Arsenic uptake by rice is influenced by microbe-mediated arsenic redox changes in the rhizosphere

Microbial-driven mechanisms of arsenic methylation during Chinese rice wine fermentation

Arsenic (As) may be a potential contaminant in Chinese rice wine. The methylation of As, which was evaluated as a possible detoxification mechanism to solve this issue. In this study, we simulated Chinese rice wine fermentation under laboratory conditions to explore As methylation behavior. The total As content of Chinese rice wine decreased by 68.6 % after fermentation. As species were transformed during fermentation; inorganic arsenic (iAs) was converted to methylated As; iAs decreased by 73.29 %, and the dimethylarsenic acid (DMA) percentage increased from 4.4 % to 19.9 %. We found that the As methylation gene (arsM) was ubiquitous in Chinese rice wine. Correlation analysis showed that physicochemical properties determined arsM abundance and DMA content during fermentation. The microbial As methylation pathway was summarized based on the annotated As functional genes from the Kyoto Encyclopedia of Genes and Genomes database. Higher relative abundances of glutathione S-transferase and arsC promoted the formation of more trivalent As substrates and further promoted methylation behavior for As detoxification during fermentation. According to the microbial arsM contribution analysis, Mycobacteroides, Rhizopus, and Jimgerdemannia were the primary As methylation microorganisms in Chinese rice wine. These results highlighted the specific As methylation process during fermentation, which could improve the control of As contamination in Chinese rice wines.

Agronomic solutions to decrease arsenic concentrations in rice

Rice plants accumulate arsenic (As), a toxic metalloid found both naturally and as a form of anthropogenic pollution in rice fields. Arsenic concentrations in rice grain may pose human health risks, particularly when consumed regularly or used in food products for infants and young children. The purpose of this review is to summarize evidence-based mitigation strategies for minimizing the As content of rice and establish recommendations for their implementation. Mitigation strategies include irrigation management practices that introduce aerobic periods, applying soil and foliar amendments that decrease As plant-uptake, selecting and developing cultivars with lower rates of As-uptake, and post-harvest processing. In addition to a literature review, we interviewed rice producers and stakeholders to identify barriers or knowledge gaps to implementing the mitigation strategies. Alternate wetting and drying irrigation showed high effectiveness in decreasing grain As concentrations and is also climate-smart and can be cost-neutral. Combining irrigation management with select amendments maximized the decrease of grain As concentrations. Combining treatments will allow a choice of options to accommodate different farm circumstances, though nearly all field-level treatments lack experimental evidence from trials at production-scale operations (i.e., > 1 ha, with commercial management). Thus, more research is needed to develop best management strategies at the field scale in collaboration with farmers.

Application of Silica Nanoparticles Induces Different Effects on Inorganic and Methylated Arsenic Accumulation in Rice Grains: Insights from Arsenic Transformation in Soil

Silica nanoparticles (SiNPs) are promising agrochemicals for reducing pollutant accumulation in plants. However, their applications sometimes fail to reduce arsenic in rice grains. Here, we explored the mechanisms using pot experiments via foliar and soil applications, respectively. Both applications significantly decreased As(III) (19.2-35.1%) and DMA (74.4-81.3%) in grains but increased As(V) by 1.2-1.8-fold. SiNP applications reduced As(III) but promoted As(V) in porewater during the flooding period. The As(III)-oxidation gene aioA showed a 1-3 orders of magnitude higher abundance than arsenic-reduction/methylation genes, and its abundance significantly increased after both applications. SiNP applications facilitated the release of Fe-bound organic carbon into porewater and promoted bacterial growth and As(III) oxidation, leading to high As(V) availability for rice uptake. Nevertheless, foliar spraying performed better than soil amendment in reducing total arsenic in grains by inhibiting stem/nodes-to-grain translocation. Our findings highlight the microbial arsenic transformation in soil regulated by SiNPs and demonstrate the advantages of foliar spraying in the arsenic-contaminated paddy field.

Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation

The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.

Metalloid Nanomaterials Alleviate Arsenic Phytotoxicity and Grain Accumulation in Rice: Mechanisms of Abiotic Stress Tolerance and Rhizosphere Behavior

Nanoenabled agriculture technology exhibits potential in reducing arsenic uptake in rice; however, a systematic understanding of the rice-soil-microorganism process of nanomaterials (NMs) is lacking. Soil amendment of metalloid NMs, including SiO2, hydroxyapatite, S0, and Se0 at 10-100 (0.1-5.0 for Se NMs) mg/kg, increased rice biomass by 76.1-135.8% in arsenic-contaminated soil (17.0 mg/kg) and decreased arsenic accumulation in plant tissues by 9.3-78.2%. The beneficial effects were nanoscale-specific and NMs type- and concentration-dependent; 5 mg/kg Se NMs showed the greatest growth promotion and decrease in As accumulation. Mechanistically, (1) Se NMs optimized the soil bacterial community structure, enhancing the abundance of arsM by 104.2% and subsequently increasing arsenic methylation by 276.1% in rhizosphere compared to arsenic-alone treatments; (2) metabolomic analyses showed that Se NMs upregulated the biosynthesis pathway of abscisic acid, jasmonic acid, and glutathione, with subsequent downregulation of the arsenic transporter-related gene expression in roots by 42.2-73.4%, decreasing the formation of iron plaque by 87.6%, and enhancing the arsenic detoxification by 50.0%. Additionally, amendment of metalloid NMs significantly enhanced arsenic-treated rice yield by 66.9-91.4% and grain nutritional quality. This study demonstrates the excellent potential of metalloid NMs for an effective and sustainable strategy to increase food quality and safety.

Paddy Soil Flooding and Nonflooding Affect the Transcriptional Activity of Arsenic Methylation and Demethylation Communities

The intermediate product methylarsenite [MMA(III)] of arsenic (As) methylation can be methylated to dimethylarsenate (DMA), which causes rice straighthead disease via the As methylation enzyme (ArsM), demethylated to arsenite via the As demethylation enzyme (ArsI), or excreted from cells via the MMA(III) efflux enzyme (ArsP). Whereas As methylation is commonly reported in flooded soils, As demethylation is mostly mediated by aerobes. We used custom-built ROCker models (accuracies of 99.7-99.9%) to quantify the short-read sequences carrying As genes and investigate the variations in the transcriptional activity of the arsM, arsI, and arsP genes in flooded and nonflooded paddy soils. We revealed significantly (p < 0.05) greater transcriptional activity of the arsM and arsP genes in flooded than nonflooded soils, whereas the transcriptional activity of the arsI genes was comparable. MMA(III) demethylation in flooded soils is possibly coupled with denitrification, as revealed by the significantly (p < 0.05) positively correlated genes in terms of transcriptional activity. Moreover, we showed that microbes coexpressing the arsM and arsI genes were dominated by Actinomycetota and Pseudomonadota. This study sheds light on the active microbial communities involved in As methylation and demethylation in paddy soils and provides insights into the prevention of rice straighthead disease.

Conventional and biodegradable microplastics affected arsenic mobility and methylation in paddy soils through distinct chemical-microbial pathways

The presence of microplastics (MPs) in paddy soil has become a growing concern, yet the influence of MPs on arsenic (As) dynamics in paddy soil remains largely unexplored. A 98-day microcosm experiment was conducted to investigate the impact of MPs on As behavior in As-contaminated paddy soil. The results revealed that conventional microplastics (CMPs) reduced As concentration in porewater by 25-38 %, but substantially increased the percentage of methylated As (% MeAs) in soil by 8-23 times under 5 % dosages after 98-day incubation. In contrast, at the end of incubation, biodegradable microplastics (BMPs) at 5 % dosages notably increased As concentration in porewater and % MeAs in soil by 2-9 times and 11-395 times, respectively. The combination of network analysis and Random-Forest analysis implied that CMPs might inhibit As mobility through enhancing microbial As(III) oxidation and promote As methylation by enriching arsM-carrying microbes. However, BMPs promoted As release mainly accompanying with microbial iron reduction, and enhanced As methylation through enriching fermenting bacteria (i.e., Clostridiaceae) and arsM-carrying organic matter degrading bacteria (i.e., Gemmatimonas and Nocardia). These findings might provide broaden insights into As cycling induced by MPs and contribute to the prevention of combined pollution from As and MPs in paddy soil.

Controlling factors of iron plaque formation and its adsorption of cadmium and arsenic throughout the entire life cycle of rice plants

Iron (Fe) plaque, which forms on the surface of rice roots, plays a crucial role in immobilizing heavy metal(loids), thus reducing their accumulation in rice plants. However, the principal factors influencing Fe plaque formation and its adsorption capacity for heavy metal(loid)s throughout the rice plant's lifecycle remain poorly understood. Thus, this study investigated the dynamics of Fe plaque formation and its ability to adsorb cadmium (Cd) and arsenic (As) across different growth stages, aiming to identify the key drivers behind these processes. The findings reveal that the rate of radial oxygen loss (ROL) and the abundance of plaque-associated microbes are the primary drivers of Fe plaque formation, with their relative importance ranging from 1.4% to 81%. Similarly, the adsorption of As by Fe plaque is principally determined by the rate of ROL and the quantity of Fe plaque, with subsequent effects from the total Fe in rhizospheric soil, arsenate-reducing bacteria, and organic matter-degrading bacteria. The relative importance of these factors ranges from 6.0% to 11.7%. By contrast, the adsorption of Cd onto Fe plaque is primarily affected by competition for adsorption sites with ammonium in soils and the presence of organic matter-degrading bacteria, contributing 25.5% and 23.5% to the adsorption process, respectively. These findings provide significant insights into the development of Fe plaque and its absorption of heavy metal(loid)s throughout the lifecycle of rice plants.

Migration, transformation of arsenic, and pollution controlling strategies in paddy soil-rice system: A comprehensive review

Arsenic pollution in paddy fields has become a public concern by seriously threatening rice growth, food security and human health. In this review, we delve into the biogeochemical behaviors of arsenic in paddy soil-rice system, systemically revealing the complexity of its migration and transformation processes, including the release of arsenic from soil to porewater, uptake and translocation of arsenic by rice plants, as well as transformation of arsenic species mediated by microorganism. Especially, microbial processes like reduction, oxidation and methylation of arsenic, and the coupling of arsenic with carbon, iron, sulfur, nitrogen cycling through microbes and related mechanisms were highlighted. Environmental factors like pH, redox potential, organic matter, minerals, nutrient elements, microorganisms and periphyton significantly influence these processes through different pathways, which are discussed in this review. Furthermore, the current progress in remediation strategies, including agricultural interventions, passivation, phytoremediation and microbial remediation is explored, and their potential and limitations are analyzed to address the gaps. This review offers comprehensive perspectives on the complicated behaviors of arsenic and influence factors in paddy soil-rice system, and provides a scientific basis for developing effective arsenic pollution control strategies.

Quantifying the impact of factors on soil available arsenic using machine learning

Arsenic (As) can accumulate in edible plant parts and thus pose a serious threat to human health. Identifying the contributions of various factors to soil available As is crucial for evaluating environmental risks. However, research quantitatively assessing the importance of soil properties on available As is scarce. In this study, we utilized 442 datasets covering total As, available As, and properties of farmland soils. The five machine learning models were employed to predict soil available As content, and the model with the best predictive performance was selected to calculate the importance of soil properties on available As and interpret the model results. The Random Forest model exhibited the best predictive performance, with R2 for the test set of dryland and paddy fields being 0.83 and 0.82 respectively, while also outperforming other machine learning models in terms of accuracy. Concurrently, evaluating the contribution of soil properties to soil available As revealed that increases in soil total arsenic, pH, organic matter (OM), and cation exchange capacity (CEC) led to higher soil available As content. Among these factors, soil total As had the greatest impact, followed by CEC. The influence of pH on soil available As was greater in dryland compared to OM, while in paddy fields, it was smaller than OM (p < 0.01). Sensitivity analysis results indicated that reducing soil total As content had the greatest effect on available As. In both dryland and paddy field soils, reducing soil total As had the most pronounced effect on available As, leading to reductions of 10.09% and 8.48%, respectively. Therefore, prioritizing the regulation of soil total As and CEC is crucial in As contamination management practices to alter As availability in farmland soils.

Diversity and transcription of genes involved in respiratory As(V) reduction and As(III) methylation in Japanese paddy soils

BACKGROUND

Arsenic (As) metabolism by soil microorganisms has an impact on As geochemical cycling in paddy soils, which in turn affects As uptake in rice. However, little is known about the key microorganisms involved in this process in Japanese paddy soil.

RESULTS

Total RNA was extracted from Japanese paddy soils with different levels of dissolved As under flooded conditions, and the transcription of As metabolic genes (arrA, ttrA and arsM) was analyzed via a metatranscriptomic approach. The results showed that ttrA was the predominant respiratory arsenate reductase gene transcribed in these soils rather than arrA, suggesting that ttrA contributes to the reductive dissolution of As. The predominant taxa expressing ttrA differed among soils but were mostly associated with genera known for their iron- and/or sulfate-reduction activity. In addition, a wide variety of microorganisms expressed and upregulated arsM approximately 5.0- to 13.2-fold at 9 d compared with 3 d of incubation under flooded conditions in flasks.

CONCLUSIONS

Our results support the involvement of microbial activity in the geochemical cycling of As in Japanese paddy soils and suggest that ttrA may be one of the key genes involved in the formation of arsenite, an inorganic species taken up by rice.

Evaluating the impact of microorganisms in the iron plaque and rhizosphere soils of Spartina alterniflora and Suaeda salsa on the migration of arsenic in a coastal tidal flat wetland in China

The microorganism in rhizosphere systems has the potential to regulate the migration of arsenic (As) in coastal tidal flat wetlands. This study investigates the microbial community in the iron plaque and rhizosphere soils of Spartina alterniflora (S. alterniflora) and Suaeda salsa (S. salsa), as two common coastal tidal flat wetland plants in China, and determines the impact of the As and Fe redox bacteria on As mobility using field sampling and 16S rDNA high-throughput sequencing. The results indicated that As bound to crystalline Fe in the Fe plaque of S. salsa in high tidal flat. In the Fe plaque, there was a decrease in the presence of Fe redox bacteria, while the presence of As redox bacteria increased. Thus, the formation of Fe plaque proved advantageous in promoting the growth of As redox bacteria, thereby aiding in the mobility of As from rhizosphere soils to the Fe plaque. As content in the Fe plaque and rhizosphere soils of S. alterniflora was found to be higher than that of S. salsa. In the Fe plaque, As/Fe-reducing bacteria in S. alterniflora, and As/Fe-oxidizing bacteria in S. salsa significantly affected the distribution of As in rhizosphere systems. S. alterniflora has the potential to be utilized for wetland remediation purposes.

A novel sulfidogenic process via sulfur reduction to remove arsenate in acid mine drainage: Insights into the performance and microbial mechanisms

Biological sulfidogenic processes based on sulfate-reducing bacteria (SRB) are not suitable for arsenic (As)-containing acid mine drainage (AMD) treatment because of the formation of the mobile thioarsenite during sulfate reduction. In contrast, biological sulfidogenic processes based on sulfur-reducing bacteria (S0RB) produce sulfide without pH increase, which could achieve more effective As removal than the SRB-based process. However, the reduction ability and toxicity tolerance of S0RB to As remains mysterious, which may substantially affect the practical applicability of this process when treating arsenate (As(V))-containing AMD. Thus, this study aims to develop a biological sulfur reduction process driven by S0RB, and explore its long-term performance on As(V) removal and microbial community evolution. Operating under moderately acidic conditions (pH=4.0), the presence of 10 mg/L As(V) significantly suppressed the activity of S0RB, leading to the failure of As(V) removal. Surprisingly, a drop in pH to 3.0 enhanced the tolerance of S0RB to As toxicity, allowing for efficient sulfide production (396±102 mg S/L) through sulfur reduction. Consequently, effective and stable removal of As(V) (99.9 %) was achieved, even though the sulfidogenic bacteria were exposed to high levels of As(V) (42 mg/L) in long-term trials. Spectral and spectroscopic analysis showed that As-bearing sulfide minerals were present in the bioreactor. Remarkably, the presence of As(V) induced notable changes in the microbial community composition, with Desulfurella and Clostridium identified as predominate sulfur reducers. The qPCR result further revealed an increase in the concentration of functional genes related to As transport (asrA and arsB) in the bioreactor sludge as the pH decreased from 4.0 to 3.0. This suggests the involvement of microorganisms carrying asrA and arsB in an As transport process. Furthermore, metagenomic binning demonstrated that Desulfurella contained essential genes associated with sulfur reduction and As transportation, indicating its genetic potential for sulfide production and As tolerance. In summary, this study underscores the effectiveness of the biological sulfur reduction process driven by S0RB in treating As(V)-contaminated AMD. It offers insights into the role of S0RB in remediating As contamination and provides valuable knowledge for practical applications.

Sustainable water management in rice cultivation reduces arsenic contamination, increases productivity, microbial molecular response, and profitability

Arsenic (As) and silicon (Si) are two structurally competitive natural elements where Si minimises As accumulation in rice plants, and based on this two-year field trial, the study proposes adopting alternating wetting and drying (AWD) irrigation as a sustainable water management strategy allowing greater Si availability. This field-based project is the first report on AWD's impact on As-Si distribution in fluvio-alluvial soils of the entire Ganga valley (24 study sites, six divisions), seasonal variance (pre-monsoon and monsoon), rice plant anatomy and productivity, soil microbial diversity, microbial gene ontology profiling and associated metabolic pathways. Under AWD to flooded and pre-monsoon to monsoon cultivations, respectively, greater Si availability was achieved and As-bioavailability was reduced by 8.7 ± 0.01-9.2 ± 0.02% and 25.7 ± 0.09-26.1 ± 0.01%. In the pre-monsoon and monsoon seasons, the physiological betterment of rice plants led to the high rice grain yield under AWD improved by 8.4 ± 0.07% and 10.0 ± 0.07%, proving the economic profitability. Compared to waterlogging, AWD evidences as an optimal soil condition for supporting soil microbial communities in rice fields, allowing diverse metabolic activities, including As-resistance, and active expression of As-responsive genes and gene products. Greater expressions of gene ontological terms and complex biochemical networking related to As metabolism under AWD proved better cellular, genetic and environmental responsiveness in microbial communities. Finally, by implementing AWD, groundwater usage can be reduced, lowering the cost of pumping and field management and generating an economic profit for farmers. These combined assessments prove the acceptability of AWD for the establishment of multiple sustainable development goals (SDGs).

Nutrient and mycoremediation of a global menace 'arsenic': exploring the prospects of phosphorus and Serendipita indica-based mitigation strategies in rice and other crops

KEY MESSAGE

Serendipita indica induced metabolic reprogramming in colonized plants complements phosphorus-management in improving their tolerance to arsenic stress on multifaceted biological fronts. Restoration of the anthropic damage done to our environment is inextricably linked to devising strategies that are not only economically sound but are self-renewing and ecologically conscious. The dilemma of heavy metal (HM) dietary ingestion, especially arsenic (As), faced by humans and animals alike, necessitates the exploitation of such technologies and the cultivation of healthy and abundant crops. The remarkable symbiotic alliance between plants and 'mycorrhizas' has evolved across eons, benefiting growth/yield aspects as well as imparting abiotic/biotic stress tolerance. The intricate interdependence of Serendipita indica (S. indica) and rice plant reportedly reduce As accumulation, accentuating the interest of microbiologists, agriculturists, and ecotoxicological scientists apropos of the remediation mechanisms of As in the soil-AMF-rice system. Nutrient management, particularly of phosphorus (P), is also praised for mitigating As phytotoxicity by deterring the uptake of As molecules due to the rhizospheric cationic competition. Taking into consideration the reasonable prospects of success in minimizing As acquisition by rice plants, this review focuses on the physiological, metabolic, and transcriptional alterations underlying S. indica symbiosis, recuperation of As stress together with nutritional management of P by gathering case studies and presenting successful paradigms. Weaving together a volume of literature, we assess the chemical forms of As and related transport pathways, discuss As-P-rice interaction and the significance of fungi in As toxicity mitigation, predominantly the role of mycorrhiza, as well as survey of the multifaceted impacts of S. indica on plants. A potential strategy for simultaneous S. indica + P administration in paddy fields is proposed, followed by future research orientation to expand theoretic comprehension and encourage field-based implementation.

Impact of iron and sulfur cycling on the bioavailability of cadmium and arsenic in co-contaminated paddy soil

The biogeochemical cycling of iron (Fe) or sulfur (S) in paddy soil influences the cadmium (Cd) and arsenic (As) migration. However, the influence of coupled reduction effects and reaction precedence of Fe and S on the bioavailability of Cd and As is still not fully understood. This study aimed to reveal the influence of Fe and S reduction on soil Cd and As mobility under various pe + pH conditions and to elucidate the related mechanism in subtropical China. According to the findings, higher adsorption from Fe reduction caused high-crystalline goethite (pe + pH > 2.80) to become amorphous ferrihydrite, which in turn caused water-soluble Cd (62.0%) to first decrease. Cd was further decreased by 72.7% as a result of the transformation of SO42- to HS-/S2- via sulfate reduction and the formation of CdS and FeS. As release (an increase of 8.1 times) was consequently caused by the initial reduction and dissolution of iron oxide (pe + pH > 2.80). FeS had a lesser impact on the immobilization of As than sulfate-mediated As (V) reduction in the latter stages of the reduction process (pe + pH < 2.80). pe + pH values between 3 and 3.5 should be maintained to minimize the bioavailability of As and Cd in moderate to mildly polluted soil without adding iron oxides and sulfate amendments. The practical remediation of severely co-contaminated paddy soil can be effectively achieved by using Fe and S additions at different pe + pH conditions. This technique shows promise in reducing the bioavailability of Cd and As.

Dissemination of antibiotic resistance genes is regulated by iron oxides: Insight into the influence on bacterial transformation

The transportation of antibiotic resistance genes (ARGs) in manure-soil-plant continuums poses risks to human health. Horizontal gene transfer, particularly for bacterial transformation, is an important way for ARG dissemination. As crucial components in soils, iron oxides impacted the fates of various abiotic and biotic contaminants due to their active properties. However, whether they can influence the transformation of ARGs is unknown, which waits to be figured out to boost the assessment and control of ARG spread risks. In this study, we have investigated the effects of goethite, hematite, and magnetite (0-250 mg/L, with sizes < 100 nm and > 100 nm) on the transfer of ampicillin resistance genes to Escherichia coli cells. At lower iron oxide concentrations, the transformation of ARGs was first facilitated (transformation frequency reached up to 3.38-fold higher), but the facilitating effects gradually weakened and eventually disappeared as concentrations further increased. Particle size and iron oxide type were not the universal determinants controlling the transformation. At lower concentrations, iron oxides interacted with proteins and phospholipids in E. coli envelope structures, and induced the overgeneration of intracellular reactive oxygen species. Consequently, they led to pore formation and permeability enhancement on the cell membrane, thus promoting the transformation. The facilitation was also associated with the carrier-like effect of iron oxides for antibiotic resistance plasmids. At higher concentrations, the weakened facilitations were attributed to the aggregation of iron oxides. In this study, we highlight the crucial roles of the concentrations (contents) of iron oxides on the dissemination of ARGs in soils; this study may serve as a reference for ARG pollution control in future agricultural production.

Unraveling assemblage of microbial community dwelling in Dabaoshan As/Pb/Zn mine-impacted area: A typical mountain mining area of South China

Microbial community assemblage includes microorganisms from the three domains including Bacteria, Archaea, and Eukarya (Fungi), which play a crucial role in geochemical cycles of metal(loid)s in mine tailings. Mine tailings harbor vast proportions of metal(loid)s, representing a unique source of co-contamination of metal(loid)s that threaten the environment. The elucidation of the assembly patterns of microbial communities in mining-impacted ecospheres has received little attention. To decipher the microbial community assembly processes, the microbial communities from the five sites of the Dabaoshan mine-impacted area were profiled by the MiSeq sequencing of 16S rRNA (Bacteria and Archaea) genes and internal transcribed spacers (Fungi). Results indicated that the coexistence of 31 bacterial, 10 fungal, and 3 archaeal phyla, were mainly dominated by Mucilaginibacter, Cladophialophora, and Candidatus Nitrosotalea, respectively. The distribution of microorganisms was controlled by deterministic processes. The combination of Cu, Pb, and Sb was the main factor explaining the structure of microbial communities. Functional predicting analysis of bacteria and archaea based on the phylogenetic investigation of communities by reconstruction of unobserved states analyses revealed that the metabolic pathways related to arsenite transporter, arsenate reductase, and FeS cluster were important for metal detoxification. Furthermore, the ecological guilds (pathogens, symbiotrophs, and saprotrophs) of fungal communities explained 44.5 % of functional prediction. In addition, metal-induced oxidative stress may be alleviated by antioxidant enzymes of fungi communities, such as catalase. Such information provides new insights into the microbial assembly rules in co-contaminated sites.

Soil Humic Acid Stimulates Potentially Active Dissimilatory Arsenate-Reducing Bacteria in Flooded Paddy Soil as Revealed by Metagenomic Stable Isotope Probing

Dissimilatory arsenate reduction contributes a large proportion of arsenic flux from flooded paddy soil, which is closely linked to soil organic carbon input and efflux. Humic acid (HA) represents a natural ingredient in soil and is shown to enhance microbial arsenate respiration to promote arsenic mobility. However, the community and function profiles of metabolically active arsenate-respiring bacteria and their interactions with HA in paddy soil remain unclear. To probe this linkage, we performed a genome-centric comparison of potentially active arsenate-respiring bacteria in anaerobic microcosms amended with 13C-lactate and HA by combining stable-isotope probing with genome-resolved metagenomics. Indeed, HA greatly accelerated the microbial reduction of arsenate to arsenite. Enrichment of bacteria that harbor arsenate-respiring reductase genes (arrA) in HA-enriched 13C-DNA was confirmed by metagenomic binning, which are affiliated with Firmicutes (mainly Desulfitobacterium, Bacillus, Brevibacillus, and Clostridia) and Acidobacteria. Characterization of reference extracellular electron transfer (EET)-related genes in these arrA-harboring bacteria supports the presence of EET-like genes, with partial electron-transport chain genes identified. This suggests that Gram-positive Firmicutes- and Acidobacteria-related members may harbor unspecified EET-associated genes involved in metal reduction. Our findings highlight the link between soil HA and potentially active arsenate-respiring bacteria, which can be considered when using HA for arsenic removal.

The use of urea hydrogen peroxide as an alternative N-fertilizer to reduce accumulation of arsenic in rice grains

A greenhouse experiment was conducted to examine the effects of urea hydrogen peroxide (UHP) on reducing the accumulation of As in rice grains. The results show that UHP effectively triggered Fenton-like reaction by reacting with Fe2+ in the paddy soils. This significantly inhibited the activities of As(V)-reducing microbes, causing impediment of As(V)-As(III) conversion following inundation of dryland crop soils for paddy rice cultivation. As-methylating microbes were also inhibited, adversely affecting As methylation in the soils. These processes led to the reduction in phyto-availability of As in the soil solutions for uptake by rice plant roots, and consequently reduced the accumulation of As in the rice grains. In this study, an UHP application rate of 0.0625% on three occasions (tillering, heading and filling) during the rice growth period was sufficient to lower the rice grain-borne As concentration to below 0.2 mg/kg, meeting the quality standard set by the Chinese government. No additive effect on reducing grain-borne As was observed for the joint application of UHP and biochar or biochar composite. The use of UHP for soil fertilization had no adverse impact on rice yield in comparison with the application of urea at an equal amount of nitrogen.

Glutaredoxin in Rice Growth, Development, and Stress Resistance: Mechanisms and Research Advances

Rice (Oryza sativa L.) is a staple food for more than half of the global population. Various abiotic and biotic stresses lead to accumulation of reactive oxygen species in rice, which damage macromolecules and signaling pathways. Rice has evolved a variety of antioxidant systems, including glutaredoxin (GRX), that protect against various stressors. A total of 48 GRX gene loci have been identified on 11 of the 12 chromosomes of the rice genome; none were found on chromosome 9. GRX proteins were classified into four categories according to their active sites: CPYC, CGFS, CC, and GRL. In this paper, we summarized the recent research advances regarding the roles of GRX in rice development regulation and response to stresses, and discussed future research perspectives related to rice production. This review could provide information for rice researchers on the current status of the GRX and serve as guidance for breeding superior varieties.

Microbial communities in paddy soils: differences in abundance and functionality between rhizosphere and pore water, the influence of different soil organic carbon, sulfate fertilization and cultivation time, and contribution to arsenic mobility and speciation

Abiotic factors and rhizosphere microbial populations influence arsenic accumulation in rice grains. Although mineral and organic surfaces are keystones in element cycling, localization of specific microbial reactions in the root/soil/pore water system is still unclear. Here, we tested if original unplanted soil, rhizosphere soil and pore water represented distinct ecological microniches for arsenic-, sulfur- and iron-cycling microorganisms and compared the influence of relevant factors such as soil type, sulfate fertilization and cultivation time. In rice open-air-mesocosms with two paddy soils (2.0% and 4.7% organic carbon), Illumina 16S rRNA gene sequencing demonstrated minor effects of cultivation time and sulfate fertilization that decreased Archaea-driven microbial networks and incremented sulfate-reducing and sulfur-oxidizing bacteria. Different compartments, characterized by different bacterial and archaeal compositions, had the strongest effect, with higher microbial abundances, bacterial biodiversity and interconnections in the rhizosphere vs pore water. Within each compartment, a significant soil type effect was observed. Higher percentage contributions of rhizosphere dissimilatory arsenate- and iron-reducing, arsenite-oxidizing, and, surprisingly, dissimilatory sulfate-reducing bacteria, as well as pore water iron-oxidizing bacteria in the lower organic carbon soil, supported previous chemistry-based interpretations of a more active S-cycling, a higher percentage of thioarsenates and lower arsenic mobility by sorption to mixed Fe(II)Fe(III)-minerals in this soil.

Insight into the plant-associated bacterial interactions: Role for plant arsenic extraction and carbon fixation

This study investigated the interactions between rhizosphere and endosphere bacteria during phytoextraction and how the interactions affect arsenic (As) extraction and carbon (C) fixation of plants. Pot experiments, high-throughput sequencing, metabonomics, and network analysis were integrated. Results showed that positive correlations dominated the interconnections within modules (>95 %), among modules (100 %), and among keystone taxa (>72 %) in the bacterial networks of plant rhizosphere, root endosphere, and shoot endosphere. This confirmed that cooperative interactions occurred between bacteria in the rhizosphere and endosphere during phytoextraction. Modules and keystone taxa positively correlating with plant As extraction and C fixation were identified, indicating that modules and keystone taxa promoted plant As extraction and C fixation simultaneously. This is mainly because modules and keystone taxa in plant rhizosphere, root endosphere, and shoot endosphere carried arsenate reduction and C fixation genes. Meanwhile, they up-regulated the significant metabolites related to plant As tolerance. Additionally, shoot C fixation increased peroxidase activity and biomass thereby facilitating plant As extraction was confirmed. This study revealed the mechanisms of plant-associated bacterial interactions contributing to plant As extraction and C fixation. More importantly, this study provided a new angle of view that phytoextraction can be applied to achieve multiple environmental goals, such as simultaneous soil remediation and C neutrality.

Arbuscular Mycorrhizal Fungi Alter Arsenic Translocation Characteristics of Iris tectorum Maxim

Arsenic (As) pollution in wetlands, mainly as As(III) and As(V), has threatened wetland plant growth. It has been well documented that arbuscular mycorrhizal (AM) fungi can alleviate As stress in terrestrial plants. However, whether AM fungi can protect natural wetland plants from As stress remains largely unknown. Therefore, three hydroponic experiments were conducted in which Iris tectorum Maxim. (I. tectorum) plants were exposed to As(III) or As(V) stresses, to investigate the effects of mycorrhizal inoculation on As uptake, efflux, and accumulation. The results suggested that short-term kinetics of As influx in I. tectorum followed the Michaelis-Menten function. Mycorrhizal inoculation decreased the maximum uptake rate (Vmax) and Michaelis constant (Km) of plants for As(III) influx, while yielding no significant difference in As(V) influx. Generally, mycorrhizal plants released more As into environments after 72 h efflux, especially under As(V) exposure. Moreover, mycorrhizal plants exhibited potential higher As accumulation capacity, probably due to more active As reduction, which was one of the mechanisms through which AM fungi mitigate As phytotoxicity. Our study has revealed the role of aerobic microorganism AM fungi in regulating As translocation in wetland plants and supports the involvement of AM fungi in alleviating plant As stress in anaerobic wetlands.

Sustainable Immobilization of Arsenic by Man-Made Aerenchymatous Tissues in Paddy Soil

Arsenic (As) is a major environmental pollutant and poses a significant health risk to humans through rice consumption. Elevating the soil redox potential (Eh) has been shown to reduce As bioavailability and decrease As accumulation in rice grains. However, sustainable methods for managing the Eh of rice paddies are lacking. To address this issue, we propose a new approach that uses man-made aerenchymatous tissues (MAT) to increase soil Eh by mimicking O2 release from wet plant roots. Our study demonstrated that the MAT method sustainably increased the soil Eh levels from -119 to -80.7 mV (∼30%), over approximately 100 days and within a radius of around 5 cm from the surface of the MAT. Moreover, it resulted in a significant reduction (-28.5% to -63.3%) in dissolved organic carbon, Fe, Mn, and As concentrations. MAT-induced Fe(III) (oxyhydr)oxide minerals served as additional adsorption sites for dissolved As in soil porewater. Furthermore, MAT promoted the oxidation of arsenite to the less mobile arsenate by significantly enhancing the relative abundance of the aioA gene (130% increase in the 0-5 cm soil zone around MAT). The decrease in As bioavailability significantly reduced As accumulation in rice grains (-30.0%). This work offers a low-cost and sustainable method for mitigating As release in rice paddies by addressing the issue of soil Eh management.

Anoxygenic phototrophic arsenite oxidation by a Rhodobacter strain

Microbially mediated arsenic redox transformations are key for arsenic speciation and mobility in rice paddies. Whereas anaerobic anoxygenic photosynthesis coupled to arsenite (As(III)) oxidation has been widely examined in arsenic-replete ecosystems, it remains unknown whether this light-dependent process exists in paddy soils. Here, we isolated a phototrophic purple bacteria, Rhodobacter strain CZR27, from an arsenic-contaminated paddy soil and demonstrated its capacity to oxidize As(III) to arsenate (As(V)) using malate as a carbon source photosynthetically. Genome sequencing revealed an As(III)-oxidizing gene cluster (aioXSRBA) encoding an As(III) oxidase. Functional analyses showed that As(III) oxidation under anoxic phototrophic conditions correlated with transcription of the large subunit of the As(III) oxidase aioA gene. Furthermore, the non-As(III) oxidizer Rhodobacter capsulatus SB1003 heterologously expressing aioBA from strain CZR27 was able to oxidize As(III), indicating that aioBA was responsible for the observed As(III) oxidation in strain CZR27. Our study provides evidence for the presence of anaerobic photosynthesis-coupled As(III) oxidation in paddy soils, highlighting the importance of light-dependent, microbe-mediated arsenic redox changes in paddy arsenic biogeochemistry.

Differential effects of arsenite and arsenate on rice (Oryza sativa) plants differing in glutathione S-transferase gene expression

Contamination of paddy soils with arsenic (As) can cause phytotoxicity in rice and increase the accumulation of arsenic in grains. The uptake and accumulation of As in rice depends on the different As species present in the soil. Plants detoxify As by conjugating and sequestering xenobiotic compounds into vacuoles using various enzymes. However, the severity of damage induced by arsenite (As(III)) and arsenate (As(V)), as well as the roles of glutathione S-transferase in detoxifying these As species in rice, are not fully understood. In this study, we developed plant materials overexpressing a glutathione S-transferase gene OsGSTU40 under the control of the maize UBIL promoter. Through systematic investigations of both wild-type Nipponbare (Oryza sativa L., ssp. japonica) and OsGSTU40 overexpression lines under chronic or acute stress of As, we aimed to understand the toxic effects of both As(III) and As(V) on rice plants at the vegetative growth stage. We hypothesized that (i) As(III) and As(V) have different toxic effects on rice plants and (ii) OsGSTU40 played positive roles in As toxicity tolerance. Our results showed that As(III) was more detrimental to plant growth than As(V) in terms of plant growth, biomass, and lipid peroxidation in both chronic and acute exposure. Furthermore, overexpression of OsGSTU40 led to better plant growth even though uptake of As(V), but not As(III), into shoots was enhanced in transgenic plants. In acute As(III) stress, transgenic plants exhibited a lower level of lipid peroxidation than wild-type plants. The element composition of plants was dominated by the different As stress treatments rather than by the genotype, while the As concentration was negatively correlated with phosphorus and silicon. Overall, our findings suggest that As(III) is more toxic to plants than As(V) and that glutathione S-transferase OsGSTU40 differentially affects plant reactions and tolerance to different species of arsenic.

Sediment arsenic remediation by submerged macrophytes via root-released O2 and microbe-mediated arsenic biotransformation

Arsenic (As)-contaminated water restoration is extremely challenging because As remobilization from sediments can result in episodic or long-term release of As to the overlying water. In this study, by combining high-resolution imaging techniques with microbial community profiling, we examined the feasibility of utilizing the rhizoremediation of submerged macrophytes (Potamogeton crispus) to decrease As bioavailability and regulate its biotransformation in sediments. Results showed that P. crispus considerably decreased the rhizospheric labile As flux to lower than 4 pg cm^-2 s^-1 from larger than 7 pg cm^-2 s^-1, suggesting its effectiveness in promoting As retention in sediments. Iron plaques induced by radial oxygen loss from roots decreased the mobility of As by sequestering it. Additionally, Mn-oxides may act as an oxidizer for the oxidation of As(III) to As(V) in the rhizosphere, which can further increase the As adsorption owing to the strong binding affinity between As(V) and Fe-oxides. Furthermore, microbially mediated As oxidation and methylation were intensified in the microoxic rhizosphere, which decreased the mobility and toxicity of As by changing its speciation. Our study demonstrated that root-driven abiotic and biotic transformation contribute to As retention in sediments, which lays a foundation for applying macrophytes to the remediation of As-contaminated sediments.

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.

Arsenic release from microbial reduction of scorodite in the presence of electron shuttle in flooded soil

Scorodite (FeAsO₄·H₂O) is a common arsenic-bearing (As-bearing) iron mineral in near-surface environments that could immobilize or store As in a bound state. In flooded soils, microbe induced Fe(III) or As(V) reduction can increase the mobility and bioavailability of As. Additionally, humic substances can act as electron shuttles to promote this process. The dynamics of As release and diversity of putative As(V)-reducing bacteria during scorodite reduction have yet to be investigated in detail in flooded soils. Here, the microbial reductive dissolution of scorodite was conducted in an flooded soil in the presence of anthraquinone-2,6-disulfonate (AQDS). Anaeromyxobacter, Dechloromonas, Geothrix, Geobacter, Ideonella, and Zoogloea were found to be the dominant indigenous bacteria during Fe(III) and As(V) reduction. AQDS increased the relative abundance of dominant species, but did not change the diversity and microbial community of the systems with scorodite. Among these bacteria, Geobacter exhibited the greatest increase and was the dominant Fe(III)- and As(V)-reducing bacteria during the incubation with AQDS and scorodite. AQDS promoted both Fe(III) and As(V) reduction, and over 80% of released As(V) was microbially transformed to As(III). The increases in the abundance of arrA gene and putative arrA sequences of Geobacter were higher with AQDS than without AQDS. As a result, the addition of AQDS promoted microbial Fe(III) and As(V) release and reduction from As-bearing iron minerals into the environment. These results contribute to exploration of the transformation of As from As-bearing iron minerals under anaerobic conditions, thus providing insights into the bioremediation of As-contaminated soil.

Insight into universality and characteristics of nitrate reduction coupled with arsenic oxidation in different paddy soils

Nitrate reduction coupled with arsenic (As) oxidation strongly influences the bioavailability and toxicity of As in anaerobic environments. In the present study, five representative paddy soils developed from different parent materials were used to investigate the universality and characteristics of nitrate reduction coupled with As oxidation in paddy soils. Experimental results indicated that 99.8 % of highly toxic aqueous As(III) was transformed to dissolved As(V) and Fe-bound As(V) in the presence of nitrate within 2-8 d, suggesting that As was apt to be reserved in its low-toxic and nonlabile form after nitrate treatment. Furthermore, nitrate additions also significantly induced the higher abundance of 16S rRNA and As(III) oxidase (aioA) genes in the five paddy soils, especially in the soils developed from purple sand-earth rock and quaternary red clay, which increased by 10 and 3-5 times, respectively, after nitrate was added. Moreover, a variety of putative novel nitrate-dependent As(III)-oxidizing bacteria were identified based on metagenomic analysis, mainly including Aromatoleum, Paenibacillus, Microvirga, Herbaspirillum, Bradyrhizobium, Azospirillum. Overall, all these findings indicate that nitrate reduction coupled with As(III) oxidation is an important nitrogen-As coupling process prevalent in paddy environments and emphasize the significance of developing and popularizing nitrate-based biotechnology to control As pollution in paddy soils and reduce the risk of As compromising food security.

Microbial remediation and plant-microbe interaction under arsenic pollution

Arsenic contamination in aquatic and terrestrial ecosystem is a serious environmental issue. Both natural and anthropogenic processes can introduce it into the environment. The speciation of the As determine the level of its toxicity. Among the four oxidation states of As (-3, 0, +3, and + 5), As(III) and As(V) are the common species found in the environment, As(III) being the more toxic with adverse impact on the plants and animals including human health. Therefore, it is very necessary to remediate arsenic from the polluted water and soil. Different physicochemical as well as biological strategies can be used for the amelioration of arsenic polluted soil. Among the microbial approaches, oxidation of arsenite, methylation of arsenic, biosorption, bioprecipitation and bioaccumulation are the promising transformation activities in arsenic remediation. The purpose of this review is to discuss the significance of the microorganisms in As toxicity amelioration in soil, factors affecting the microbial remediation, interaction of the plants with As resistant bacteria, and the effect of microorganisms on plant arsenic tolerance mechanism. In addition, the exploration of genetic engineering of the bacteria has a huge importance in bioremediation strategies, as the engineered microbes are more potent in terms of remediation activity along with quick adaptively in As polluted sites.

Effects of microplastics on arsenic uptake and distribution in rice seedlings

The potential of microplastics (MPs) and nanoplastics (NPs) to act as a carrier for heavy metals derived from the environment is of rising concern to the health of global ecosystems. Here, we investigated the effects of particle size of polystyrene micro/nano plastics on the uptake, accumulation, and toxicity of As in rice seedlings in a hydroponic system. Significant differences in As uptake and accumulation in different plant tissue were observed between the plants co-exposed to 82 nm NPs + As and 200 nm MPs + As. The NPs + As co-exposure led to higher As accumulation in rice leaves (12.4-36.7 %), while larger sized MPs + As(V) treatment reduced As accumulation in rice leaves. Furthermore, the co-exposure of NPs/MPs + As mitigated the rice growth inhibition caused by As toxicity. These results will provide insight into elucidating the potentially effects of nano/microplastics on As uptake and accumulation in crop plants for assessing the hazards of micro-and nanoplastics as pollutants in the food chain and environment.

Dark Side of Ammonium Nitrogen in Paddy Soil with Low Organic Matter: Stimulation of Microbial As(V) Reduction and As(III) Transfer from Soil to Rice Grains

The bioavailability of arsenic (As) is influenced by ammonium (NH₄⁺-N) fertilization, but the underlying mechanisms controlling As transformation in soil-rice systems are still not fully understood. The effects of two NH₄⁺-N fertilizers, urea and NH₄HCO₃, on the transformation of As in a paddy soil with low organic matter content and transfer in rice plants were investigated. Treatments with urea and NH₄HCO₃ significantly increased arsenite (As(III)) concentration in porewater, bioavailable As in rhizosphere soil, and the relative abundance of the As(V) respiratory reductase gene (arrA) and As(III) methyltransferase gene (arsM). Furthermore, the relative expression of As transporter genes in rice roots, such as OsLsi1, OsLsi2, and OsLsi3, was upregulated, and the translocation efficiency of As(III) from rice roots to brown rice was promoted. Subsequently, As(III) accumulation in brown rice significantly increased. Therefore, attention should be paid to As-contaminated paddy fields with NH₄⁺-N fertilization.

Responses of diversity and arsenic-transforming functional genes of soil microorganisms to arsenic hyperaccumulator (Pteris vittata L.)/pomegranate (Punica granatum L.) intercropping

Intercropping of arsenic (As) hyperaccumulator (Pteris vittata L.) with crops can reduce the As concentration in soil and the resulting ecological and health risks, while maintaining certain economic benefits. However, it is still unclear how As-transforming functional bacteria and dominant bacteria in the rhizosphere of P. vittata affect the microbial properties of crop rhizosphere soil, as well as how As concentration and speciation change in crop rhizosphere soil under intercropping. This is of great significance for understanding the biogeochemical cycle of As in soil and crops. This study aimed to use high-throughput sequencing and quantitative polymerase chain reaction (qPCR) to analyze the effects of different rhizosphere isolation patterns on the bacterial diversity and the copy number of As-transforming functional genes in pomegranate (Punica granatum L.) rhizosphere soil. The results showed that the abundance of bacteria in the rhizosphere soil of pomegranate increased by 16.3 %, and the soil bacterial community structure significantly changed. C_Alphaproteobacteria and o_Rhizobiales bacteria significantly accumulated in the rhizosphere of pomegranate. The copy number of As methylation (arsM) gene in pomegranate rhizosphere soil significantly increased by 63.37 %. The concentrations of nonspecifically sorbed As (F1), As associated with amorphous Fe (hydr)oxides (F3), and the total As (FT) decreased; the proportion of As (III) in pomegranate rhizosphere soil decreased; and the proportion of As (V) increased in pomegranate rhizosphere soil. c_Alphaproteobacteria and o_Rhizobiales accumulated in crop rhizosphere soil under the intercropping of P. vittata with crops. Also, the copy number of As methylation functional genes in crop rhizosphere soil significantly increased, which could reduce As (III) proportion in crop rhizosphere soil. These changes favored simultaneous agricultural production and soil remediation. The results provided the theoretical basis and practical guidance for the safe utilization of As-contaminated soil in the intercropping of As-hyperaccumulator and cash crops.

Distinct response of arsenic speciation and bioavailability to different exogenous organic matter in paddy soil

Land application of organic waste has been increasingly encouraged since it could sequester carbon to mitigate climate change. Considering the susceptibility of arsenic (As) bioavailability in soils to organic matter, understanding the influence of different exogenous organic matter on As biogeochemical behavior in rice-soil system is crucial to reasonably recycle organic waste on soils and ensure the food safety. In this study, impacts of two typical organic matter amendments, rice straw and humic substance, on the As speciation and bioavailability in paddy soil were investigated. Results showed that addition of both rice straw and humic substance could increase the dissolved organic carbon (DOC) content in soil solution by 16.4%-34.4% and 21.7%-53.2%, respectively, but the response of As speciation and bioavailability was quite different, showing the decoupling between As release and DOC. Rice straw addition increased As release to porewater by 28.0%-28.4%, particularly at the initial 0-18 days after the soil was flooded, but humic substance presented the opposite effect, decreasing As release by 27.4%-43.1% which was mainly attributable to the As^III immobilization. This study suggests that the organic matter with high contents of labile heteroaliphatic/aliphatic carbon, being easily to be biodegraded, should not be applied on As contaminated soils.

Responses to arsenic stress of rice varieties coinoculated with the heavy metal-resistant and rice growth-promoting bacteria Pseudomonas stutzeri and Cupriavidus taiwanensis

Arsenic (As)-contaminated rice paddy fields are spreading globally, and thus, rice grains with low As accumulation at a safe level for consumption is profoundly needed. Rice is highly susceptible to As accumulation, and the responses to As vary among rice varieties. Here, combinations of the As^III-oxidizing bacteria Pseudomonas stutzeri strains 4.25, 4.27, or 4.44 and Cupriavidus taiwanensis KKU2500-3 were investigated with respect to their responses to As toxicity and rice growth promotion during the early growth stage. All bacterial strains enhanced antioxidant enzyme activities, including SOD, CAT, APX, GPX, and GR, under As stress in vitro. Uninoculated and coinoculated rice seedlings of three rice varieties (KDML105, RD6, RD10) were cultivated in hydroponic solution without and with a combination of toxic As^III and less toxic As^V for 30 days. Compared with uninoculated seedlings, the inoculated seedlings showed higher growth parameters and lower As contents in roots, shoots and throughout the plants. The bioconcentration factor (BCF) and translocation factor were reduced in inoculated seedlings. The effective response of rice to As toxicity influenced by bacteria was highest in KDML105, followed by RD6 and RD10. The root sulfide content was correlated with As accumulation in roots, shoots, and total seedlings and the BCFs. P. stutzeri 4.44 and C. taiwanensis KKU2500-3 were the most promising combinations for application in KDML105 cultivation under As-contaminated conditions. Understanding the basic response of rice coinoculated with effective bacteria at the early stage will provide guidelines for rice cultivation under As conditions at other scales.

Immobile Iron-Rich Particles Promote Arsenic Retention and Regulate Arsenic Biotransformation in Treatment Wetlands

Remediation of arsenic (As)-contaminated wastewater by treatment wetlands (TWs) remains a technological challenge due to the low As adsorption capacity of wetland substrates and the release of adsorbed As to pore water. This study investigated the feasibility of using immobile iron-rich particles (IIRP) to promote As retention and to regulate As biotransformation in TWs. Iron-rich particles prepared were immobilized in the interspace of a gravel substrate. TWs with IIRP amendment (IIRP-TWs) achieved a stable As removal efficiency of 63 ± 4% over 300 days, while no As removal or release was observed in TWs without IIRP after 180 days of continuous operation. IIRP amendment provided additional adsorption sites and increased the stability of adsorbed As due to the strong binding affinity between As and Fe oxides. Microbially mediated As(III) oxidation was intensified by iron-rich particles in the anaerobic bottom layer of IIRP-TWs. Myxococcus and Fimbriimonadaceae were identified as As(III) oxidizers. Further, metagenomic binning suggested that these two bacterial taxa may have the capability for anaerobic As(III) oxidation. Overall, this study demonstrated that abiotic and biotic effects of IIRP contribute to As retention in TWs and provided insights into the role of IIRP for the remediation of As contamination.

Sustainable removal of soil arsenic by naturally-formed iron oxides on plastic tubes

Arsenic (As) pollution in paddy fields is a major threat to rice safety. Existing As remediation techniques are costly, require external chemical addition and degrade soil properties. Here, we report the use of plastic tubes as a recyclable tool to precisely extract As from contaminated soils. Following insertion into flooded paddy soils, polyethylene tube walls were covered by thin but massive Fe coatings of 76.9-367 mg Fe m^-2 in 2 weeks, which adsorbed significant amounts of As. The formation of tube-wall Fe oxides was driven by local Fe-oxidizing bacteria with oxygen produced by oxygenic phototrophs (e.g., Cyanobacteria) or diffused from air through the tube wall. The tubes with As-bound Fe oxides can be easily separated from soil and then washed and reused. We tested the As removal efficiency in a pot experiment to remove As from ~ 20 cm depth/40 kg soils in a 2-year experiment and achieved an overall removal efficiency of 152 mg As m^-2 soil year^-1, comparable to phytoremediation with the As hyperaccumulator Pteris vittata. The cost of Fe hooks was estimated at 8325 RMB ha^-1 year^-1, and the profit of growing rice (around 16080 RMB ha^-1 year^-1 can be still maintained. The As accumulated in rice tissues was markedly decreased in the treatment (>11.1 %). This work provides a low-cost and sustainable soil remediation method for the targeted removal of As from soils and a useful tool for the study and management of the biogeochemical Fe cycle in paddy soils.

Arsenic accumulation in rice: Alternative irrigation regimes produce rice safe from arsenic contamination

The natural occurrence of arsenic (As) in groundwater & soils and its bioaccumulation in rice grains is a major health concern worldwide. To combat the problem, best combination of irrigation management and suitable rice variety altering As content in grains must be ensured. With this aim, a field trial was conducted with two rice varieties and water management including alternate wetting and drying (AWD) and continuous flooding (CF) irrigation regimes with As contaminated groundwater (AsW) and temporarily stored groundwater (TSG) and river water for only CF (as control). Results revealed that As content in different portions of paddy plant was significantly different (P < 0.001) with irrigation practices and rice varieties. AWD irrigation with TSG accumulated lower As in rice grains compared with CF-AsW for both varieties. Data showed that AWD-TSG practice led to 61.37% and 60.34% grain As reduction for BRRI dhan28 and BRRI dhan29, respectively, compared with CF-AsW. For Principle Component Analysis (PCA), first principle component (PC1) explained 91.7% of the variability and irrigation water As, soil total and available As, straw As, root As and husk As were the dominating parameters. With significant (P < 0.05) variation in yields between the genotypes, AWD increased grain yield by 29.25% in BRRI dhan29 Compared with CF. However, translocation factor (TF) and bioconcentration factor (BCF) for both varieties were less than one for all the treatments. The addition of this study to our knowledge base is that, AWD-TSG with BRRI dhan29 can be an As-safe practice without compromising yields.

Time-Dependent Biosensor Fluorescence as a Measure of Bacterial Arsenic Uptake Kinetics and Its Inhibition by Dissolved Organic Matter

Microbe-mediated transformations of arsenic (As) often require As to be taken up into cells prior to enzymatic reaction. Despite the importance of these microbial reactions for As speciation and toxicity, understanding of how As bioavailability and uptake are regulated by aspects of extracellular water chemistry, notably dissolved organic matter (DOM), remains limited. Whole-cell biosensors utilizing fluorescent proteins are increasingly used for high-throughput quantification of the bioavailable fraction of As in water. Here, we present a mathematical framework for interpreting the time series of biosensor fluorescence as a measure of As uptake kinetics, which we used to evaluate the effects of different forms of DOM on uptake of trivalent arsenite. We found that thiol-containing organic compounds significantly inhibited uptake of arsenite into cells, possibly through the formation of aqueous complexes between arsenite and thiol ligands. While there was no evidence for competitive interactions between arsenite and low-molecular-weight neutral molecules (urea, glycine, and glyceraldehyde) for uptake through the aquaglyceroporin channel GlpF, which mediates transport of arsenite across cell membranes, there was evidence that labile DOM fractions may inhibit arsenite uptake through a catabolite repression-like mechanism. The observation of significant inhibition of arsenite uptake at DOM/As ratios commonly encountered in wetland pore waters suggests that DOM may be an important control on the microbial uptake of arsenite in the environment, with aspects of DOM quality playing an important role in the extent of inhibition. IMPORTANCE The speciation and toxicity of arsenic in environments like rice paddy soils and groundwater aquifers are controlled by microbe-mediated reactions. These reactions often require As to be taken up into cells prior to enzymatic reaction, but there is limited understanding of how microbial arsenic uptake is affected by variations in water chemistry. In this study, we explored the effect of dissolved organic matter (DOM) quantity and quality on microbial As uptake, with a focus on the role of thiol functional groups that are well known to form aqueous complexes with arsenic. We developed a quantitative framework for interpreting fluorescence time series from whole-cell biosensors and used this technique to evaluate effects of DOM on the rates of microbial arsenic uptake. We show that thiol-containing compounds significantly decrease rates of As uptake into microbial cells at environmentally relevant DOM/As ratios, revealing the importance of DOM quality in regulating arsenic uptake, and subsequent biotransformation, in the environment.

Double-edged effects of elevating temperature on the aging of exogenous arsenic in flooded paddy soils

Temperature variation can have a significant impact on arsenic (As) bioavailability in paddy soils. However, details regarding the transformation of exogenous As during the aging process in paddy soils at various temperatures remain unclear. This work investigated the effects of temperature on the As extractability and As species transformation of three paddy soils spiked with exogenous arsenate at 60 mg kg^-1 under flooded aging and explored the related chemical and microbial mechanisms. The results showed that 0.05 M NH₄H₂PO₄-extractable As decreased over time during flooded aging for 192 days, and it decreased by approximately one-third at 35 °C compared with 15 °C and 25 °C at the same aging time, indicating that higher temperatures facilitated the decrease in As extractability. As(V) reduction mainly occurred at 35 °C because the abundance and As(V)-reducing capacity of the predominant indigenous bacteria, the Bacillus sp strains, and the abundance of the arrA gene were significantly higher than those at 15 °C and 25 °C. The reduction of As(V) to As(III) and aging occurred simultaneously. The kinetic models were established, and the rate constants of the reduction and aging processes were obtained. Soil properties significantly affected the aging and reduction processes of extractable As(V). Our study indicated that elevating temperature had dual effects on the environmental risk of As in the flooded aging process. The previous definition of "aging" based on cationic metals needs to be updated according to the transformation characteristics of As species in flooded conditions. Our results addressed the necessity of impeding the reduction of As(V) in paddy soils under global warming.

Impact of different manure-derived dissolved organic matters on the fate of arsenic-antibiotic in co-contaminated paddy soils

Manure application increases the transfer risk of antibiotic resistance to farmland. Especially, its impact remains unclear when it occurs in arsenic (As)-contaminated paddy soils, which is considered as a global environmental problem. In this work, we investigated the fate of antibiotic resistance genes (ARGs) in As-antibiotic co-contaminated paddy soils under the application of manure from different sources (pig manure, cow dung, and chicken manure). Differences in the aliphatic carbon and electron-donating capacities of these dissolved organic matters (DOM) regulated the transformation of iron and As by both biotic and abiotic processes. The regulation by pig manure was stronger than that by cow dung and chicken manure. DOM regulation increased the abundance of As-related functional genes (arsC, arrA, aioA, and arsM) in the soil and accelerated the transformation of As speciation, the highest proportion of As(III) being 45%-61%. Meanwhile, the continuous selection pressure provided by the highly toxic As(III) increased the risk of ARGs and mobile genetic elements (MGEs) via horizontal gene transfer. As-resistant bacteria, including Bacillus, Geobacter, and Desulfitobacterium, were finally considered as potential host bacteria for ARGs and MGEs. In summary, this study clarified the synergistic mechanism of As-antibiotic on the fate of ARGs in co-contaminated paddy soils, and provided practical guidance for the proper application of organic fertilizers.

Silicon enhances abundances of reducing microbes in rhizoplane and decreases arsenite uptake by rice (Oryza sativa L.)

Although silicon (Si) transporters-mediated uptake of arsenic (As) by rice roots is well-documented, how Si influences As behaviors in rhizosphere and rhizoplane before As entry into roots is still unclear. Here we used three rice genotypes to explore the effect of silicic acid on the root uptake of As as impacted by chemical and microbial changes in bulk soil, rhizosphere, rhizoplane and endosphere. The results show that exogenous Si decreased root arsenite [As(III)] absorption, which was attributed to Si-mediated alteration of traits in chemical plaque and microbial films on the rhizoplane. The pH, Eh, As and Fe in the porewater were not influenced by Si. However, Si enhanced the concentrations of As(III) (16-49%) and Fe (15-80%) in the rhizoplane while decreasing As(III) concentrations in the roots (19-39%) and grains (22-29%). The diversities and richness of microbes in soils and plants were not affected by Si. The microbial connections were negatively influenced by Si in bulk and rhizosphere soils, but positively impacted in rhizoplane and endosphere. Both the abundance of reducing microbes, Anaeromyxobacter and Geobacteraceae, and the level of As(III) and Fe in rhizoplane were significantly increased by the addition of Si, thereby restraining As(III) from uptake into roots. This study provides new insights into the microbial mechanisms of Si-mediated As uptake by rice.

Zinc Fertilizers Modified the Formation and Properties of Iron Plaque and Arsenic Accumulation in Rice (Oryza sativa L.) in a Life Cycle Study

This study examined the effect of three forms of zinc fertilizers on arsenic (As) accumulation and speciation in rice tissues over the life cycle of this cereal crop in a paddy soil. The formation and properties of iron plaque on rice roots at the maximum tillering stage and the mature stage were also determined. Elevated As at 5 mg/kg markedly lowered the rice yield by 86%; however, 100 mg/kg Zn fertilizers significantly increased the rice yield by 354-686%, regardless of the Zn form. Interestingly, only Zn²⁺ significantly lowered the total As in rice grains by 17% to 3.5 mg/kg and As(III) by 64% to around 0.5 mg/kg. Zinc amendments substantially hindered and, in the case of zinc oxide bulk particles (ZnOBPs), fully prevented the crystallization of iron oxides (Fe₃O₄ and Fe₂O₃) and silicon oxide (SiO₂) and altered the composition of iron plaques on rice roots. SiO₂ was first reported to be a significant component of iron plaque. Overall, ZnOBPs, ZnO nanoparticles, and Zn²⁺ displayed significant yet distinctive effects on the properties of iron plaque and As accumulation in rice grains, providing a fresh perspective on the potentially unintended consequences of different Zn fertilizers on food safety.

Microbial Community Structure of Arsenic-Bearing Groundwater Environment in the Riverbank Filtration Zone

Arsenic (As) contamination of groundwater is a global public health problem. Microorganisms have a great effect on the migration and transformation of arsenic. Studying the effect of microbial community structure and function on arsenic release in the groundwater environment of the riverbank filtration zone has important theoretical and practical significance. In this paper, in-situ monitoring technology and molecular biology technology were used to study the microbial community in the process of river water infiltration in the Shenyang Huangjia water source, China. The results showed that the structure, diversity and abundance of the microbial community in groundwater were closely related to the arsenic content. Proteobacteria was the dominant phylum in groundwater of the study area, and Acinetobacter, Pseudomonas, Sulfuritalea, Sphingomonas and Hydrogenophaga etc. were the main dominant bacterial genera. In addition to reducing and oxidizing arsenic, these functional microorganisms also actively participated in the biogeochemical cycle of elements such as iron, manganese, nitrogen and sulfur. There was a significant correlation between dominant bacteria and environmental factors. Fe/Mn had a significant positive correlation with As, which brought potential danger to the water supply in high iron and manganese areas.

Leveraging arsenic resistant plant growth-promoting rhizobacteria for arsenic abatement in crops

Arsenic is a toxic metalloid categorized under class 1 carcinogen and is detrimental to both plants and animals. Agricultural land in several countries is contaminated with arsenic, resulting in its accumulation in food grains. Increasing global food demand has made it essential to explore neglected lands like arsenic-contaminated lands for crop production. This has posed a severe threat to both food safety and security. Exploration of arsenic-resistant plant growth-promoting rhizobacteria (PGPR) is an environment-friendly approach that holds promise for both plant growth promotion and arsenic amelioration in food grains. However, their real-time performance is dependent upon several biotic and abiotic factors. Therefore, a detailed analysis of associated mechanisms and constraints becomes inevitable to explore the full potential of available arsenic-resistant PGPR germplasm. Authors in this review have highlighted the role and constraints of arsenic-resistant PGPR in reducing the arsenic toxicity in food crops, besides providing the details of arsenic transport in food grains.

Silicon fertilization influences microbial assemblages in rice roots and decreases arsenic concentration in grain: A five-season in-situ remediation field study

Microbial mechanism of in-situ remediation of arsenic (As) in As-contaminated paddy fields by silicon (Si) fertilization has been rarely reported, especially under continuous rice cultivation and Si applications. In this study, two Si fertilizers were applied for three phases in five consecutive rice seasons to investigate the long-lasting impacts on in-situ remediation of As, and the underpinning microbial mechanism of root-associated compartments (bulk soil, rhizosphere and endosphere) was explored using the last double-cropping rice. Repeated application of Si fertilizers as base manure had a long-lasting effect on reducing As concentrations in rice grains. Application of Si fertilizer at an adequate amount resulted in an extended in-situ remediation effect from endosphere to rhizosphere. The microbial diversity and richness in rhizosphere soil and endosphere were significantly impacted by Si fertilization, the effects depending on application doses and prolonged seasons. Si fertilization can immobilize As in the root or rhizosphere, and Fe concentrations and the As- and Fe-transforming microorganisms (i.e. Geobacteraceae) are the determinants of As uptake in rice. We recommend more extensive supplementation of Si fertilizer at a higher rate to decrease grain As concentration for in-situ remediation. This study sheds light on the microbial-mediated mechanism underlying Si fertilization effect on decreased As uptake in paddy fields.

The chemical-microbial release and transformation of arsenic induced by citric acid in paddy soil

Citric acid (CA) is the major exudate of rice roots, yet the effects of CA on arsenic (As) transformation and microbial community in flooded paddy soil have not been clearly elucidated. In this study, microcosms were established by amending CA to As contaminated paddy soils, mimicking the rhizosphere environment. Results showed that 0.5% CA addition significantly enhanced As mobilization after one-hour incubation, increased total As in porewater by about 20-fold. CA addition induced arsenate release into porewater, and subsequently formed ternary complex of As, iron and organic matters, inhibiting further As transformation (including arsenate reduction and arsenite methylation). Furthermore, the results of linear discriminant analysis (LDA) effect size (LEfSe) and network analysis revealed that CA addition significantly enriched bacteria associated with arsenic and iron reductions, such as Clostridium (up to 35-fold) and Desulfitobacterium (up to 4-fold). Our results suggest that CA exhibits robust ability to mobilize As through both chemical and microbial processes, increasing the risk of As accumulation by rice. This study sheds light on our understanding of As mobilization and transformation in rhizosphere soil, potentially providing effective strategies to restrict As accumulation in food crops by screening or cultivating varieties with low CA exuding.

Phosphorus-arsenic interaction in the 'soil-plant-microbe' system and its influence on arsenic pollution

Elevated arsenic (As) in soil is of public concern due to the carcinogenicity. Phosphorus (P) strongly influences the adsorption, absorption, transport, and transformation of As in the soil and in organisms due to the similarity of the chemical properties of P and As. In soil, P, particularly inorganic P, can release soil-retained As (mostly arsenate) by competing for adsorption sites. In plant and microbial systems, P usually reduces As (mainly arsenate) uptake and affects As biotransformation by competing for As transporters. The intensity and pattern of PAs interaction are highly dependent on the forms of As and P, and strongly influenced by various biotic and abiotic factors. An understanding of the PAs interaction in 'soil-plant-microbe' systems is of great value to prevent soil As from entering the human food chain. Here, we review PAs interactions and the main influential factors in soil, plant, and microbial subsystems and their effects on the As release, absorption, transformation, and transport in the 'soil-plant-microbe' system. We also analyze the application potential of P fertilization as a control for As pollution and suggest the research directions that need to be followed in the future.