Copper stress in flooded soil: Impact on enzyme activities, microbial community composition and diversity in the rhizosphere of Salix integra

Identification of Pb-responsive GST transcripts in Salix integra and Pb tolerance of transgenic plants overexpressing SiGSTU55

The escalating severity of soil Pb pollution has intensified the focus on phytoremediation technologies. The biomass advantages of woody plants offer broader prospects for their application in phytoremediation. Fast-growing woody plant Salix integra exhibit significant potential for remediating Pb pollution. Previous research by our team identified GST gene as the gene with most abundant differential expression transcripts in S. integra responding to Pb stress. Leveraging transcriptomic data of S. integra responding to Pb, we identified 22 Pb-responsive SiGST transcripts. Temporal expression analysis under Pb stress revealed 14 transcripts with significant Pb responsiveness, 8 of which were enriched in the "glutathione metabolism" pathway. Using similarity analysis with proteins from 10 Salicaceae species, we selected the most specific SiGSTU55 protein for further functional validation. Overexpression studies in Arabidopsis thaliana and poplar, along with Pb treatment experiments, demonstrated that SiGSTU55 enhances Pb tolerance in transgenic A. thaliana by stimulating root growth and in transgenic poplar by boosting GST activity, GSH, and PC contents under Pb stress, resulting in significantly greater height growth of transgenic poplar in Pb-containing soil. This study not only identified Pb-responsive SiGSTs in S. integra but also confirmed the capacity of the highly specific SiGSTU55 gene to enhance Pb tolerance in transgenic plants. It offers a reference for research into heavy metal tolerance of GST genes in other plants and establishes a foundation for the application of woody plants in remediating Pb-contaminated soil.

Enhancement of repeated inoculation strategy with a domesticated bacterial consortium on the biodegradation of high-level crude oil in soil

Repeated inoculation of hydrocarbon degrading microbes should be powerful to improve the survival of inoculant, which is vital to achieve efficient remediation of petroleum contaminated soil. This paper aims to study the repeated inoculation (with different inoculum size and time interval) enhanced bioremediation of high-level petroleum contaminated soil with a domesticated bacterial consortium. The copy number of bacterium and alkB gene, soil enzyme activities and microbial community structure during the remediation were systematically analyzed to preliminarily reveal the mechanism of repeated inoculation affecting remediation for the first time. The results revealed that repeated inoculation remarkably improved the total petroleum hydrocarbon (TPH) removal in soil (86.5 % in HC120) compared with a single inoculation (68.9 % in HA120). The TPH removal of repeated inoculation with high inoculum size (HC) on the 60th day was close to that of once inoculation (HA) on the 120th day, suggesting that repeated inoculation led to faster degradation. Interestingly, the effect of inoculation with low dose and more times (LC120, 78.5 %) was equal to that with high dose and less times (HB120, 78.0 %), even much better than that with high dose and once inoculation (HA120). Treatment HC had a significant impact on the soil bacterial diversity and community structure, and the dominant species in the inoculants, such as Stenotrophomonas and Pseudomonas, which was low abundance in the blank group (CK), still maintained high abundance during the remediation process. The soil catalase activities and the number of alkB gene were the highest in HC. Correlation analysis implied that repeated inoculation of hydrocarbon degrading bacteria did improve the survival of inoculant, soil enzyme activities and maintain the number of degrading bacteria, thus promoting the TPH removal. These findings will facilitate the practical application of bioremediation technology to contaminated environment, which has important environmental and economic benefits.

Application of soil amendments to reduce the transfer of trace metal elements from contaminated soils of Lubumbashi (Democratic Republic of the Congo) to vegetables

The extraction of copper and cobalt from mines has led to the contamination of agricultural soils by trace metal elements (TMEs) (e.g. Cu: 204 to 1355 mg/kg). The mining industry is one of the sources of metal discharges into the environment, contributing to water, soil, and air contamination and causing metabolic disorders in the inhabitants of the city of Lubumbashi (R.D. Congo). This study assessed the effectiveness of organocalcareous soil improvers applied to TME-contaminated soils to reduce their transfer to plants. Following a factorial design, increasing doses of organic soil improvers (chicken droppings and sawdust) and agricultural lime were applied to the soils of three market gardens (high, medium, and low Cu contamination). The experiment was monitored for 60 days. Soil physicochemical properties (pH, TOC, and total and available copper, cobalt, lead, cadmium, and zinc (mg/kg)) were determined for the three gardens and in the vegetable biomass. The daily consumption index of the vegetables was determined based on total TME content. The results show that organocalcareous soil improvers did not promote plant growth and survival on soils with high and medium levels of copper contamination. However, on soils with low copper content, organocalcareous soil improvers improved germination and plant survival and reduced the transfer of metals from the soil to the plants. The best germination and plant survival rates were obtained with the lightly contaminated market garden. In addition, the organo-limestone amendments applied to the soils slightly increased the soil pH from acidic to slightly acidic, with pH values ranging from (5.43 ± 0.07 to 7.26 ± 0.33). The daily vegetable consumption index obtained for cobalt in the low-contaminated garden ranged from (0.029 to 0.465 mg/60 kg/day), i.e. from 0.5 to 8.45 times higher than the FAO/WHO limit, unlike the other trace metals (Cd, Cu and Pb) for which the daily consumption index found was lower than the FAO/WHO limit. Organocalcareous soil improvers can only be applied to soils with low levels of TME contamination, but for soils with medium to high levels of metal contamination, new soilless production techniques such as hydroponics or bioponics are needed.

Investigating the Mechanism of Cadmium-Tolerant Bacterium Cellulosimicrobium and Ryegrass Combined Remediation of Cadmium-Contaminated Soil

Cadmium (Cd) pollution has been rapidly increasing due to the global rise in industries. Cd not only harms the ecological environment but also endangers human health through the food chain and drinking water. Therefore, the remediation of Cd-polluted soil is an imminent issue. In this work, ryegrass and a strain of Cd-tolerant bacterium were used to investigate the impact of inoculated bacteria on the physiology and biochemistry of ryegrass and the Cd enrichment of ryegrass in soil contaminated with different concentrations of Cd (4 and 20 mg/kg). The results showed that chlorophyll content increased by 24.7% and 41.0%, while peroxidase activity decreased by 56.7% and 3.9%. In addition, ascorbic acid content increased by 16.7% and 6.3%, whereas glutathione content decreased by 54.2% and 6.9%. The total Cd concentration in ryegrass increased by 21.5% and 10.3%, and the soil's residual Cd decreased by 86.0% and 44.1%. Thus, the inoculation of Cd-tolerant bacteria can improve the antioxidant stress ability of ryegrass in Cd-contaminated soil and change the soil's Cd form. As a result, the Cd enrichment in under-ground and above-ground parts of ryegrass, as well as the biomass of ryegrass, is increased, and the ability of ryegrass to remediate Cd-contaminated soil is significantly improved.

Rhizosphere microbiome of plants used in phytoremediation of mine tailing dams

Rhizospheric microbial communities improve the effectiveness of hyperaccumulators in the phytoremediation of heavy metals. However, limited access to tailing dams and inadequate assessment of plants' phytoremediation potential limit the characterization of native accumulators, hindering the effectiveness of local remediation efforts. This study evaluates the heavy metal sequestration potentials of Pennisetum purpureum, Leucaena leucocephala, and Pteris vittata and their associated rhizospheric microbial communities at the Marlu and Pompora tailing dams in Ghana. The results indicate shoot hyperaccumulation of Cd (334.5 ± 6.3 mg/kg) and Fe (10,647.0 ± 12.6 mg/kg) in P. purpureum and L. leucocephala, respectively. Analysis of rhizospheric bacterial communities revealed the impact of heavy metal contamination on bacterial community composition, associating Fe and Cd hyperaccumulation with Bacillus, Arthrobacter, and Sphingomonas species. This study reports the hyperaccumulation potentials of L. leucocephala and P. purpureum enhanced by associated rhizosphere bacterial communities, suggesting their potential application as an environmentally friendly remediation process of heavy metals contaminated lands.

Biochemical and multi-omics analyses of response mechanisms of rhizobacteria to long-term copper and salt stress: Effect on soil physicochemical properties and growth of Avicennia marina

Mangroves are of important economic and environmental value and research suggests that their carbon sequestration and climate change mitigation potential is significantly larger than other forests. However, increasing salinity and heavy metal pollution significantly affect mangrove ecosystem function and productivity. This study investigates the tolerance mechanisms of rhizobacteria in the rhizosphere of Avicennia marina under salinity and copper (Cu) stress during a 4-y stress period. The results exhibited significant differences in antioxidant levels, transcripts, and secondary metabolites. Under salt stress, the differentially expressed metabolites consisted of 30% organic acids, 26.78% nucleotides, 16.67% organic heterocyclic compounds, and 10% organic oxides as opposed to 27.27% organic acids, 24.24% nucleotides, 15.15% organic heterocyclic compounds, and 12.12% phenyl propane and polyketides under Cu stress. This resulted in differential regulation of metabolic pathways, with phenylpropanoid biosynthesis being unique to Cu stress and alanine/aspartate/glutamate metabolism and α-linolenic acid metabolism being unique to salt stress. The regulation of metabolic pathways enhanced antioxidant defenses, nutrient recycling, accumulation of osmoprotectants, stability of plasma membrane, and chelation of Cu, thereby improving the stress tolerance of rhizobacteria and A. marina. Even though the abundance and community structure of rhizobacteria were significantly changed, all the samples were dominated by Proteobacteria, Chloroflexi, Actinobacteriota, and Firmicutes. Since the response mechanisms were unbalanced between treatments, this led to differential growth trends for A. marina. Our study provides valuable inside on variations in diversity and composition of bacterial community structure from mangrove rhizosphere subjected to long-term salt and Cu stress. It also clarifies rhizobacterial adaptive mechanisms to these stresses and how they are important for mitigating abiotic stress and promoting plant growth. Therefore, this study can serve as a reference for future research aimed at developing long-term management practices for mangrove forests.

Identification of Novel QTL for Mercury Accumulation in Maize Using an Enlarged SNP Panel

Mercury (Hg) pollution not only poses a threat to the environment but also adversely affects the growth and development of plants, with potential repercussions for animals and humans through bioaccumulation in the food chain. Maize, a crucial source of food, industrial materials, and livestock feed, requires special attention in understanding the genetic factors influencing mercury accumulation. Developing maize varieties with low mercury accumulation is vital for both maize production and human health. In this study, a comprehensive genome-wide association study (GWAS) was conducted using an enlarged SNP panel comprising 1.25 million single nucleotide polymorphisms (SNPs) in 230 maize inbred lines across three environments. The analysis identified 111 significant SNPs within 78 quantitative trait loci (QTL), involving 169 candidate genes under the Q model. Compared to the previous study, the increased marker density and optimized statistical model led to the discovery of 74 additional QTL, demonstrating improved statistical power. Gene ontology (GO) enrichment analysis revealed that most genes participate in arsenate reduction and stress responses. Notably, GRMZM2G440968, which has been reported in previous studies, is associated with the significant SNP chr6.S_155668107 in axis tissue. It encodes a cysteine proteinase inhibitor, implying its potential role in mitigating mercury toxicity by inhibiting cysteine. Haplotype analyses provided further insights, indicating that lines carrying hap3 exhibited the lowest mercury content compared to other haplotypes. In summary, our study significantly enhances the statistical power of GWAS, identifying additional genes related to mercury accumulation and metabolism. These findings offer valuable insights into unraveling the genetic basis of mercury content in maize and contribute to the development of maize varieties with low mercury accumulation.

Threshold response of ecosystem water use efficiency to soil water in an alpine meadow

Ecosystem water use efficiency (WUE) is a coupled index of carbon (gross ecosystem productivity, GEP) and water fluxes (transpiration, Tr or evapotranspiration, ET), reflecting how ecosystem uses water efficiently to increase its carbon uptake. Though ecosystem WUE is generally considered to decrease with increasing precipitation levels, it remains elusive whether and how it nonlinearly responds to extreme water changes. Here, we performed a 5-year precipitation halving experiment in an alpine meadow, combined with extremely interannual precipitation fluctuations, to create a large range of soil water variations. Our results showed that WUETr and WUEET consistently showed a quadratic pattern in response to soil water. Such quadratic patterns were steadily held at different stages of growing seasons, with minor changes in the optimal water thresholds (25.0-28.4 %). Below the water threshold, more soil water stimulated GEP but reduced Tr and ET by lowering soil temperature, resulting in a positive response of ecosystem WUE to soil water. Above the threshold, soil water stimulated GEP less than Tr (ET), leading to a negative response of ecosystem WUE to soil water. However, biological processes, including plant cover and belowground biomass as well as vertical root biomass distribution, had less effect on ecosystem WUE. Overall, this work is among the first to reveal the nonlinearity and optimal water thresholds of ecosystem WUE across a broad range of soil water, suggesting that future extreme precipitation events will more frequently surpass the water threshold and differently change the coupling relationships of carbon and water fluxes in alpine grasslands.

Copper reduces the virulence of bacterial communities at environmentally relevant concentrations

Increasing environmental concentrations of metals as a result of anthropogenic pollution are significantly changing many microbial communities. While there is evidence metal pollution can result in increased antibiotic resistance, the effects of metal pollution on the virulence of bacterial communities remains largely undetermined. Here, we experimentally test whether metal stress alters the virulence of bacterial communities. We do this by incubating three wastewater influent communities under different environmentally relevant copper concentrations for three days. We then quantify the virulence of the community phenotypically using the Galleria mellonella infection model, and test if differences are due to changes in the rate of biomass accumulation (productivity), copper resistance, or community composition (quantified using 16S amplicon sequencing). The virulence of the communities was found to be reduced by the highest copper concentration, but not to be affected by the lower concentration. As well as reduced virulence, communities exposed to the highest copper concentration were less diverse and had lower productivity. This work highlights that metal pollution may decrease virulence in bacterial communities, but at a cost to diversity and productivity.

Transcriptome-Wide Identification and Response Pattern Analysis of the Salix integra NAC Transcription Factor in Response to Pb Stress

The NAC (NAM-ATAF1/2-CUC) transcription factor family is one of the largest plant-specific transcription factor families, playing an important role in plant growth and development and abiotic stress response. As a short-rotation woody plant, Salix integra (S. integra) has high lead (Pb) phytoremediation potential. To understand the role of NAC in S. integra Pb tolerance, 53 SiNAC transcripts were identified using third-generation and next-generation transcriptomic data from S. integra exposed to Pb stress, and a phylogenetic analysis revealed 11 subfamilies. A sequence alignment showed that multiple subfamilies represented by TIP and ATAF had a gene that produced more than one transcript under Pb stress, and different transcripts had different responses to Pb. By analyzing the expression profiles of SiNACs at 9 Pb stress time points, 41 of 53 SiNACs were found to be significantly responsive to Pb. Short time-series expression miner (STEM) analysis revealed that 41 SiNACs had two significant Pb positive response patterns (early and late), both containing 10 SiNACs. The SiNACs with the most significant Pb response were mainly from the ATAF and NAP subfamilies. Therefore, 4 and 3 SiNACs from the ATAF and NAP subfamilies, respectively, were selected as candidate Pb-responsive SiNACs for further structural and functional analysis. The RT-qPCR results of 7 transcripts also confirmed the different Pb response patterns of the ATAF and NAP subfamilies. SiNAC004 and SiNAC120, which were randomly selected from two subfamilies, were confirmed to be nuclear localization proteins by subcellular localization experiments. Functional prediction analysis of the associated transcripts of seven candidate SiNACs showed that the target pathways of ATAF subfamily SiNACs were "sulfur metabolism" and "glutathione metabolism", and the target pathways of NAP subfamily SiNACs were "ribosome" and "phenylpropanoid biosynthesis". This study not only identified two NAC subfamilies with different Pb response patterns but also identified Pb-responsive SiNACs that could provide a basis for subsequent gene function verification.

Using soil enzyme Vmax as an indicator to evaluate the ecotoxicity of lower-ring polycyclic aromatic hydrocarbons in soil: Evidence from fluorescein diacetate hydrolase kinetics

Fluorescein diacetate hydrolase (FDA hydrolase) is a reliable biochemical biomarker of changes in soil microbial activity and quality. However, the effect and mechanism of lower-ring polycyclic aromatic hydrocarbons (PAHs) on soil FDA hydrolase are still unclear. In this work, we investigated the effects of two typical lower-ring PAHs, naphthalene (Nap) and anthracene (Ant), on the activity and kinetic characteristics of FDA hydrolases in six soils differing in their properties. Results demonstrated that the two PAHs severely inhibited the activities of the FDA hydrolase. The values of V_max and K_m dropped by 28.72-81.24 % and 35.84-74.47 % at the highest dose of Nap, respectively, indicating an uncompetitive inhibitory mechanism. Under Ant stress, the values of V_max decreased by 38.25-84.99 %, and the K_m exhibited two forms, unchanged and decreased (74.00-91.61 %), indicating uncompetitive and noncompetitive inhibition. The inhibition constant (K_i) of the Nap and Ant ranged from 0.192 to 1.051 and 0.018 to 0.087 mM, respectively. The lower K_i of Ant compared to Nap indicated a higher affinity for enzyme-substrate complex, resulting in higher toxicity of Ant than Nap to soil FDA hydrolase. The inhibitory effect of Nap and Ant on soil FDA hydrolase was mainly affected by soil organic matter (SOM). SOM influenced the affinity of PAHs with enzyme-substrate complex, which resulted in a difference in PAHs toxicity to soil FDA hydrolase. The enzyme kinetic V_max was a more sensitive indicator than enzyme activity to evaluate the ecological risk of PAHs. This research offers a strong theoretical foundation for quality control and risk evaluation of PAH-contaminated soils through a soil enzyme-based approach.

Root exudates increased arsenic mobility and altered microbial community in paddy soils

Root exudates are crucial for plants returning organic matter to soils, which is assumed to be a major source of carbon for the soil microbial community. This study investigated the influence of root exudates on the fate of arsenic (As) with a lab simulation experiment. Our findings suggested that root exudates had a dose effect on the soil physicochemical properties, As speciation transformation and the microbial community structure at different concentrations. The addition of root exudates increased the soil pH while decreased the soil redox potential (Eh). These changes in the soil pH and Eh increased As and ferrous (Fe(II)) concentrations in soil porewater. Results showed that 40 mg/L exudates addition significantly increased arsenite (As(III)) and arsenate (As(V)) by 541 and 10 times respectively within 30 days in soil porewater. The relative abundance of Fe(III)-reducing bacteria Geobacter and Anaeromyxobacter increased with the addition of root exudates, which enhanced microbial Fe reduction. Together these results suggest that investigating how root exudates affect the mobility and transformation of As in paddy soils is helpful to systematically understand the biogeochemical cycle of As in soil-rice system, which is of great significance for reducing the health risk of soil As contamination.

Beneficial Microorganisms Improve Agricultural Sustainability under Climatic Extremes

The challenging alterations in climate in the last decades have had direct and indirect influences on biotic and abiotic stresses that have led to devastating implications on agricultural crop production and food security. Extreme environmental conditions, such as abiotic stresses, offer great opportunities to study the influence of different microorganisms in plant development and agricultural productivity. The focus of this review is to highlight the mechanisms of plant growth-promoting microorganisms (especially bacteria and fungi) adapted to environmental induced stresses such as drought, salinity, heavy metals, flooding, extreme temperatures, and intense light. The present state of knowledge focuses on the potential, prospective, and biotechnological approaches of plant growth-promoting bacteria and fungi to improve plant nutrition, physio-biochemical attributes, and the fitness of plants under environmental stresses. The current review focuses on the importance of the microbial community in improving sustainable crop production under changing climatic scenarios.

Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship

Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.

Activation and tolerance of Siegesbeckia Orientalis L. rhizosphere to Cd stress

This experiment investigated the changes of rhizosphere soil microenvironment for hyperaccumulation-soil system under Cd stress in order to reveal the mechanism of hyperaccumulation and tolerance. Thus, Cd fractions, chemical compositions, and biochemical characteristics in rhizosphere soil of Siegesbeckia orientalis L. under Cd stress conditions of 0, 5, 10, 25, 50, 100, and 150 mg kg-1 were investigated through a root bag experiment, respectively. As a result, Cd induced the acidification of S. orientalis rhizosphere soil, and promoted the accumulation of dissolved organic carbon (DOC) and readily oxidizable organic carbon (ROC), which increased by 28.39% and 6.98% at the maximum compared with control. The percentage of labile Cd (acid-soluble and reducible Cd) in soil solution increased significantly (P < 0.05) from 31.87% to 64.60% and from 26.00% to 34.49%, respectively. In addition, rhizosphere microenvironment can alleviate the inhibition of Cd on soil microorganisms and enzymes compare with bulk soils. Under medium and low concentrations of Cd, the rhizosphere soil microbial biomass carbon (MBC), basal respiration, ammonification and nitrification were significantly increased (P < 0.05), and the activities of key enzymes were not significantly inhibited. This suggests that pH reduction and organic carbon (DOC and ROC) accumulation increase the bioavailability of Cd and may have contributed to Cd accumulation in S. orientalis. Moreover, microorganisms and enzymes in rhizosphere soils can enhance S. orientalis tolerance to Cd, alleviating the nutrient imbalance and toxicity caused by Cd pollution. This study revealed the changes of physicochemical and biochemical properties of rhizosphere soil under Cd stress. Rhizosphere soil acidification and organic carbon accumulation are key factors promoting Cd activation, and microorganisms and enzymes are the responses of Cd tolerance.

Respecting catalytic efficiency of soil arylsulfatase as soil Sb contamination bio-indicator by enzyme kinetic strategy

Antimony (Sb), a toxic metalloid, is ubiquitous in the environment and threatens human and ecological health. Soil arylsulfatase (ARS) activity indicates heavy metal pollution. However, the enzyme's substrate concentration can affect the toxicity evaluation of heavy metals using enzyme activity. Enzyme kinetic parameters directly reflect the potency of heavy metals, and the magnitude of these parameters does not change with the substrate concentration of soil enzyme. In this work, seventeen soils were exposed to Sb contamination to investigate the change of kinetic parameters of soil arylsulfatase under Sb stress. Results showed that Sb inhibited soil arylsulfatase activity. The maximum reaction rate (V_max) of soil arylsulfatase was reduced by 11.58-46.72% in 16 tested soils and unchanged in S15 when exposed to Sb. The Michaelis constant (K_m) presented three trends: unchanged, increased by 28.46-41.27%, and decreased by 19.71-29.91% under Sb stress. The catalytic efficiency (K_a as the ratio of V_max to K_m) decreased by 12.56-55.17% in all soils except for S12 and S16. Antimony acted as a non-competitive and linear mixed inhibitor by decreasing ARS activity in S1-S12, S14, and S17-S18 soils, as an uncompetitive inhibitor in S13 and S16 soils and as a competitive inhibitor in S15. The competitive and uncompetitive inhibition constants (K_ic and K_iu) were 0.058-0.142 mM and 0.075-0.503 mM. The ecological dose values of Sb to catalytic efficiency (K_a) of ARS (ED₁₀-K_a) ranged from 50 to 1315 mg kg^-1. Soil pH and total phosphorus (TP) contents were the dominant factors responsible for Sb toxicity on K_a by affecting the interaction of inhibitor (Sb) with enzyme-substrate (ES) complex. The findings of this study advance the current knowledge on Sb toxicity to soil enzymes and have significant implications for the risk assessment of Sb in soils.

Plant–Microbe Interactions under the Action of Heavy Metals and under the Conditions of Flooding

Heavy metals and flooding are among the primary environmental factors affecting plants and microorganisms. This review separately considers the impact of heavy metal contamination of soils on microorganisms and plants, on plant and microbial biodiversity, and on plant–microorganism interactions. The use of beneficial microorganisms is considered one of the most promising methods of increasing stress tolerance since plant-associated microbes reduce metal accumulation, so the review focuses on plant–microorganism interactions and their practical application in phytoremediation. The impact of flooding as an adverse environmental factor is outlined. It has been shown that plants and bacteria under flooding conditions primarily suffer from a lack of oxygen and activation of anaerobic microflora. The combined effects of heavy metals and flooding on microorganisms and plants are also discussed. In conclusion, we summarize the combined effects of heavy metals and flooding on microorganisms and plants.

Nitrogen and sulfur fertilizers promote the absorption of lead and cadmium with Salix integra Thunb. by increasing the bioavailability of heavy metals and regulating rhizosphere microbes

Fertilization is an effective agronomic strategy to improve the efficiency of phytoextraction by Salix integra Thunb. However, the specific effects of the simultaneous application of nitrogen (N) and sulfur (S) fertilizers in the rhizosphere remain unclear. We investigated the bioavailability of lead (Pb) and Cadmium (Cd) along with the microbial metabolic functions and community structure in the rhizosphere soil of S. integra after the application of N (0, 100, and 200 kg·ha⁻¹·year⁻¹) and S (0, 100, and 200 kg·ha⁻¹·year⁻¹) fertilizers for 180 days. The simultaneous application of N and S fertilizers significantly enhanced the absorption of Pb and Cd by S. integra, whereas this effect was not observed for the single application of N or S fertilizer. The contents of acid-soluble Pb and Cd in the rhizosphere soil significantly increased after either single or combined fertilize applications. The microbial metabolic activity was enhanced by the N and S fertilizers, whereas the microbial diversity markedly decreased. The metabolic patterns were mainly affected by the concentration of N fertilizer. The dominant fungi and bacteria were similar under each treatment, although the relative abundances of the dominant and special species differed. Compared to the N200S100 and N200S200 treatments, the N100S100 and N100S200 treatments resulted in fewer pathogenic fungi and more rhizosphere growth-promoting bacteria, which promoted phytoremediation by S. integra. Redundancy analysis indicated that the pH and nitrate content were the key factors affecting the structure of the microbial community. Collectively, the results suggest interactive effects between N and S fertilizers on the rhizosphere soil, providing a potential strategy for plant-microbial remediation by S. integra.

Immobilization of cadmium by mercapto-functionalized palygorskite under stimulated acid rain: Stability performance and micro-ecological response

The interaction of cadmium (Cd) pollution and acid rain stress has seriously threatened soil ecosystem and human health. However, there are still few effective amendments for the in-situ remediation in the Cd-contaminated acidified soil. In this study, the performance and mechanisms of palygorskite (PAL) and mercapto-functionalized PAL (MPAL) on Cd immobilization were investigated, and the stability as well as effects on soil micro-ecology under stimulated acid rain were also explored. Results showed that MPAL could react with Cd to form stable Cd-sulfhydryl and Cd-O complexes. The reduction of bioavailable Cd by MPAL was 121.19-164.86% higher than that by PAL. Notably, the Cd immobilization by MPAL remained stable within 90 days in which the concentrations of HOAc-extractable Cd were reduced by 18.28-25.12%, while the reducible and residual fractions were increased by 9.26-18.53% and 54.16%-479.01%, respectively. The sequential acid rain leaching demonstrated that soil after MPAL treatments had a strong H⁺ resistance, and the immobilized Cd showed prominent stability. In addition, activities of acid phosphatase, catalase and invertase in MPAL treated soil were significantly enhanced by 34.60%, 22.09% and 48.87%, respectively. After MPAL application, bacterial diversity was further improved with diversified sulfur metabolism biomarkers. The decreased abundance of Cd resistance genes including cadA, cadC, czcA, czcB, czcR and zipA also indicated that soil micro-ecology was improved by MPAL. These results showed that MPAL was an effective and eco-friendly amendment for the immobilization of Cd in contaminated soil.

Effects of Tetracycline and Copper on Water Spinach Growth and Soil Bacterial Community

The effects of tetracycline (TC) and copper (Cu) on the growth of water spinach and the bacterial community structure in soil were examined in this study. The results revealed that a single Cu treatment decreased water spinach development more severely than TC, and that the toxic effects of TC and Cu on water spinach were synergistic at low doses and antagonistic at high concentrations. The single Cu treatment had the largest influence on the activities of three antioxidant enzymes (Superoxide Dismutase (SOD), Peroxidase (POD), Catalase (CAT)) and the content of Malondialdehyde (MDA) in water spinach leaves, followed by the TC and Cu composed treatment, with the single TC treatment having the least effect. The results of 16Sr RNA sequence analysis showed that the richness and diversity of soil bacterial communities were reduced by either a single TC or Cu treatment. Cu had a greater effect on the composition of the microbial community at genus level than TC. In conclusion, Cu had a greater influence on the growth of water spinach and soil microbial community composition than TC. TC and Cu exhibited synergistic effects at low concentrations and antagonistic effects at high concentrations on relevant indicators when Cu concentration was fixed.

Effects of copper oxide nanoparticles on Salix growth, soil enzyme activity and microbial community composition in a wetland mesocosm

A model wetland with Salix was established to investigate the effects of CuO nanoparticles (NPs; the equivalent amount of Cu at 0, 100 and 500 mg/kg) on plant, soil enzyme activity and microbial community. Ionic Cu (100, 500 mg/kg) and bulk-sized CuO particles (BPs, 500 mg/kg) were included as controls. The results suggested the CuO NPs at 500 mg/kg and ionic Cu treatments inhibited the plant growth, while CuO NPs at 100 mg/kg and CuO BPs at 500 mg/kg played a facilitating role. CuO NPs significantly decreased the activities of peroxidase and polyphenol oxidase, while ionic Cu treatments increased peroxidase activity, BPs and ionic Cu (500 mg/kg) increased the polyphenol oxidase activity. Bacterial community richness and diversity were reduced in all Cu treatments; however, CuO NPs and BPs at 500 mg/kg significantly increased the richness and diversity of fungal community.Soil microbial community was significantly altered by Cu types and dose. In comparison with ionic Cu and CuO BPs, CuO NPs uniquely enriched the microbial community and the fungal families.Overall, it demonstrate that both particle size and dose regulate the impact of CuO on wetland ecology, which deepens our understanding on the ecological risks of CuO NPs in freshwater forested wetland.

Differential response of Oryza sativa L. and Phragmites australis L. plants in trace elements contaminated soils under flooded and unflooded conditions

Drastic changes in the water regime of trace elements (TEs) contaminated soils under semiarid conditions, from completely dry to flooding situations, may alter the solubility of the contaminants and, therefore, their potential mobility and availability to plants. Certain macrophyte species have shown a promising suitability for their use in the phytoremediation of TEs contaminated soils under fluctuating flooded-unflooded conditions, as a consequence of their high resistance and tolerance to contamination. Similarly, different water conditions occur during rice (Oryza sativa) cultivation, a species often used as a model plant for TEs toxicity studies. The aim of this work was to study the tolerance and oxidative response to TEs of common reed (Phragmites australis) and rice grown in contaminated mining soils, when exposed to different water saturation conditions. Both species (common reed and rice) were cultivated in three different contaminated soils from the Sierra Minera of La Unión-Cartagena (SE-Spain) under contrasting water saturation conditions (flooded and unflooded) in a pot experiment. Soil EC and elevated metal (mainly Cd and Zn) soluble concentrations conditioned the survival of the plants. Whereas, As accumulation in the aerial part of both species influenced the most oxidative stress homeostasis. Common reed showed to be a good candidate for its use in the phytostabilization of TEs contaminated soils under both flooded and unflooded conditions.

Effects of Vegetation Restoration on Soil Enzyme Activity in Copper and Coal Mining Areas

Mining areas are suffering from serious environmental hazards, such as soil erosion, water pollution as well as land degradation. In this study, two types of mining areas in Anhui Province, China-one a copper mining area and the other a coal mining area-were selected to compare the soil properties under different vegetation restoration conditions, which can be generally classified into reclaimed and non-reclaimed areas. Soil catalase and urease activities and soil chemical properties were chosen to be the main indicators of soil quality. Principal component analysis was used to evaluate the overall soil fertility in the copper and coal mining areas. Results showed that in the copper mining area soil catalase activity was between 12.36 and 19.17 μg g^-1 h^-1 and urease activity was between 0.03 and 12.05 μg g^-1 h^-1. And in coal mining area, soil catalase activity was between 3.52 and 9.72 μg g^-1 h^-1 and urease activity was between 2.71 and 10.81 μg g^-1 h^-1. Moreover, soil catalase and urease activities in degraded areas were lower than those in reclaimed areas. Soil catalase activity and soil urease activity were significantly correlated with total potassium and total nitrogen, respectively. Soil quality in land types with vegetation restoration was higher than in non-reclaimed areas and old subsidence areas, while soil quality in the copper mining area was generally higher than in the coal mining area. Thus, the optimum measure in this region to ameliorate these degraded soils is vegetation restoration, which helps not only to improve the environment, but also to enhance soil quality in these degraded lands.

Kinetics and catalytic efficiency of soil fluorescein diacetate hydrolase under the pesticide parathion stress

Fluorescein diacetate hydrolase (FDA-H) is an accurate biochemical method measuring the total microbial activity in soil, which indicates soil quality under ambient environmental changes such as pesticide parathion (PTH). However, the influence of PTH on the kinetics of FDA-H is still unknown. In this study, fifteen farmland soils were exposed to acute PTH pollution to investigate how the kinetic characteristics of FDA-H change with PTH concentration. Results showed that PTH strongly inhibited the FDA-H activities. The values of maximum reaction velocity (V_max) ranged from 0.29 to 2.18 × 10^-2 mM g^-1 soil h^-1 and declined by 42.30%-71.01% under PTH stress. The Michaelis constant (K_m) values ranged between 2.90 and 14.17 × 10^-2 mM and exhibited three forms including unchanged, increased (38.16-242.65%) and decreased (13.41-39.23%) when exposed to PTH. Based on the changes in two kinetic parameters, the inhibition of PTH on FDA-H was classified as three types, i.e., noncompetitive, linear mixed and uncompetitive inhibition. The competitive inhibition constant (K_ic) and noncompetitive constant (K_iu) ranged from 0.064 to 0.447 mM and 0.209 to 0.723 mM, respectively, which were larger than the K_m in values. The catalytic efficiency (V_max/K_m) of FDA-H is a sensitive integrated parameter to evaluate the PTH toxicity due to the higher inhibition ratio than the V_max. The PTH toxicity to FDA-H decreased with increase of soil organic matter and total nitrogen contents. This implied that the PTH toxicity could be alleviated by an increasing content of soil organic matter due to its buffering capacity to PTH. Besides, soils with a higher content of total nitrogen could provide stable environment for FDA-H to maintain its functionality under PTH pollution. Thus, the results of this study have great implications to the risk assessment of parathion in soils.

Effect of different vegetation on copper accumulation of copper-mine abandoned land in tongling, China

Mining activity and abandoned mine land are one of the major sources of heavy metal pollution. Thus, ecological rehabilitation of abandoned mine lands is crucial to control heavy metal pollution. This research aims to explore the influencing factors and effects of different vegetation on copper (Cu) accumulation and soil amelioration. In this study, the abandoned land of Tongguanshan Cu mine in Tongling city, Anhui province, China, was chosen as the test area, and nine sampling points were established. Samples of soil and plants were collected from each plot, and the impacts of Cu pollution on soil enzymes and other features were analyzed, as well as the correlation between Cu accumulation of different plants and soil properties. The results showed that Cu content of soil in the Tongguanshan area varied greatly with the depth of the soil profile. Moreover, Cu in the soil can inhibit soil enzyme activities; and the correlation coefficients of total soil Cu with urease and catalase were -0.83 and -0.73, respectively. Clearly, the accumulation of Cu in plants was positively correlated with Cu content in soil. It was found that Pueraria lobata had the best remediation effect on soil Cu pollution in a short period of time. Hence the preliminary tests clearly indicate that phytoremediation in abandoned mine lands can not only reduce heavy metal pollution, but also enhance soil nutrition and enzyme activity, helping to ameliorate degraded land and promote regional socioeconomic sustainable development.

Effect of sterilization on cadmium immobilization and bacterial community in alkaline soil remediated by mercapto-palygorskite

Cadmium (Cd) pollution in alkaline soil in some areas of northern China has seriously threatened wheat production and human health. However, there are still few effective amendments for alkaline soil, and the mechanism of amendments with a good immobilization effect remains unclear. In this study, soil sterilization experiments were conducted to investigate the effects of soil microorganisms on the immobilization of a novel amendment-mercapto palygorskite (MPAL) in Cd-contaminated alkaline soils. The results showed that the mercapto on the MPAL surface was not affected by autoclaving. Compared with the control, the available Cd concentration in 0.025% MPAL treatments decreased by 18.80-29.23% after 1 d of aging and stabled after 10 d of aging. Importantly, the immobilization of MPAL on Cd in sterilized soil was significantly better than that in natural soil due to the changes in Cd fractions. Compared with MPAL-treated natural soil, exchangeable Cd fraction and carbonate-bound Cd fraction in MPAL-treated sterilized soil decreased by 20.79-27.09% and 20.05-26.45%, while Fe/Mn oxide-bound Cd fraction and organic matter-bound Cd fraction increased by 17.77-22.68% and 18.85-27.32%. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis found that the potential functions of the microbial community in normal and sterilized soil were different significantly. Soil sterilization increased the soil pH and decreased the arylsulfatase activity, but did not change the soil zeta potential and available sulfur. The changes in Cd fractions in MPAL-treated sterilized soil may be related to the reduction in the bacterial community and the changes in function microbial, but not to the soil properties. In addition, MPAL application had little effects on the bacterial community, soil pH value, zeta potential, available sulfur, and arylsulfatase. These results showed that the immobilization of MPAL on Cd in alkaline soil was stable and effective, and was not affected by soil sterilization and soil microorganism reduction.

Copper bioavailability, uptake, toxicity and tolerance in plants: A comprehensive review

Copper (Cu) is an essential element for humans and plants when present in lesser amount, while in excessive amounts it exerts detrimental effects. There subsists a narrow difference amid the indispensable, positive and detrimental concentration of Cu in living system, which substantially alters with Cu speciation, and form of living organisms. Consequently, it is vital to monitor its bioavailability, speciation, exposure levels and routes in the living organisms. The ingestion of Cu-laced food crops is the key source of this heavy metal toxicity in humans. Hence, it is necessary to appraise the biogeochemical behaviour of Cu in soil-plant system with esteem to their quantity and speciation. On the basis of existing research, this appraisal traces a probable connexion midst: Cu levels, sources, chemistry, speciation and bioavailability in the soil. Besides, the functions of protein transporters in soil-plant Cu transport, and the detrimental effect of Cu on morphological, physiological and nutrient uptake in plants has also been discussed in the current manuscript. Mechanisms related to detoxification strategies like antioxidative response and generation of glutathione and phytochelatins to combat Cu-induced toxicity in plants is discussed as well. We also delimits the Cu accretion in food crops and allied health perils from soils encompassing less or high Cu quantity. Finally, an overview of various techniques involved in the reclamation and restoration of Cu-contaminated soils has been provided.

Indicators for assessment of soil quality: a mini-review

Soil quality is the competence of soil to perform necessary functions that are able to maintain animal and plant productivity of the soil. Soil consists of various physical, chemical, and biological parameters, and all these parameters are involved in the critical functioning of soil. There is a need for continuous assessment of soil quality as soil is a complex and dynamic constituent of Earth's biosphere that is continuously changing by natural and anthropogenic disturbances. Any perturbations in the soil cause disturbances in the physical (soil texture, bulk density, etc.), chemical (pH, salinity, organic carbon, etc.), and biological (microbes and enzymes) parameters. These physical, chemical, and biological parameters can serve as indicators for soil quality assessment. However, soil quality assessment cannot be possible by evaluating only one parameter out of physical, chemical, or biological. So, there is an emergent need to establish a minimum dataset (MDS) which shall include physical, chemical, and biological parameters to assess the quality of the given soil. This review attempts to describe various physical, chemical, and biological parameters, combinations of which can be used in the establishment of MDS.

Indigenous Bacteria Have High Potential for Promoting Salix integra Thunb. Remediation of Lead-Contaminated Soil by Adjusting Soil Properties

Salix integra Thunb., a fast-growing woody plant species, has been used for phytoremediation in recent years. However, little knowledge is available regarding indigenous soil microbial communities associated with the S. integra phytoextraction process. In this study, we used an Illumina MiSeq platform to explore the indigenous microbial composition after planting S. integra at different lead (Pb) contamination levels: no Pb, low Pb treatment (Pb 500 mg kg^–1), and high Pb treatment (Pb 1500 mg kg^–1). At the same time, the soil properties and their relationship with the bacterial communities were analyzed. The results showed that Pb concentration was highest in the root reaching at 3159.92 ± 138.98 mg kg^–1 under the high Pb treatment. Planting S. integra decreased the total Pb concentration by 84.61 and 29.24 mg kg^–1, and increased the acid-soluble Pb proportion by 1.0 and 0.75% in the rhizosphere and bulk soil under the low Pb treatment compared with unplanted soil, respectively. However, it occurred only in the rhizosphere soil under the high Pb treatment. The bacterial community structure and microbial metabolism were related to Pb contamination levels and planting of S. integra, while the bacterial diversity was only affected by Pb contamination levels. The dominant microbial species were similar, but their relative abundance shifted in different treatments. Most of the specific bacterial assemblages whose relative abundances were promoted by root activity and/or Pb contamination were suitable for use in plant-microbial combination remediation, especially many genera coming from Proteobacteria. Redundancy analysis (RDA) showed available nitrogen and pH having a significant effect on the bacteria relating to phytoremediation. The results indicated that indigenous bacteria have great potential in the application of combined S. integra-microbe remediation of lead-contaminated soil by adjusting soil properties.