Responses of microbial community composition and function to biochar and irrigation management and the linkage to Cr transformation in paddy soil

The potential of ferrihydrite-synthetic humic-like acid composite as a soil amendment for metal-contaminated agricultural soil: Immobilization mechanisms by combining abiotic and biotic perspectives

In-situ passivation technique has attracted increasing attention for metal-contaminated agricultural soil remediation. However, metal immobilization mechanisms are mostly illustrated based on metal speciation changes and alterations in soil physicochemical properties from a macroscopic and abiotic perspective. In this study, a ferrihydrite-synthetic humic-like acid composite (FH-SHLA) was fabricated and applied as a passivator for a 90-day soil incubation. The heavy metals immobilization mechanisms of FH-SHLA were investigated by combining both abiotic and biotic perspectives. Effects of FH-SHLA application on soil micro-ecology were also evaluated. The results showed that the 5%FH-SHLA treatment significantly decreased the DTPA-extractable Pb, Cd and Zn by 80.75%, 46.82% and 63.63% after 90 days of incubation (P < 0.05), respectively. Besides, 5% FH-SHLA addition significantly increased soil pH, soil organic matter content and cation exchange capacity (P < 0.05). The SEM, FTIR, and XPS characterizations revealed that the abiotic metal immobilization mechanisms by FH-SHLA included surface complexation, precipitation, electrostatic attraction, and cation-π interactions. For biotic perspective, in-situ microorganisms synergistically participated in the immobilization process via sulfide precipitation and Fe mineral production. FH-SHLA significantly altered the diversity and composition of the soil microbial community, and enhanced the intensity and complexity of the microbial co-occurrence network. Both metal bioavailability and soil physiochemical parameters played a vital role in shaping microbial communities, while the former contributed more. Overall, this study provides new insight into the heavy metal passivation mechanism and demonstrates that FH-SHLA is a promising and environmentally friendly amendment for metal-contaminated soil remediation.

Biochar loaded with root exudates of hyperaccumulator Leersia hexandra Swartz facilitated Cr(VI) reduction by shaping soil functional microbial communities

Cr(VI) contamination is widely recognized as one of the major environmental hazards. To address the problem of remediation of soil Cr(VI) contamination and utilization of waste peanut shells, this study comprehensively investigated the effects of peanut shell-derived biochar loaded with root exudates of hyperaccumulator Leersia hexandra Swartz on Cr(VI) reduction and microbial community succession in soil. This study confirmed that root exudate-loaded peanut shell biochar reduced soil pH while simultaneously increasing DOC, sulfide, and Fe(II) concentrations, thereby facilitating the reduction of Cr(VI), achieving a reduction efficiency of 81.8%. Based on XPS and SEM elemental mapping analyses, Cr(VI) reduction occurred concurrently with the Fe and S redox cycles. Furthermore, the microbial diversity, abundance of the functional genera (Geobacter, Arthrobacter, and Desulfococcus) and the metabolic functions associated with Cr(VI) reduction were enhanced by root exudate-loaded biochar. Root exudate-loaded biochar can promote both direct Cr(VI) reduction mediated by the Cr(VI)-reducing bacteria Arthrobacter, and indirect Cr(VI) reduction through Cr/S/Fe co-transformation mediated by the sulfate-reducing bacteria Desulfococcus and Fe(III)-reducing bacteria Geobacter. This study demonstrates the effectiveness of peanut shell biochar loaded with root exudates of hyperaccumulator Leersia hexandra Swartz to promote soil Cr(VI) reduction, reveals the mechanism how root exudate-loaded biochar shapes functional microbial communities to facilitate Cr(VI) reduction, and proposes a viable strategy for Cr(VI) remediation and utilization of peanut shell.

Biochar co-pyrolyzed from peanut shells and maize straw improved soil biochemical properties, rice yield, and reduced cadmium mobilization and accumulation by rice: Biogeochemical investigations

Biochar is an eco-friendly amendment for the remediation of soils contaminated with cadmium (Cd). However, little attention has been paid to the influence and underlying mechanisms of the co-pyrolyzed biochar on the bioavailability and uptake of Cd in paddy soils. The current study explored the effects of biochar co-pyrolyzed from peanut shells (P) and maize straw (M) at different mixing ratios (1:0, 1:1, 1:2, 1:3, 0:1, 2:1 and 3:1, w/w), on the bacterial community and Cd fractionation in paddy soil, and its uptake by rice plant. Biochar addition, particularly P1M3 (P/M 1:3), significantly elevated soil pH and cation exchange capacity, transferred the mobile Cd to the residual fraction, and reduced Cd availability in the rhizosphere soil. P1M3 application decreased the concentration of Cd in different rice tissues (root, stem, leaf, and grain) by 30.0%- 49.4%, compared to the control. Also, P1M3 enhanced the microbial diversity indices and relative abundance of iron-oxidizing bacteria in the rhizosphere soil. Moreover, P1M3 was more effective in promoting the formation of iron plaque, increasing the Cd sequestration by iron plaque than other treatments. Consequently, the highest yield and lowest Cd accumulation in rice were observed following P1M3 application. This study revealed the feasibility of applying P1M3 for facilitating paddy soils contaminated with Cd.

Exploring the synergistic interplay of sulfur metabolism and electron transfer in Cr(VI) and Cd(II) removal by Clostridium thiosulfatireducens: Genomic and mechanistic insights

In this study, a sulfate-reducing bacterium, Clostridium thiosulfatireducens (CT) was reported and the performance and removal mechanism of Cr(VI) and Cd(II) removal were investigated. It is noteworthy that the dsrAB gene is absent in this strain, but the strain is capable of producing sulfide. The conversion rate of Cr(VI) by CT was 84.24 % at a concentration of 25 mg/L, and the conversion rate of Cd(II) was 94.19 % at a concentration of 28 mg/L. The complete genome is 6,106,624 bp and the genome consisted of a single chromosome. The GC content of the chromosomes was 29.65 %. The mechanism of heavy metal removal by CT bacteria mainly includes biosorption, electron transfer and redox, with reduction combined with S2- precipitation as the main pathway. The product characterization results showed that the formation of mainly ionic crystals and precipitates (CdS, Cd(OH)2, Cr(OH)3, Cr2O3) after adsorption. Genome-wide techniques have shown that the clearance of Cr(VI) and Cd(II) by CT is largely dependent on sulfate transport, sulfur metabolism, and energy metabolism to some extent. In addition, genes related to ATP binding, electron carrier activity, transporter protein genes, and DNA repair are also important factors to improve the heavy metal resistance and transformation ability of CT strains. Both the Fe-S cycle and the ROS-resistant system can enhance the electron transfer activity and thus slow down the damage of heavy metals to microorganisms. This study fills the gap in the understanding of the basic properties and heavy metal transformation mechanism of CT.

Quantification of the effect of biochar application on heavy metals in paddy systems: Impact, mechanisms and future prospects

Biochar (BC) has shown great potential in remediating heavy metal(loid)s (HMs) contamination in paddy fields. Variation in feedstock sources, pyrolysis temperatures, modification methods, and application rates of BC can result in great changes in its effects on HM bioavailability and bioaccumulation in soil-rice systems and remediation mechanisms. Meanwhile, there is a lack of application guidelines for BC with specific properties and application rates when targeting rice fields contaminated with certain HMs. To elucidate this topic, this review focuses on i) the effects of feedstock type, pyrolysis temperature, and modification method on the properties of BC; ii) the changes in bioavailability and bioaccumulation of HMs in soil-rice systems applying BC with different feedstocks, pyrolysis temperatures, modification methods, and application rates; and iii) exploration of potential remediation mechanisms for applying BC to reduce the mobility and bioaccumulation of HMs in rice field systems. In general, the application of Fe/Mn modified organic waste (OW) derived BC for mid-temperature pyrolysis is still a well-optimized choice for the remediation of HM contamination in rice fields. From the viewpoint of remediation efficiency, the application rate of BC should be appropriately increased to immobilize Cd, Pb, and Cu in rice paddies, while the application rate of BC for immobilizing As should be <2.0 % (w/w). The mechanism of remediation of HM-contaminated rice fields by applying BC is mainly the direct adsorption of HMs by BC in soil pore water and the mediation of soil microenvironmental changes. In addition, the application of Fe/Mn modified BC induced the formation of iron plaque (IP) on the root surface of rice, which reduced the uptake of HM by the plant. Finally, this paper describes the prospects and challenges for the extension of various BCs for the remediation of HM contamination in paddy fields and makes some suggestions for future development.

Mechanism of Cr(VI) bioreduction by Clostridium sp. LQ25 under Fe(III) reducing conditions

The Cr(VI) bioreduction has attracted widespread attention in the field of Cr(VI) pollution remediation due to its environmental friendliness. Further in-depth research on the reduction mechanisms is necessary to enhance the efficiency of Cr(VI) bioreduction. However, the limited research on Cr(VI) bioreduction mechanisms remains a bottleneck for the practical application of Cr(VI) reduction. In this study, The Cr(VI) reduction of strain LQ25 was significantly improved when Fe(III) was used as an electron acceptor, which increased by 1.6-fold maximum within the set Cr(VI) concentration range. Based on this, the electron transfer process of Cr(VI) reduction was analyzed using strain LQ25. Based on genomic data, flavin proteins were found to interact closely with electron transfer-related proteins using protein-protein interaction (PPi) analysis. Transcriptome analysis revealed that flavin synthesis genes (ribE, ribBA, and ribH) and electron transfer flavoprotein genes (fixA, etfA, fixB, and etfB) were significantly upregulated when Fe(III) was used as the electron acceptor. These results indicate that the fermentative dissimilatory Fe(III)-reducing bacterial strain LQ25 mainly uses flavin as an electron shuttle for electron transfer, which differs from the common use of cytochrome c in respiratory bacteria. These findings on the mechanism of Cr(VI) bioreduction provide technical support for improving the efficiency of Cr(VI) reduction which promote the practical application of Cr(VI) bioreduction in the field of Cr(VI) pollution remediation.

Reduction of Chromate via Biotic and Abiotic Pathways in the Presence of Three Co-contaminating Electron Acceptors

Bioreduction of Cr(VI) to Cr(III) is a promising technology for removing Cr(VI), but Cr(VI) reduction alone cannot support microbial growth. This study investigated the reduction of Cr(VI) in the presence of three electron acceptors that typically coexist with Cr(VI): NO3-, SO42-, and Fe(III). All three systems could reduce Cr(VI) to Cr(III), but the fate of Cr, its impacts on reduction of the other acceptors, and its impact on the microbial community differed. Although Cr(VI) was continuously removed in the NO3--reduction systems, batch tests showed that denitrification was inhibited primarily through impeding nitrite reduction. The SO42- and Fe(III) reduction systems reduced Cr(VI) using a combination of biotic and abiotic processes. Across all three systems, the abundance of genera capable of reducing Cr(VI) increased following the introduction of Cr(VI). Conversely, the abundance of genera that cannot reduce or resist Cr(VI) decreased, leading to restructuring of the microbial community. Furthermore, the abundance of sulfide oxidizers and Fe(II) oxidizers substantially increased after the introduction of chromate. This study provides fundamental knowledge about how Cr(VI) bioreduction interacts with bioreductions of three other co-contaminating electron acceptors.

Deciphering the impacts of chromium contamination on soil bacterial communities: A comparative analysis across various soil types

Addressing the widespread concern of chromium (Cr) pollution, this study investigated its impacts on bacterial communities across eight soil types, alongside the potential Cr transformation-related genes. Utilizing real-time PCR, 16S rRNA gene sequencing and gene prediction, we revealed shifts in bacterial community structure and function at three Cr exposure levels. Our results showed that the bacterial abundance in all eight soil types was influenced by Cr to varying extents, with yellow‒brown soil being the most sensitive. The bacterial community composition of different soil types exhibited diverse responses to Cr, with only the relative abundance of Proteobacteria decreasing with increasing Cr concentration across all soil types. Beta diversity analysis revealed that while Cr concentration impacted the assembly process of bacterial communities to a certain extent, the influence on the compositional structure of bacterial communities was primarily driven by soil type rather than Cr concentration. The study also identified biomarkers for each soil type under three Cr levels, offering a basis for monitoring changes in Cr pollution. By predicting crucial functional genes related to Cr transformation, it was observed that the relative abundance of chrA (chromate transporter) in yellow‒brown soil significantly exceeded that in all other soil types, suggesting its potential for Cr adaptation. The study also revealed correlations among soil physicochemical properties, Cr concentration, and these functional genes, providing a foundation for future research aimed at more precise functional analysis and the development of effective soil remediation strategies.

Immobilization of zinc and cadmium by biochar-based sulfidated nanoscale zero-valent iron in a co-contaminated soil: Performance, mechanism, and microbial response

Mining and smelting of mineral resources causes excessive accumulation of potentially toxic metals (PTMs) in surrounding soils. Here, biochar-based sulfidated nanoscale zero-valent iron (SNZVI/BC) was designed via a one-step liquid phase reduction method to immobilize cadmium (Cd) and zinc (Zn) in a copolluted arable soil. A 60 d soil incubation experiment revealed that Cd and Zn immobilization efficiency by 6 % SNZVI/BC (25.2-26.2 %) was higher than those by individual SNZVI (13.9-18.0 %) or biochar (14.0-19.3 %) based on the changes in diethylene triamine pentaacetic acid (DTPA)-extractable PTM concentrations in soils, exhibiting a synergistic effect. Cd2+ or Zn2+ replaced isomorphously Fe2+ in amorphous ferrous sulfide, as revealed by XRD, XPS, and high-resolution TEM-EDS, forming metal sulfide precipitates and thus immobilizing PTMs. PTM immobilization was further enhanced by adsorption by biochar and oxidation products (Fe2O3 and Fe3O4) of SNZVI via precipitation and surface complexation. SNZVI/BC also increased the concentration of dissolved organic carbon and soil pH, thus stimulating the abundances of beneficial bacteria, i.e., Bacilli, Clostridia, and Desulfuromonadia. These functional bacteria further facilitated microbial Fe(III) reduction, production of ammonium and available potassium, and immobilization of PTMs in soils. The predicted function of the soil microbial community was improved after supplementation with SNZVI/BC. Overall, SNZVI/BC could be a promising functional material that not only immobilized PTMs but also enhanced available nutrients in cocontaminated soils.

Effects of chromate on nitrogen removal and microbial community in two-stage vertical-flow constructed wetlands

Nitrogen and chromium (Cr(VI)) pollution in waterbodies pose great threats to human health, and a cost-effective alternative with Cr(VI) and nitrogen simultaneous removal is still needed. This study investigated the influence of Cr(VI) on nitrogen removal in the two-stage vertical-flow constructed wetlands (TS-VFCWs) along with iron ore and woodchip, and explored relationship between Cr(VI) and nitrogen removal. The results showed that efficient Cr(VI) and nitrogen removal were simultaneously achieved in TS-VFCWs together with iron-ore and woodchip under 2 mg/L-Cr(VI), whereas 10 mg/L-Cr(VI) gave significant and recoverable inhibition of nitrogen removal. Cr(VI) supplementation promoted the beneficiation of Cr(VI)-reducing/resistant bacteria IMCC26207 and Bryobacter on iron-ore. Woodchip enriched Cr(VI)-reducing bacteria Streptomyces and Thiobacillus. XRD and XPS showed that abundant bound-Cr existed in the surface of iron ore and woodchip, and Cr(III) precipitation/oxide was the major product. High abundances of nitrifying and autotrophic/heterotrophic denitrifying bacteria ensured good nitrogen removal at Cr(VI) stress.

Remediation materials for the immobilization of hexavalent chromium in contaminated soil: Preparation, applications, and mechanisms

Hexavalent chromium is a toxic metal that can induce severe chromium contamination of soil, posing a potential risk to human health and ecosystems. In recent years, the immobilization of Cr(VI) using remediation materials including inorganic materials, organic materials, microbial agents, and composites has exhibited great potential in remediating Cr(VI)-contaminated soil owing to the environmental-friendliness, short period, simple operation, low cost, applicability on an industrial scale, and high efficiency of these materials. Therefore, a systematical summary of the current progress on various remediation materials is essential. This work introduces the production (sources) of remediation materials and examines their characteristics in detail. Additionally, a critical summary of recent research on the utilization of remediation materials for the stabilization of Cr(VI) in the soil is provided, together with an evaluation of their remediation efficiencies toward Cr(VI). The influences of remediation material applications on soil physicochemical properties, microbial community structure, and plant growth are summarized. The immobilization mechanisms of remediation materials toward Cr(VI) in the soil are illuminated. Importantly, this study evaluates the feasibility of each remediation material application for Cr(VI) remediation. The latest knowledge on the development of remediation materials for the immobilization of Cr(VI) in the soil is also presented. Overall, this review will provide a reference for the development of remediation materials and their application in remediating Cr(VI)-contaminated soil.

Effect of microbial communities on nitrogen and phosphorus metabolism in rivers with different heavy metal pollution

Small urban and rural rivers usually face heavy metal pollution as a result of urbanization and industrial and agricultural activities. To elucidate the metabolic capacity of microbial communities on nitrogen and phosphorus cycle in river sediments under different heavy metal pollution backgrounds, this study collected samples in situ from two typical rivers, Tiquan River and Mianyuan River, with different heavy metal pollution levels. The microbial community structure and metabolic capacity of nitrogen and phosphorus cycles of sediment microorganisms were analyzed by high-throughput sequencing. The results showed that the major heavy metals in the sediments of the Tiquan River were Zn, Cu, Pb, and Cd with the contents of 103.80, 30.65, 25.95, and 0.44 mg/kg, respectively, while the major heavy metals in the sediments of the Mianyuan River were Cd and Cu with the contents of 0.60 and 27.81 mg/kg, respectively. The dominant bacteria Steroidobacter, Marmoricola, and Bacillus in the sediments of the Tiquan River had positive correlations with Cu, Zn, and Pb while are negatively correlated with Cd. Cd had a positive correlation with Rubrivivax, and Cu had a positive correlation with Gaiella in the sediments of the Mianyuan River. The dominant bacteria in the sediments of the Tiquan River showed strong phosphorus metabolic ability, and the dominant bacteria in the sediments of the Mianyuan River showed strong nitrogen metabolic ability, corresponding to the lower total phosphorus content in the Tiquan River and the higher total nitrogen content in the Mianyuan River. The results of this study showed that resistant bacteria became dominant bacteria due to the stress of heavy metals, and these bacteria showed strong nitrogen and phosphorus metabolic ability. It can provide theoretical support for the pollution prevention and control of small urban and rural rivers and have positive significance for maintaining the healthy development of rivers.

Water Management Impacts on Chromium Behavior and Uptake by Rice in Paddy Soil with High Geological Background Values

Chromium (Cr) is an expression toxic metal and is seriously released into the soil environment due to its extensive use and mining. Basalt is an important Cr reservoir in the terrestrial environment. Cr in paddy soil can be enriched by chemical weathering. Therefore, basalt-derived paddy soils contain extremely high concentrations of Cr and can enter the human body through the food chain. However, the water management conditions' effect on the transformation of Cr in basalt-derived paddy soil with high geological background values was less recognized. In this study, a pot experiment was conducted to investigate the effects of different water management treatments on the migration and transformation of Cr in a soil-rice system at different rice growth stages. Two water management treatments of continuous flooding (CF) and alternative wet and dry (AWD) and four different rice growth stages were set up. The results showed that AWD treatment significantly reduced the biomass of rice and promoted the absorption of Cr in rice plants. During the four growth periods, the root, stem and leaf of rice increased from 11.24-16.11 mg kg^-1, 0.66-1.56 mg kg^-1 and 0.48-2.29 mg kg^-1 to 12.43-22.60 mg kg^-1, 0.98-3.31 mg kg^-1 and 0.58-2.86 mg kg^-1, respectively. The Cr concentration in roots, stems and leaves of AWD treatment was 40%, 89% and 25% higher than CF treatment in the filling stage, respectively. The AWD treatment also facilitated the potential bioactive fractions conversion to the bioavailable fraction, compared with the CF treatment. In addition, the enrichment of iron-reducing bacteria and sulfate-reducing bacteria with AWD treatment also provided electron iron for the mobilization of Cr, thus affecting the migration and transformation of Cr in the soil. We speculated that the reason for this phenomenon may be the bioavailability of Cr was affected by the biogeochemical cycle of iron under the influence of alternating redox. This indicates that AWD treatment may bring certain environmental risks in contaminated paddy soil with high geological background, and it is necessary to be aware of this risk when using water-saving irrigation to plant rice.

Effects of Cr Stress on Bacterial Community Structure and Composition in Rhizosphere Soil of Iris tectorum under Different Cultivation Modes

With the rapid development of industry, Cr has become one of the major heavy metal pollutants in soil, severely impacting soil microecology, among which rhizosphere microorganisms can improve the soil microenvironment to promote plant growth. However, how rhizosphere bacterial communities respond to Cr stress under different cultivation modes remains to be further studied. Therefore, in this study, a greenhouse pot experiment combined with 16S rRNA high-throughput sequencing technology was used to study the effects of Cr stress at 200 mg kg−1 on the bacterial community structure and diversity in the rhizosphere soil of Iris tectorum under different cultivation modes. The results showed that the rhizosphere bacterial community diversity index (Shannon and Simpson) and abundance index (Ace and Chao) increased significantly with wetland plant diversity under Cr stress. Moreover, the bacterial community changed by 20.1% due to the addition of Cr, further leading to a 15.9% decrease in the common species of the bacterial community, among which Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteriota accounted for more than 74.8% of the total sequence. However, with the increase in plant diversity, the abundance of rhizosphere-dominant bacteria and plant growth-promoting bacteria communities increased significantly. Meanwhile, the symbiotic network analysis found that under the two cultivation modes, the synergistic effect between the dominant bacteria was significantly enhanced, and the soil microenvironment was improved. In addition, through redundancy analysis, it was found that C, N, and P nutrients in uncontaminated soil were the main driving factors of bacterial community succession in the rhizosphere of I. tectorum, and Cr content in contaminated soil was the main driving factor of bacterial community succession in I. tectorum rhizosphere. In summary, the results of this study will provide a basis for the response of the rhizosphere bacterial community to Cr and the interaction between wetland plants and rhizosphere bacteria in the heavy metal restoration of wetland plants under different cultivation modes.

Citric acid secretion from rice roots contributes to reduction and immobilization of Cr(VI) by driving microbial sulfur and iron cycle in paddy soil

Root exudates released by plants can promote microbial growth and activity, thereby affecting the transformation and availability of soil pollutants. However, the effects of the root exudates of rice plants on chromium (Cr) transformation in paddy soils and the underlying mechanisms are yet to be elucidated properly. The present study investigated how rice root exudates interact with rhizosphere microorganisms to influence the transformation of Cr and explored the key components in root exudates that affect Cr(VI) reduction. The results showed that the addition of root exudate and citric acid markedly decreased soil pH and increased dissolved organic carbon content that created favorable conditions and provided sufficient electron donors for Cr(VI) reduction, thereby greatly facilitating the reduction of Cr(VI) and the transformation of HOAc-extractable Cr into more stable oxidizable and residual Cr. Additionally, Desulfovibrio-related sulfate-reducing bacteria, Thiobacillus-related sulfide-oxidizing bacteria, and Geobacter-related Fe(III)-reducing bacteria were enriched with the addition of root exudate and citric acid. Among them, sulfate would be reduced by Desulfovibrio to sulfide, which would be further utilized by Thiobacillus to reduce Cr(VI), thereby enabling the continuous reduction of Cr(VI); simultaneously, Geobacter would sustain the reduction of Cr(VI) by reducing Fe(III) to Fe(II). Furthermore, based on the high-level secretion of citric acid in response to Cr(VI) exposure and the similar effects of root exudates and citric acid on Cr(VI) reduction, it is proposed that citric acid is the key component in rice root exudates that affects Cr(VI) reduction. These results suggest that root exudates (citric acid as the key component) contribute to the reduction and immobilization of Cr(VI) by driving microbial S and Fe cycles, with Desulfovibrio, Thiobacillus, and Geobacter being the keystone genera. The study provides a novel insight into the Fe/S/Cr co-transformation processes with microbial involvement, and the artificial root exudate mixtures designed to reduce Cr(VI).