural production continues to increase; however, little is known about the stereoselective and toxic responses of soil microorganisms to cis-epoxiconazole in the soil microenvironment. High-throughput sequencing and metabolomics were integrated to investigate the stereoselective response of soil microbial community structure, metabolic profile to cis-epoxiconazole exposure, and the correlation between the microbiomes and different metabolites. Soil microbial community structure and soil metabolic profile were significantly altered and exhibited significant enantioselectivity. The alpha diversity (Chao, Shannon, and Simpson diversity) of bacterial and fungus was not significantly affected, whereas the beta diversity (Bray-Curtis dissimilarity and PLS-DA) of bacterial and fungus was significantly altered in treatment of cis-epoxiconazole and its enantiomers (p-value < 0.05). The variation in bacterial and fungus community structure was the highest under (+)-enantiomer exposure, followed by exposure to racemate and (-)-enantiomer. Soil metabolomic analysis revealed that exposure to high or low doses of cis-epoxiconazole and its enantiomers resulted in different degrees of reprogramming of the soil metabolic pool. The 39 significantly changed metabolites mainly included small molecular organic acids, amino acids and their intermediates, and purine and adenosine intermediates. Six metabolic pathways were significantly disrupted. Different correlation patterns were observed between the significantly altered metabolites and microbes (p-value < 0.05) by Pearson correlation-based analysis. In conclusion, as xenobiotic pollutant, epoxiconazole altered the structure and metabolism of soil microorganisms with significant stereoselectivity mainly driven by 2R, 3S-(+)-cis-epoxiconazole. This study provided a more robust assessment of the risks of epoxiconazole exposure to soil microorganisms. Given the importance of the soil environment in agricultural production, characterization of the soil microbiome and metabolome can provide new insights into the ecological risks posed by exposure to the chiral triazole pesticide cis-epoxiconazole and its enantiomers.