Field-scale studies on the change of soil microbial community structure and functions after stabilization at a chromium-contaminated site

Genome and transcriptomic analysis of the adaptation of Escherichia coli to environmental stresses

In natural niches, bacteria are forced to spend most of their lives under various environmental stresses, such as nutrient limitation, heavy metal pollution, heat and antibiotic stress. To cope with adverse environments, bacterial genome can during the life cycle, produce potential adaptive mutants. The genomic changes, especially mutations, in the genes that encode RNA polymerase and transcription factors, might lead to variations in the transcriptome. These variations enable bacteria to cope with environmental stresses through physiological adaptation in response to stress. This paper reviews the recent contributions of genomic and transcriptomic analyses in understanding the adaption mechanism of Escherichia coli to environmental stresses. Various genomic changes have been observed in E. coli strains in laboratory or under natural stresses, including starvation, heavy metals, acidic conditions, heat shock and antibiotics. The mutations include slight changes (one to several nucleotides), deletions, insertions, chromosomal rearrangements and variations in copy numbers. The transcriptome of E. coli largely changes due to genomic mutations. However, the transcriptional profiles vary due to variations in stress selections. Cellular adaptation to the selections is associated with transcriptional changes resulting from genomic mutations. Changes in genome and transcriptome are cooperative and jointly affect the adaptation of E. coli to different environments. This comprehensive review reveals that coordination of genome mutations and transcriptional variations needs to be explored further to provide a better understanding of the mechanisms of bacterial adaptation to stresses.

Response patterns of the microbiome during hexavalent chromium remediation by Tagetes erecta L

Chromium pollution, particularly hexavalent chromium [Cr(VI)], may threaten the environment and human health. This study investigated the potential of Tagetes erecta L. (Aztec marigold) for phytoremediation of soil contaminated with Cr(VI), and focused on the effects of varying concentrations of Cr(VI) on both the physicochemical properties of soil and microbiome of Tagetes erecta L. We observed that Tagetes erecta L. showed tolerance to Cr(VI) stress and maintained normal growth under these conditions, as indicated by bioconcentration factors of 0.33-0.53 in shoots and 0.39-0.70 in roots. Meanwhile, the structure and diversity of bacterial communities were significantly affected by Cr(VI) pollution. Specifically, Cr(VI) had a more significant effect on the microbial community structure in the endophytic of Tagetes erecta L. than in the rhizosphere (p < 0.05). The genera Devosia and Methylobacillus were positively correlated with Cr(VI) concentrations. Biomarkers such as Bacilli and Pseudonocardia were identified under the different Cr(VI)-contaminated treatments using LEfSe. In addition, the interaction and stability of the endophytic microbiome were enhanced under Cr(VI) stress. This study explored the interactions between heavy metals, microorganisms, and plants, providing valuable insights for developing in situ bioremediation of Cr(VI)-contaminated soils.

Effect of EDDS on the rhizosphere ecology and microbial regulation of the Cd-Cr contaminated soil remediation using king grass combined with Piriformospora indica

The negative impacts of soil heavy metals composite pollution on agricultural production and human health are becoming increasingly prevalent. The applications of green chelating agents and microorganisms have emerged as promising alternate methods for enhancing phytoremediation. The regulatory effects of root secretion composition, microbial carbon source utilization, key gene expression, and soil microbial community structure were comprehensively analyzed through a combination of HPLC, Biolog EcoPlates, qPCR, and high-throughput screening techniques. The application of EDDS resulted in a favorable rhizosphere ecological environment for the king grass Piriformospora indica, characterized by a decrease in soil pH by 0.41 units, stimulation of succinic acid and fumaric acid secretion, and an increase in carbon source metabolic activity of amino acids and carbohydrates. Consequently, this improvement enhanced the bioavailability of Cd/Cr and increased the biomass of king grass by 25.7%. The expression of dissimilatory iron-reducing bacteria was significantly upregulated by 99.2%, while there was no significant difference in Clostridium abundance. Furthermore, the richness of the soil rhizosphere fungal community (Ascomycota: 45.8%, Rozellomycota: 16.7%) significantly increased to regulate the proportion of tolerant microbial dominant groups, promoting the improvement of Cd/Cr removal efficiency (Cd: 23.4%, Cr: 18.7%). These findings provide a theoretical basis for the sustainable development of chelating agent-assisted plants-microorganisms combined remediation of heavy metals in soil.

Microplastics alter Cr accumulation and fruit quality in Cr(VI) contaminated soil-cucumber system during the lifecycle: Insight from rhizosphere bacteria and root metabolism

Both microplastics and Cr(VI) potentially threaten soil and crops, but little is known about their interaction in the soil-plant system. This study investigated the effect and mechanism of polyethylene (PE), polyamide (PA), and polylactic acid (PLA) microplastics on Cr bioaccumulation and toxicity in a Cr(VI) contaminated soil-cucumber system during the lifecycle. The results show that microplastics had a greater effect on Cr accumulation in cucumber roots, stems, and leaves than in fruits. PE microplastics increased, but PA and PLA microplastics decreased the Cr accumulation in cucumber. Microplastics, especially high-dose, small, and aged microplastics, exacerbated the effects of accumulated Cr in cucumber on fresh weight and fruit yield. The nutrient contents in fruits except soluble sugars were reduced by microplastics. The random forest regression model shows that the microplastic type was the most important factor causing changes in the soil-cucumber system except for Cr(VI) addition. Under Cr(VI) and microplastic co-exposure, bacteria that could simultaneously tolerate Cr(VI) stress and degrade microplastics were enriched in the rhizosphere soil. The partial least squares path model shows that microplastics reduced the beneficial effect of the bacterial community on cucumber growth. Microplastics, especially PLA microplastics, alleviated the adverse effects of Cr(VI) stress on root metabolism.

Effect of Phanerochaete chrysosporium induced phosphate precipitation on bacterial diversity during the soil remediation process

Biomineralization by phosphate minerals and phosphate solubilizing fungi (PSF) has attracted great interest as a novel remediation method for heavy metal(loid) co-contaminated soil. It was very essential to investigate the microenvironment response with the application of amendments. In this study, three grain sizes of hydroxyapatites (HAP) and Phanerochaete chrysosporium (P. chrysosporium) were used to investigate the change in heavy metal(loid) fractions, soil physicochemical properties, and bacterial community during the remediation of Mangchang and Dabaoshan acidic mine soils. The results showed that the residual fractions in the two soils increased significantly after 35 days of remediation, especially that of As and Zn in Dabaoshan soils were presented at over 87%. In addition, soil pH, organic matter (OM), and available phosphorous (AP) were almost improved. 16S rRNA sequencing analysis indicated that the introduction of culture medium and P. chrysosporium alone changed bacterial abundance, but the addition of HAP changed the bacterial diversity and community composition by altering environmental conditions. The amendments in the research showed good performance on immobilizing heavy metal(loid)s and reducing their bioavailability. Moreover, the research suggested that environmental factors and soil inherent properties could influence the microbial community structure and composition.

Phase transformation of Cr(VI) host-mineral driven by citric acid-aided mechanochemical approach for advanced remediation of chromium ore processing residue-contaminated soil

The slow release of Cr(VI) from chromium ore processing residue-contaminated soil (COPR-soil) poses a significant environmental and health risk, yet advanced remediation techniques are still insufficient. Here, the slow-release behavior of Cr(VI) in COPR-soil is observed and attributed to the embedded Cr(VI) in the lattice of vaterite due to the isomeric substitution of CrO42- for CO32-. A citric acid-aided mechanochemical approach with FeS2/ZVI as reductive material was developed and found to be highly effective in remediating COPR-soil. Almost all Cr(VI) in COPR-soil, including Cr(VI) embedded in the minerals, are reduced with a reduction efficiency of 99.94%. Cr(VI) reduction kinetics indicate that the Cr(VI) reduction rate constant in the presence of citric acid was 4.8 times higher compared to its absence. According to the Raman spectroscopy, X-ray diffraction (XRD), and Electron Probe X-ray Micro-Analyzer (EPMA) analysis, the reduction of Cr(VI) embedded in vaterite was mainly attributed to the citric acid-induced protonation effect. That is, under the protonation effect, the embedded Cr(VI) could be released from vaterite through its phase transformation to calcite, whose affinity to Cr(VI) is low. While the reduction of released Cr(VI) could be promoted due to the complexation of citric acid with disulfide groups on FeS2/ZVI. The results of long-term stability tests demonstrated that the remediated COPR-soil exhibited excellent long-term stability, which may also be associated with improved utilization of available carbon and electron donors by the Cr(VI) reducing bacteria (Proteobacteria)-dominated microbial community in the presence of citric acid, thereby promoting to establish a stable reducing microenvironment. Collectively, these findings will further our understanding of the reduction remediation of COPR-soil, especially in the case of Cr(VI) embedded in minerals.

Zinc oxide nanoparticles alleviate chromium-induced oxidative stress by modulating physio-biochemical aspects and organic acids in chickpea (Cicer arietinum L.)

Extensive chromium (Cr) release into water and soil severely impairs crop productivity worldwide. Nanoparticle (NP) technology has shown potential for reducing heavy metal toxicity and improving plant physicochemical profiles. Herein, we investigated the effects of exogenous zinc oxide NPs (ZnO-NPs) on alleviating Cr stress in Cr-sensitive and tolerant chickpea genotypes. Hydroponically grown chickpea plants were exposed to Cr stress (0 and 120 μM) and ZnO-NPs (25 μM, 20 nm size) twice at a 7-day interval. Cr exposure reduced physiochemical profiles, ion content, cell viability, and gas exchange parameters, and it increased organic acid exudate accumulation in roots and the Cr content in the roots and leaves of the plants. However, ZnO-NP application significantly increased plant growth, enzymatic activities, proline, total soluble sugar, and protein and gas exchange parameters and reduced malondialdehyde and hydrogen peroxide levels, Cr content in roots, and organic acid presence to improve root cell viability. This study provides new insights into the role of ZnO-NPs in reducing oxidative stress along with Cr accumulation and mobility due to low levels of organic acids in chickpea roots. Notably, the Cr-tolerant genotype exhibited more pronounced alleviation of Cr stress by ZnO-NPs. These findings highlight the potential of ZnO-NP in regulating plant growth, reducing Cr accumulation, and promoting sustainable agricultural development.

Mixed nitrate and metal contamination influences operational speciation of toxic and essential elements

Environmental contamination constrains microbial communities impacting diversity and total metabolic activity. The former S-3 Ponds contamination site at Oak Ridge Reservation (ORR), TN, has elevated concentrations of nitric acid and multiple metals from decades of processing nuclear material. To determine the nature of the metal contamination in the sediment, a three-step sequential chemical extraction (BCR) was performed on sediment segments from a core located upgradient (EB271, non-contaminated) and one downgradient (EB106, contaminated) of the S-3 Ponds. The resulting exchangeable, reducing, and oxidizing fractions were analyzed for 18 different elements. Comparison of the two cores revealed changes in operational speciation for several elements caused by the contamination. Those present from the S-3 Ponds, including Al, U, Co, Cu, Ni, and Cd, were not only elevated in concentration in the EB106 core but were also operationally more available with increased mobility in the acidic environment. Other elements, including Mg, Ca, P, V, As, and Mo, were less operationally available in EB106 having decreased concentrations in the exchangeable fraction. The bioavailability of essential macro nutrients Mg, Ca, and P from the two types of sediment was determined using three metal-tolerant bacteria previously isolated from ORR. Mg and Ca were available from both sediments for all three strains; however, P was not bioavailable from either sediment for any strain. The decreased operational speciation of P in contaminated ORR sediment may increase the dependence of the microbial community on other pools of P or select for microorganisms with increased P scavenging capabilities. Hence, the microbial community at the former S-3 Ponds contamination site may be constrained not only by increased toxic metal concentrations but also by the availability of essential elements, including P.

Sources, impacts, factors affecting Cr uptake in plants, and mechanisms behind phytoremediation of Cr-contaminated soils

Chromium (Cr) is released into the environment through anthropogenic activities and has gained significant attention in the recent decade as environmental pollution. Its contamination has adverse effects on human health and the environment e.g. decreases soil fertility, alters microbial activity, and reduces plant growth. It can occur in different oxidation states, with Cr(VI) being the most toxic form. Cr contamination is a significant environmental and health issue, and phytoremediation offers a promising technology for remediating Cr-contaminated soils. Globally, over 400 hyperaccumulator plant species from 45 families have been identified which have the potential to remediate Cr-contaminated soils through phytoremediation. Phytoremediation can be achieved through various mechanisms, such as phytoextraction, phytovolatilization, phytodegradation, phytostabilization, phytostimulation, and rhizofiltration. Understanding the sources and impacts of Cr contamination, as well as the factors affecting Cr uptake in plants and remediation techniques such as phytoremediation and mechanisms behind it, is crucial for the development of effective phytoremediation strategies. Overall, phytoremediation offers a cost-effective and sustainable solution to the problem of Cr pollution. Further research is needed to identify plant species that are more efficient at accumulating Cr and to optimize phytoremediation methods for specific environmental conditions. With continued research and development, phytoremediation has the potential to become a widely adopted technique for the remediation of heavy metal-contaminated soils.

Spatiotemporal distribution and pollution control of pollutants in a Cr(VI)-contaminated site located in Southern China

Soil and groundwater Cr(VI) pollution resulting from improper disposal and accidental spills is a critical problem worldwide. In this study, a comprehensive study was conducted to assess the hydrogeological conditions of a contaminated site, obtain spatiotemporal distribution and trend forecasts of pollutant Cr(VI), and determine the feasibility of applying clayey engineered barriers for pollution control. The results showed that the hydraulic conductivity (K) of the clayey barrier (1.56E-5 m/d) is several orders of magnitude lower than that of the stratum beneath the contaminated site, with K values ranging from 0.0014 to 4.76 m/d. Cr(VI) exhibits high mobility and a much higher concentration in the vadose zone, with maximum values of 6100 mg/kg in topsoil and 2090 mg/L in the perched aquifer. The simulation results indicated that the groundwater in the vicinity of the contaminated site, as well as downstream of the Lianshui River, is seriously threatened by Cr(VI). Notably, the pollution plume could occur downstream of the Lianshui River after 8 years. The retention efficiency of clayey engineered barriers will decrease over time, at 61.6% after 8 years and 33% after 20 years. This work contributes to an in-depth understanding of Cr(VI) migration at contaminated sites.

Application of magnetic-nanoparticle functionalized whole-cell biosensor array for bioavailability and ecotoxicity estimation at urban contaminated sites

The bioavailability and ecotoxicity of pollutants are important for urban ecological systems and human health, particularly at contaminated urban sites. Therefore, whole-cell bioreporters are used in many studies to assess the risks of priority chemicals; however, their application is restricted by low throughput for specific compounds and complicated operations for field tests. In this study, an assembly technology for manufacturing Acinetobacter-based biosensor arrays using magnetic nanoparticle functionalization was developed to solve this problem. The bioreporter cells maintained high viability, sensitivity, and specificity in sensing 28 priority chemicals, seven heavy metals, and seven inorganic compounds in a high-throughput manner, and their performance remained acceptable for at least 20 d. We also tested the performance by assessing 22 real environmental soil samples from urban areas in China, and our results showed positive correlations between the biosensor estimation and chemical analysis. Our findings prove the feasibility of the magnetic nanoparticle-functionalized biosensor array to recognize the types and toxicities of multiple contaminants for online environmental monitoring at contaminated sites.

Facilitating New Chromium Reducing Microbes to Enhance Hexavalent Chromium Reduction by In Situ Sonoporation-Mediated Gene Transfer in Soils

Chromium (Cr) is a heavy metal with a high toxicity and pathogenicity. Microbial reduction is an effective strategy to remove Cr(VI) at contaminated sites but suffers from the low populations and activities of Cr-reducing microorganisms in soils. This study proposed an in situ sonoporation-mediated gene transfer approach, which improved soil Cr(VI) reduction performance by delivering exogenous Cr-transporter chrA genes and Cr-reducing yieF genes into soil microorganisms with the aid of ultrasound. Besides the increasing populations of Cr-resistant bacteria and elevated copy numbers of chrA and yieF genes after sonoporation-mediated gene transfer, three new Cr-reducing strains were isolated, among which Comamonas aquatica was confirmed to obtain Cr-resistant capability. In addition, sonoporation-mediated gene transfer was the main driving force significantly shaping soil microbial communities owing to the predominance of Cr-resistant microbes. This study pioneered and evidenced that in situ soil sonoporation-mediated gene transfer could effectively deliver functional genes into soil indigenous microbes to facilitate microbial functions for enhanced bioremediation, e.g., Cr-reduction in this study, showing its feasibility as a chemically green and sustainable remediation strategy for heavy metal contaminated sites.

Nano zero-valent iron enhances the absorption and transport of chromium in rice (Oryza sativa L.): Implication for Cr risks management in paddy fields

Chromium (Cr) accumulating in soil caused serious pollution to cultivated land. At present, nano zero-valent iron (nZVI) is considered to be a promising remediation material for Cr-contaminated soil. However, the nZVI impact on the behavior of Cr in the soil-rice system under high natural geological background value remains unknown. We studied the effects of nZVI on the migration and transformation of Cr in paddy soil-rice by pot experiment. Three different doses of nZVI (0, 0.001 % and 0.1 % (w/w)) treatments and one dose of 0.1 % (w/w) nZVI treatment without plant rice were set up. Under continuous flooding conditions, nZVI significantly increased rice biomass compared with the control. At the same time, nZVI significantly promoted the reduction of Fe in the soil, increased the concentration of oxalate Fe and bioavailable Cr, then facilitated the absorption of Cr in rice roots and the transportation to the aboveground part. In addition, the enrichment of Fe(III)-reducing bacteria and sulfate-reducing bacteria in soil provided electron donors for Cr oxidation, which helps to form bioavailable Cr that is easily absorbed by plants. The results of this study can provide scientific basis and technical support for the remediation of Cr -polluted paddy soil with high geological background.

Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils

Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.

Arbuscular mycorrhizal fungi-induced tolerance to chromium stress in plants

Chromium (Cr) is one of the toxic elements that harms all forms of life, including plants. Industrial discharges and mining largely contribute to Cr release into the soil environment. Excessive Cr pollution in arable land significantly reduces the yield and quality of important agricultural crops. Therefore, remediation of polluted soil is imperative not only for agricultural sustainability but also for food safety. Arbuscular mycorrhizal fungi (AMF) are widespread soil-borne endophytic fungi that form mutualistic relationships with the vast majority of land plants. In mycorrhizal symbiosis, AMF are largely dependent on the host plant-supplied carbohydrates and lipids, in return, AMF aid the host plants in acquiring water and mineral nutrients, especially phosphorus, nitrogen and sulfur from distant soils, and this distinguishing feature of the two-way exchange of resources is a functional requirement for such mutualism and ecosystem services. In addition to supplying nutrients and water to plants, the AMF symbiosis enhances plant resilience to biotic and abiotic stresses including Cr stress. Studies have revealed vital physiological and molecular mechanisms by which AMF alleviate Cr phytotoxicity and aid plants in nutrient acquisition under Cr stress. Notably, plant Cr tolerance is enhanced by both the direct effects of AMF on Cr stabilization and transformation, and the indirect effects of AMF symbiosis on plant nutrient uptake and physiological regulation. In this article, we summarized the research progress on AMF and associated mechanisms of Cr tolerance in plants. In addition, we reviewed the present understanding of AMF-assisted Cr remediation. Since AMF symbiosis can enhance plant resilience to Cr pollution, AMF may have promising prospects in agricultural production, bioremediation, and ecological restoration in Cr-polluted soils.

Remediation of Cr(VI) contaminated soil by chitosan stabilized FeS composite and the changes in microorganism community

In-suit immobilization is one of the major strategies to remediate heavy metals contaminated soil with the effectiveness largely depends on the characteristics of the added chemical reagents/materials. In this study, chitosan stabilized FeS composite (CS-FeS) was prepared to evaluate the performance of remediating the high and toxic hexavalent chromium contaminated soil from the effectiveness and microbial response aspects. The characterization analysis confirmed the successful preparation of composite, and the introduction of chitosan successfully stabilized FeS to protect it from rapid oxidation as compared to bare FeS particles. With the addition dosage at 0.1%, about 85.6% and 81.3% of Cr(VI) was reduced in 3 d based on toxicity characteristic leaching procedure (TCLP) and CaCl₂ extraction, and the reduction efficiency increased to 96.6% and 94.8% in 7 d, respectively. The Cr(VI) was non-detected in the TCLP leachates with increase the CS-FeS composites to 0.5%. The percentages of HOAc-extractable Cr decreased from 25.17% to 6.12% accompanied with the increase in the residual Cr from 4.26% to 13.77% and improvement of soil enzyme activity under CS-FeS composites addition. Cr(VI) contamination reduced the diversity of microbial community in soil. Three dominate prokaryotic microorganisms, namely Proteobacteria, Actinobacteria and Firmicutes, were observed in Cr-contaminated soil. The addition of CS-FeS composites increased the microbial diversity especially for that in relative lower abundance. The relative abundance of Proteobacteria and Firmicute related to Cr-tolerance and reduction increased in CS-FeS composites added soils. Taking together, these results demonstrated the potential and promising of using the CS-FeS composites for Cr(VI) polluted soil remediation.

Viability and transcriptional responses of multidrug resistant E. coli to chromium stress

The viability of multidrug resistant (MDR) bacteria in environment is critical for the spread of antimicrobial resistance. In this study, two Escherichia coli strains, MDR LM13 and susceptible ATCC25922, were used to elucidate differences in their viability and transcriptional responses to hexavalent chromium (Cr(VI)) stress. The results show that the viability of LM13 was notably higher than that of ATCC25922 under 2-20 mg/L Cr(VI) exposure with bacteriostatic rates of 3.1%-57%, respectively, for LM13 and 0.9%-93.1%, respectively, for ATCC25922. The levels of reactive oxygen species and superoxide dismutase in ATCC25922 were much higher than those in LM13 under Cr(VI) exposure. Additionally, 514 and 765 differentially expressed genes were identified from the transcriptomes of the two strains (log₂|FC| > 1, p < 0.05). Among them, 134 up-regulated genes were enriched in LM13 in response to external pressure, but only 48 genes were annotated in ATCC25922. Furthermore, the expression levels of antibiotic resistance genes, insertion sequences, DNA and RNA methyltransferases, and toxin-antitoxin systems were generally higher in LM13 than in ATCC25922. This work shows that MDR LM13 has a stronger viability under Cr(VI) stress, and therefore may promote the dissemination of MDR bacteria in environment.

Di-2-ethylhexyl phthalate (DEHP) degradation and microbial community change in mangrove rhizosphere gradients

Di-2-ethylhexyl phthalate (DEHP) is a widespread persistent organic pollutant in the environment. As an ultimate barrier preventing pollutant entry into the ocean, mangrove plays an important role in coastal ecosystem. However, little information is known about DEHP degradation in mangrove rhizosphere. In this study, a rhizobox was used to separate four consecutive rhizosphere compartments with distance of 0-2, 2-4, 4-6, and > 6 mm to the rhizoplane of Kandelia obovata and investigate DEHP gradient degradation behavior in rhizosphere. Sediments closer to the rhizoplane exhibited higher DEHP degradation efficiencies (74.4 % in 0-2 mm layer). More precisely, mangrove rhizosphere promoted the benzoic acid pathway and non-selectively accelerated the production of mono(2-ethylhexyl) phthalate, phthalic acid and benzoic acid. Higher sediment organic matter content, lower pH and less humus in rhizosphere benefited DEHP hydrolysis. In addition, rhizosphere significantly increased microbial biomass and activities comparing to bulk sediments. Some bacterial lineages with potential DEHP degradation capability exhibited a distance-dependent pattern that decreased with the distance to the rhizoplane, including Bacillales, Acidothermaceae, Gammaproteobacteria, and Sphingobacteriales. Our findings suggested that mangrove rhizosphere could accelerate DEHP degradation by altering sediment physicochemical properties and microbial composition, showing positive effects on coastal ecosystem services for eliminating phthalate acid ester contamination.

Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site

Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.

Diagnostic strategy for the combined effects of microplastics and potentially toxic elements on microbial communities in catchment scale

Combined effects of potentially toxic materials (PTMs) released from production activities on microbial communities in environmental flimsy area are poorly recognised. Microplastics (MPs) and potentially toxic elements (PTEs) were investigated in soils and river sediments in a headwater catchment from the Qinghai-Tibet Plateau. Their co-effects on microbial communities and the controlling factors affecting communities were further explored. Results showed that MPs and PTEs significantly accumulated in soils and sediments. Among which fragment-shaped MPs and copper (Cu) dominated, with mean contents of 1.11 × 10⁴ and 1.81 × 10⁴ items kg^-1 and 13.80 and 7.33 mg kg^-1 in soils and sediments, respectively. Distribution index (0.54) suggested that fiber-shaped MPs preferred to transport into rivers and deposited in sediments. The film mulching contributed significantly to the occurrence of fragment-shaped MPs, while Cu may be derived from industrial wastewater. The antagonistic effect between fiber-shaped MPs and zinc (Zn) on soil microbial structure was found based on their obtuse angle in canonical correlation analysis. While the synergistic effect between total phosphorus (TP) and Cu on diversity was detected by interaction detector model (q(TP ∩ Cu) >q(TP) >q(Cu), p < 0.05). Soil TP and Cu were identified as controlling factors influencing diversity through random forest model and factor detector (q(TP) = 0.49, q(Cu) = 0.36, p < 0.05), which may be related to direct nutrient supply and microbial resistance, respectively. The negative effects of MPs on structure might be counteracted by increasing Zn content, while the co-existence of TP and Cu further increased diversity. A diagnostic framework, which involves background data collection, sampling analysis, characterisation and relationship investigation, was proposed to explore the co-effects of complex pollution and factors on communities. This study may provide strategies to mitigate the negative effects on microorganisms in the environment.

Selenium and molybdenum synergistically alleviate chromium toxicity by modulating Cr uptake and subcellular distribution in Nicotiana tabacum L

Chromium (Cr) is a harmful heavy metal that poses a serious threat to plants and animals. Selenium (Se) and molybdenum (Mo) are two beneficial elements for plant growth and resistance. However, their interactive effects on Cr uptake and distribution are poorly understood. Therefore, a hydroponics experiment was conducted to explore the effects of the use of Se and Mo alone and simultaneously on mitigating Cr toxicity. In this study, Nicotiana tabacum L. seedlings were exposed to control, 50 µM Cr, 50 μM Cr + 2 μM Se, 50 μM Cr + 1 μM Mo, or 50 μM Cr + 2 μM Se + 1 μM Mo in Hoagland solution. After 2 weeks, the plant biomass, Cr, Se and Mo contents, photosynthesis, leaf ultrastructure, antioxidant system, subcellular distribution and associated gene expression in Nicotiana tabacum L. were determined. The results showed that simultaneous use of Se and Mo promoted tobacco growth under Cr stress, as evidenced by reducing reactive oxygen species (ROS) content and reducing Cr translocation factor (TF) and inducing a 51.3% reduction in Cr content in shoots. Additionally, Se-Mo interactions increased the levels of glutathione (GSH) and phytochelatin (PC) and the distribution of Cr in the cell walls and organelles. Furthermore, the relative expression of PCS1 was upregulated, while those of NtST1 and MSN1 were downregulated. The results concluded that the simultaneous use of Se and Mo effectively alleviated Cr toxicity in Nicotiana tabacum L., which not only offers an efficient way for crops to resist Cr toxicity but also provides evidence for the benefit of Se combined with Mo.

Microbial community succession in soils under long-term heavy metal stress from community diversity-structure to KEGG function pathways

Currently, understanding the structure and function of the microbial community is the key step in artificially constructing microbial communities to control soil heavy metal pollution. Abundant/rare microbial communities play different roles in different levels of concentrations. However, the correlation between heavy metals and rare/abundant subgroups is poorly understood. In this study, we used a metagenomics approach to comprehensively investigate the evolutionary changes in microbial diversity, structure, and function under different heavy metal concentration stress in soils surrounding gold tailings. The results show that the main pollutants were Pb, As, and Zn. Indigenous microorganisms have different responses to heavy metal concentrations. Bacteria are the main components of indigenous microorganisms, mainly including Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. With the increase of heavy metal pollution, the relative abundance of Proteobacteria increased, and that of Actinobacteria decreased. Archaea was significantly inhibited by heavy metal stress and was more sensitive to heavy metal concentration. The response of fungi to heavy metal concentration was not obvious. The results of KEGG pathways showed that carbon fixation was inhibited with increasing heavy metal concentrations, while nitrogen metabolism was in contrast. Abundant subcommunity had a greater correlation mainly with metal resistance mechanisms, and rare subcommunity plays a key role for soil nutrient cycling such as N, S cycling in soils contaminated. Overall, this study provides a comprehensive analysis of the effects of heavy metal stress at different concentrations on microorganisms in farmland around gold tailings and reveals the relationship between heavy metals on KEGG pathways.

Response of soil microbial communities to petroleum hydrocarbons at a multi-contaminated industrial site in Lanzhou, China

Total petroleum hydrocarbon (TPH) contamination poses threats to ecological systems and human health. Many studies have reported its negative impacts on soil microbes, but limited information is known about microbial change and response to multiple TPH contamination events. In this study, we investigated TPH contamination level, microbial community structure and functional genes at a multi-contaminated industrial site in Lanzhou, where a benzene spill accident caused the drinking water crisis in 2014. TPHs distribution in soils and groundwater indicated multiple TPH contamination events in history, and identified the spill location where high TPH level (6549 mg kg^-1) and high ratio of low-molecular-weight TPHs (>80%) were observed. In contrast, TPH level was moderate (349 mg kg^-1) and the proportion of low-molecular-weight TPHs was 44% in soils with a long TPH contamination history. After the spill accident, soil bacterial communities became significant diverse (p = 0.047), but the dominant microbes remained the same as Pseudomonadaceae and Comamonadaceae. The abundance of hydrocarbon-degradation related genes increased by 10-1000 folds at the site where the spill accident occurred in multi-contaminated areas and was significantly related to 2-ring PAHs. Such changes of microbial community and hydrocarbon-degradation related genes together indicated the resilience of soil indigenous microbes toward multiple contamination events. Our results proved the significant change of bacterial community and huge shift of hydrocarbon-degradation related genes after the spill accident (multiple contamination events), and provided a deep insight into microbial response at industrial sites with a long period of contamination history.

Remediation of Cr(VI)-Contaminated Soil by Biochar-Supported Nanoscale Zero-Valent Iron and the Consequences for Indigenous Microbial Communities

Biochar/nano-zero-valent iron (BC-nZVI) composites are currently of great interest as an efficient remediation material for contaminated soil, but their potential to remediate Cr-contaminated soils and effect on soil microecology is unclear. The purpose of this study was to investigate the effect of BC-nZVI composites on the removal of Cr(VI) from soil, and indigenous microbial diversity and community composition. The results showed that after 15 days of remediation with 10 g/kg of BC-nZVI, 86.55% of Cr(VI) was removed from the soil. The remediation of the Cr-contaminated soil with BC-nZVI resulted in a significant increase in OTUs and α-diversity index, and even a significant increase in the abundance and diversity of indigenous bacteria and unique bacterial species in the community by reducing the toxic concentration of Cr, changing soil properties, and providing habitat for survival. These results confirm that BC-nZVI is effective in removing Cr(VI) and stabilizing Cr in soil with no significant adverse effects on soil quality or soil microorganisms.

Response of microbial community structure to chromium contamination in Panax ginseng-growing soil

Chromium (Cr) contamination in soil poses a serious security risk for the development of medicine and food with ginseng as the raw material. Microbiome are critical players in the functioning and service of soil ecosystems, but their feedback to Cr-contaminated ginseng growth is still poorly understood. To study this hypothesis, we evaluated the effects of microbiome and different Cr exposure on the soil microbial community using Illumina HiSeq high-throughput sequencing. Our results indicated that 2467 OTUs and 1785 OTUs were obtained in 16S and ITS1 based on 97% sequence similarity, respectively. Bacterial and fungal diversity were affected significantly in Cr-contaminated soil. Besides, Cr contamination significantly changed the composition of the soil bacterial and fungal communities, and some biomarkers were identified in the different classification level of the different Cr-contaminated treatments using LEfSe. Finally, a heatmap of Spearman's rank correlation coefficients and canonical discriminant analysis (CDA) indicated that Chloroflexi, Gemmatimonadetes, Acidobacteria, Verrucomicobia, and Parcubacteria in phylum level and Acidimicrobiia, Gemmatimonadetes, and Deltaproteobacteria in class level were positively correlated with AK, AP, and NO₃^--N (p < 0.05 or p < 0.01), but negatively correlated with total Cr and available Cr (p < 0.05 or p < 0.01). Similarly, in the fungal community, Tubaria, Mortierellaceae, and Rhizophagus in the phylum level and Glomeromycetes, Agaricomycetes, and Exobasidiomycetes in the class level were positively correlated with AK, AP, and NO₃^--N (p < 0.05 or p < 0.01), but negatively correlated with total Cr and available Cr (p < 0.05 or p < 0.01). Our findings provide new insight into the effects of Cr contamination on the microbial communities in ginseng-growing soil.

Immobilization of hexavalent chromium in contaminated soil by nano-sized layered double hydroxide intercalated with diethyldithiocarbamate: Fraction distribution, plant growth, and microbial evolution

Soil contamination by hexavalent chromium (Cr(VI)) poses great risks to human health and ecosystem safety. We introduced a new cheap and efficient layered double hydroxide intercalated with diethyldithiocarbamate (DDTC-LDH) for in-situ remediation of Cr(VI)-contaminated soil. The content of Cr(VI) in contaminated soil (134.26 mg kg^-1) was rapidly reduced to 1.39 mg kg^-1 within 10 days by 0.5% of DDTC-LDH. This result attains to or even exceeds the effectiveness of most of reported soil amendments for Cr(VI) removal in soils. The production cost of DDTC-LDH ($4.02 kg^-1) was relatively low than some common materials, such as nano zero-valent iron ($22.80-140.84 kg^-1). The growth of water spinach became better with the increase of DDTC-LDH dose from 0% to 0.5%, suggesting the recovery of soil function. DDTC-LDH significantly altered the structure and function of soil microbial communities. The species that have Cr(VI)-resistant or Cr(VI)-reductive ability were enriched in DDTC-LDH remediated soils. Network analysis revealed a significant functional niche differentiation of soil microbial communities. In addition to the enhancement of Cr(VI) reduction, the stimulation of plant growth promoting traits, including siderophore biosynthesis, oxidation resistance to reactive oxygen species, and phosphorus availability by DDTC-LDH was another essential mechanism for the immediate remediation of Cr(VI)-contaminated soil.

Long-term and high-bioavailable potentially toxic elements (PTEs) strongly influence the microbiota in electroplating sites

Multiple potentially toxic elements (PTEs) wastes are produced in the process of electroplating, which pollute the surrounding soils. However, the priority pollutants and critical risk factors in electroplating sites are still unclear. Hence, a typical demolished electroplating site (operation for 31 years) in the Yangtze River Delta was investigated. Results showed that the soil was severely polluted by Cr(VI) (1711.3 mg kg^-1), Ni (6754.0 mg kg^-1) and Pb (2784.4 mg kg^-1). The spatial distribution of soil PTEs performed by ArcGIS illustrated that the soil pollution varied with plating workshops. Hard Cr electroplating workshops (HCE), decorative Cr electroplating workshops (DCE) and sludge storage station (SS) were the hot spots in the site. Besides, the toxicity characteristic leaching procedure (TCLP) - extractable Cr and Ni contents in different workshops were significantly related (P < 0.05) to their bioavailable fractions (exchangeable fraction (F1) + bound to carbonate fraction (F2)), which pose potential risk to humans. Although the soil total Pb concentration was high, its mobility was very low (<0.007%). Moreover, the soil microbial community dynamics under the stress of long term and high contents of PTEs were further revealed. The soil microbiota was significantly disturbed by long term and high concentration of PTEs. A bit of bacteria (Caulobacter) and fungi (Cladosporium and Monocillium) showed tolerance potential to multiple metals. Furthermore, the canonical correspondence analysis (CCA) showed that the bioavailable fractions (F1 + F2) of Cr and Ni were the most critical environmental variables affecting microbiota. Therefore, remediation strategies are required urgently to reduce the bioavailability of soil Cr and Ni. The results of this study provide an overview of the pollution distribution and microbial dynamics of a typical plating site, laying a foundation for ecological remediation of electroplating sites in Yangtze River Delta of China.

Key Cr species controlling Cr stability in contaminated soils before and chemical stabilization at a remediation engineering site

Linking chromium (Cr) speciation with its stability in soils is vital because insoluble Cr(VI) and chemically adsorbed Cr(VI) could hinder the remediation efficiency and release Cr(VI) for a prolonged period of time. In this study, we investigated key Cr species to probe the mechanisms controlling the release of insoluble Cr(VI) at Cr-contaminated sites using synchrotron-based X-ray absorption near-edge structure (XANES) for the first time. Chromite, stichtite and Cr-silicate were predominant forms of Cr(III). Insoluble Cr(VI) was hosted by layered double hydroxides (LDHs) such as brownmilerite and hydrotalcite. Anion competition tests documented a substitution of absorbed Cr(VI) by SO₄^2- and NO₃^-. Acid extraction released 6.7-25.7% more Cr(VI) than anion extraction, possibly attributing to the erosion of LDH and CaCrO₄ in calcite rather than Cr-bearing minerals. Brown and red soils released maximally 62% and 44% of total Cr(VI) by 10 mol/(kg soil) and 2 mol/(kg soil) of H⁺, respectively. SO₄^2-, H₂O and H⁺ contributed to more release of total Cr(VI) in brown soils (22%, 33% and 7%) than red soils (25%, 17% and 2%). More crystalline Cr structures were found after chemical stabilization, indicating a higher Cr stability in chemically stabilized soils. Cr and Mn exhibited an overlapped distribution pattern in both contaminated and chemically stabilized soils, hinting at the re-oxidation of Cr(III). Insoluble Cr(VI) could be released by acidic rainfalls and soil organic matters, posing potential threats to Cr long-term stability in field-scale remediation.

Chromium biogeochemical behaviour in soil-plant systems and remediation strategies: A critical review

Chromium (Cr) is a toxic heavy metal that is heavily discharged into the soil environment due to its widespread use and mining. High Cr levels may pose toxic hazards to plants, animals and humans, and thus have attracted global attention. Recently, much progress has been made in elucidating the mechanisms of Cr uptake, transport and accumulation in soil-plant systems, aiming to reduce the toxicity and ecological risk of Cr in soil; however, these topics have not been critically reviewed and summarised to date. Accordingly, based on available data-especially from the last five years (2017-2021)-this review traces a plausible link among Cr sources, levels, chemical forms, and phytoavailability in soil; Cr accumulation and translocation in plants; and Cr phytotoxicity and detoxification in plants. Additionally, given the toxicity and hazard posed by Cr(VI) in soils and the application of reductant materials to reduce Cr(VI) to Cr(III) for the remediation of Cr(VI)-contaminated soils, the reduction and immobilisation mechanisms by organic and inorganic reductants are summarised. Finally, some priority research challenges concerning the biogeochemical behaviour of Cr in soil-plant systems are highlighted, as well as the environmental impacts resulting from the application of reductive materials and potential research prospects.

The response of bacterial communities to V and Cr and novel reducing bacteria near a vanadium‑titanium magnetite refinery

Soil contamination with multiple heavy metals has always been a pressing issue, but little attention has been given to V and Cr and their chemical fractions' impacts on microorganisms because Cr₂O₃ usually occurs as an associated mineral in vanadium mines. To investigate this issue, samples (N1-N6) less affected by anthropogenic activities were selected for microbial analysis. The area near the refinery was heavily contaminated according to the PLI (pollution load index). Actinobacteriota, Proteobacteria, and Chloroflexi were the dominant phyla in the soil. The diversity of bacteria was positively influenced by V and Cr and negatively influenced by pH, while the abundance was positively correlated with soil nutrients. Interestingly, the influence of heavy metals in the residual fraction on the microbial community structure and functional metabolism was higher than that in the oxidizable fraction, which may be due to the relatively low heavy metal valence of the oxidizable fraction, suggesting that low valence binding forms of multivalence elements have little effect on microorganisms in the soil. Ultimately, two strains with great efficiency in reducing V and Cr were screened, and co-occurrence network characteristics with significant positive interactions suggested that Bacillus can coordinate community structure in the same niche. This research will help to explore the bioavailability of heavy metals and further achieve the bioremediation of heavy metal contamination in soil.

In situ remediation of Cr(VI) contaminated groundwater by ZVI-PRB and the corresponding indigenous microbial community responses: a field-scale study

The performance of a permeable reactive barrier (PRB) for the in situ remediation of hexavalent chromium [Cr(VI)] contaminated groundwater, and the resulted responses in the indigenous microbial community, were investigated in a field-scale study. The PRB consisted of a mixture of zero-valent iron (ZVI), gravel and sand. The results showed that the PRB segment with 20% active reaction medium (ZVI) was able to successfully reduce Cr(VI) via chemical reduction from 27.29-242.65 mg/L to below the clean-up goal of 0.1 mg/L, and can be scaled-up under field conditions. It was found that the ZVI induced significant changes in the indigenous microbial community structure and compositions in the area of the PRB and those areas downgradient. The competitive growth among Cr(VI)-reducing bacteria (the reduced abundance of Hydrogenophaga, Pseudomonas, Exiguobacterium and Rhodobacter, along with the enrichment of Rivibacter and Candidatus_Desulforudis) were observed in PRB. In addition, Cr(VI)-reducing bacteria (Hydrogenophaga, Pseudomonas, Exiguobacterium and Rhodobacter) were enriched in the downgradient of PRB, indicating that Cr(VI) can be further bio-reduced to Cr(III). The Cr(VI) bio-reduction could serve as a secondary mechanism for further removal of Cr(VI) from contaminated groundwater, suggesting that the actual lifetime of a PRB can be prolonged, which is important for the design and economic assessment of a PRB. Further analysis revealed that pH, dissolved oxygen, Cr(VI) level, the oxidation-reduction potential, and temperature were the main environmental factors influencing the subsurface microbial community compositions.

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.