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

Niche Differentiation of Arsenic-Transforming Microbial Groups in the Rice Rhizosphere Compartments as Impacted by Water Management and Soil-Arsenic Concentrations

Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, pore water, and grain samples. Results confirmed several As-biotransformation processes in the rice rhizosphere compartments, and distinct assemblage of As-reducing and methylating bacteria was observed between the root-plaque and rhizosphere. Results confirmed higher potential for microbial As-reduction and As-methylation in continuously flooded, long term As-contaminated fields, which accumulated highest concentrations of As^III and methyl-As concentrations in pore water and rice grains. Water management treatment significantly altered As-speciation in the rhizosphere, and intermittent flooding reduced methyl-As and As^III concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different microbial functional groups demonstrating niche separation. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial functional groups. It was also evident that As transformation was coupled to different biogeochemical cycling processes (nutrient assimilation, carbon metabolism etc.) in the compartments and between treatments, revealing functional non-redundancy of rice-rhizosphere microbiome in response to local biogeochemical conditions and As contamination. This study provided novel insights on As-biotransformation processes and their implications on As-chemistry at the root-soil interface and their responses to water management, which could be applied for mitigating As-bioavailability and accumulation in rice grains.

New Arsenite Oxidase Gene (aioA) PCR Primers for Assessing Arsenite-Oxidizer Diversity in the Environment Using High-Throughput Sequencing

Gene encoding the large subunit of As(III) oxidase (AioA), an important component of the microbial As(III) oxidation system, is a widely used biomarker to characterize As(III)-oxidizing communities in the environment. However, many studies were restricted to a few sequences generated by clone libraries and Sanger sequencing, which may have underestimated the diversity of As(III)-oxidizers in natural environments. In this study, we designed a primer pair, 1109F (5'-ATC TGG GGB AAY RAC AAY TA-3') and 1548R (5'-TTC ATB GAS GTS AGR TTC AT-3'), targeting gene sequence encoding for the conserved molybdopterin center of the AioA protein, yielding amplicons approximately 450 bp in size that are feasible for highly parallel amplicon sequencing. By utilizing in silico analyses and the experimental construction of clone libraries using Sanger sequencing, the specificity and resolution of 1109F/1548R are approximated with two other previously published and commonly used primers, i.e., M1-2F/M3-2R and deg1F/deg1R. With the use of the 1109F/1548R primer pair, the taxonomic composition of the aioA genes was similar both according to the Sanger and next-generation sequencing (NGS) platforms. Furthermore, high-throughput amplicon sequencing using the primer pair, 1109F/1548R, successfully identified the well-known As(III)-oxidizers in paddy soils and sediments, and they also revealed the differences in the community structure and composition of As(III)-oxidizers in above two biotopes. The random forest analysis showed that the dissolved As(III) had the highest relative influence on the Chao1 index of the aioA genes. These observations demonstrate that the newly designed PCR primers enhanced the ability to detect the diversity of aioA-encoding microorganisms in environments using highly parallel short amplicon sequencing.

Patterns of microbial arsenic detoxification genes in low-arsenic continental paddy soils

Microbes mediate the arsenic detoxification in paddy soils, determining the fate of arsenic in soils and its availability to rice plants, yet little is known about the structures and abundances of functional genes as well as the driving forces in low-arsenic paddy fields. To depict the arsenic detoxification functional gene patterns, 429 soil samples were collected from 39 paddy fields across four climatic zones in China, with the arsenic contents ranged from 9.76 to 19.74 mg kg^-1. GeoChip, a microarray-based metagenomic technique, was used to analyze the functional genes involved in arsenic detoxification. A total of three arsenic detoxification gene families were detected, aoxB, arxA (arsenite oxidase), and arsM (methyltransferase). Both the diversity and abundance of functional genes varied significantly among sampling sites (p < 0.05) and decreased along the arsenic gradient. Arsenic detoxification genes were carried by bacteria, archaea, and eukaryotes. Redundancy analysis showed that soil samples were grouped according to both climatic zones they located in and arsenic gradients at the continental scale. Soil pH, average annual temperature (AAT), arsenic, annual average precipitation (AAP), and CEC were the most important factors in shaping the functional structure. Structural equation modeling showed that AAT (r = 0.21), pH (r = -0.20), and arsenic contents (r = -0.11) directly affected the arsenic detoxification gene abundances. These findings provide an overall picture of microbial communities involved in arsenic detoxification in paddy soils and reveal the importance of climatic factors in shaping functional genes across a large spatial scale.

Living to the High Extreme: Unraveling the Composition, Structure, and Functional Insights of Bacterial Communities Thriving in the Arsenic-Rich Salar de Huasco Altiplanic Ecosystem

Microbial communities inhabiting extreme environments such as Salar de Huasco (SH) in northern Chile are adapted to thrive while exposed to several abiotic pressures and the presence of toxic elements such as arsenic (As). Hence, we aimed to uncover the role of As in shaping bacterial composition, structure, and functional potential in five different sites in this altiplanic wetland using a shotgun metagenomic approach. The sites exhibit wide gradients of As (9 to 321 mg/kg), and our results showed highly diverse communities and a clear dominance exerted by the Proteobacteria and Bacteroidetes phyla. Functional potential analyses show broadly convergent patterns, contrasting with their great taxonomic variability. As-related metabolism, as well as other functional categories such as those related to the CH4 and S cycles, differs among the five communities. Particularly, we found that the distribution and abundance of As-related genes increase as the As concentration rises. Approximately 75% of the detected genes for As metabolism belong to expulsion mechanisms; arsJ and arsP pumps are related to sites with higher As concentrations and are present almost exclusively in Proteobacteria. Furthermore, taxonomic diversity and functional potential are reflected in the 12 reconstructed high-quality metagenome assembled genomes (MAGs) belonging to the Bacteroidetes (5), Proteobacteria (5), Cyanobacteria (1), and Gemmatimonadetes (1) phyla. We conclude that SH microbial communities are diverse and possess a broad genetic repertoire to thrive under extreme conditions, including increasing concentrations of highly toxic As. Finally, this environment represents a reservoir of unknown and undescribed microorganisms, with great metabolic versatility, which needs further study. IMPORTANCE As microbial communities inhabiting extreme environments are fundamental for maintaining ecosystems, many studies concerning composition, functionality, and interactions have been carried out. However, much is still unknown. Here, we sampled microbial communities in the Salar de Huasco, an extreme environment subjected to several abiotic stresses (high UV radiation, salinity and arsenic; low pressure and temperatures). We found that although microbes are taxonomically diverse, functional potential seems to have an important degree of convergence, suggesting high levels of adaptation. Particularly, arsenic metabolism showed differences associated with increasing concentrations of the metalloid throughout the area, and it effectively exerts a significant pressure over these organisms. Thus, the significance of this research is that we describe highly specialized communities thriving in little-explored environments subjected to several pressures, considered analogous of early Earth and other planets, that have the potential for unraveling technologies to face the repercussions of climate change in many areas of interest.

Effect of Fe-Mn-La-modified biochar composites on arsenic volatilization in flooded paddy soil

As can be volatilized naturally; however, this has adverse environmental effects. In this study, we investigated As volatilization in flooded paddy soil with the addition of biochar (BC) and Fe-Mn-La-modified BC composites (FMLBCs). The addition of BC and FMLBCs caused decreases in total As volatilization in the soil over 7 weeks. Maximum volatilization was achieved in the third week followed by stabilization. Volatilization decreased by 21.9%, 18.8%, 20.8%, and 31.1% with the addition of BC, FMLBC₁, FMLBC₂, and FMLBC₃ (BC/Fe/Mn/La weight ratios different), respectively, in lightly contaminated soil, and by 15.2%, 20.5%, 17.6%, and 25.4%, respectively, in highly contaminated soil. The FMLBCs decreased the exchangeable As fractions and increased the non-swappable As in the soil. Furthermore, the addition of FMLBCs significantly reduced the As(III) concentration in a suspended solution (P < 0.05), whereas no significant changes were observed in the As(V) or methyl arsenic acid concentrations. Soil enzyme activity increased and the relative abundances of Proteobacteria and Actinobacteria changed with the addition of FMLBCs. Therefore, the mechanism by which FMLBCs affected As volatilization likely included the following two aspects: (1) FMLBCs affected the transformation and distribution of soil As and decreased As dissolution, crystallization, and methylation; (2) FMLBCs influenced soil properties, which directly affected microorganism activity, thereby affecting As volatilization. FMLBCs therefore can decrease As volatilization properties and be used to control As volatilization in As-contaminated paddy soils.

High arsenic levels increase activity rather than diversity or abundance of arsenic metabolism genes in paddy soils

Arsenic (As) metabolism genes are generally present in soils but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes (ars) including arsR, acr3, arsB, arsC, arsM, arsI, arsP, and arsH as well as energy-generating As respiratory oxidation (aioA) and reduction (arrA) genes. Somewhat unexpectedly, the relative DNA abundances and diversity of ars, aioA, and arrA genes were not significantly different between low and high (∼10 vs ∼100 mg kg^-1) As soils. By comparison to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars genes abundance only when its concentration was higher than 410 mg kg^-1. In contrast, between low and high As soils, metatranscriptomics revealed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community-wide as opposed to taxon-specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil, or other environments, should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level and thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.

Bioaugmentation with As-transforming bacteria improves arsenic availability and uptake by the hyperaccumulator plant Pteris vittata (L)

Inorganic arsenic (As) is a toxic and carcinogenic pollutant that has long-term impacts on environmental quality and human health. Pteris vittata plants hyperaccumulate As from soils. Soil bacteria are critical for As-uptake by P. vittata. We examined the use of taxonomically diverse soil bacteria to modulate As speciation in soil and their effect on As-uptake by P. vittata. Aqueous media inoculated with Pseudomonas putida MK800041, P. monteilii MK344656, P. plecoglossicida MK345459, Ochrobactrum intermedium MK346993 or Agrobacterium tumefaciens MK346997 resulted in the oxidation of 5-30% As(III) and a 49-79% reduction of As(V). Soil inoculated with P. monteilii increased extractable As(III) and As(V) from 0.5 and 0.09 in controls to 0.9 and 0.39 mg As kg^-1 soil dry weight, respectively. Moreover, and P. vittata plants inoculated with P. monteilii, P. plecoglossicida, O. intermedium strains, and A. tumefaciens strains MK344655, MK346994, MK346997, significantly increased As-uptake by 43, 32, 12, 18, 16, and 14%, respectively, compared to controls. The greatest As-accumulation (1.9 ± 0.04 g kg^-1 frond Dwt) and bioconcentration factor (16.3 ± 0.35) was achieved in plants inoculated with P. monteilii. Our findings indicate that the tested bacterial strains can increase As-availability in soils, thus enhancing As-accumulation by P. vittata. Novelty statement Pteris vittata, a well-known As-hyperaccumulator, has the remarkable ability to accumulate higher levels of As in their above-ground biomass. The As-tolerant bacteria-plant interactions play a significant role in bioremediation by mediating As-redox and controlling As-availability and uptake by P. vittata. Our studies indicated that most of the tested bacterial strains isolated from As-impacted soil significantly enhanced As-uptake by P. vittata. P. monteilii oxidized 20% of As(III) and reduced 50% of As(V), increased As-extraction from soils, and increased As-uptake by 43% greater compared with control. Therefore, these strains associated with P. vittata can be used in large-scale field applications to remediate As-contaminated soil.

Mobility of arsenic in the growth media of rice plants (Oryza sativa subsp. japonica. 'Koshihikari') with exposure to copper oxide nanoparticles in a life-cycle greenhouse study

The increasing arsenic (As) concentration in agriculture media poses increasing risks to both environment and human health. Arsenic mobility determines its bioavailability and entry into the food chain. Nanoparticle application may help to control As mobility in crop cultivation media, and thus decreasing As bioavailability for plants. This research studied the adsorption kinetics of As(V) on copper oxide nanoparticles (nCuO) and nCuO dissolution in a hydroponic solution, and the effects of nCuO on As mobility in a greenhouse system exposed to As(V) addition of 10 mg/kg and nCuO at 0.1-100 mg/L for a life-cycle growth of rice. Arsenic adsorption was dependent on both the total mass and the concentration of nCuO as well as the initial concentration of As(V), while nCuO dissolution was mainly dependent on nCuO concentration regardless of As(V). Arsenic in the simulated paddy was quickly mobilized from soil to aqueous phase during week 1, and further interacted with components in water phase, sediment-water interfacial transition and rice plants. Copper (Cu) and As speciation in the soil were observed by X-Ray Absorption Near Edge Spectrometry. Dissolved Cu was complexed with organic ligands. As(V) was adsorbed to kaolinite, or reduced to As(III) and adsorbed to ferrihydrite. Percent As removal from water phase in the growth container was determined by both nCuO application and As(V) initial concentration. Based on our previous finding that As accumulation in rice grains was significantly decreased by nCuO at 50 mg/L and the results of this study on As adsorption capacity of nCuO and As removal from water due to nCuO application, nCuO at 50 mg/L was proposed to be an appropriate application in rice paddy to immobilize As. Further research is needed in actual agriculture to verify the appropriate nCuO application and get an integrated beneficial effect for rice plants and humans.

New insight into the mechanism of graphene oxide-enhanced phytotoxicity of arsenic species

Graphene oxide (GO) has exhibited significant potential to improve crop cultivation and yield. The application of GO in agriculture will inevitably result in interactions with conventional contaminants, causing potential changes to environmental behavior and toxicity of conventional contaminants. This study explored the joint phytotoxicity of GO and arsenic species (arsenite [As (III)], arsenate [As (V)]) to monocot (Triticum aestivum L.) and dicot (Solamun lycopersicum) plant species. Under the environmentally relevant concentrations, GO (1 mg/L) significantly increased the phytotoxicity of As (III) and As (V) (1 mg/L), with effects being both As- and plant species-specific. One mechanism of enhanced arsenic phytotoxicity could be GO-induced up-regulation of the aquaporin and phosphate transporter related genes expression, which would lead to the increased accumulation of As (III) and As (V) in plants. In addition, co-exposure with GO resulted in more severe oxidative stress than single As exposure, which could subsequently induce damage in root plasma membranes and compromise key arsenic detoxification pathways such as complexation with glutathione and efflux. Co-exposure to GO and As also led to more significant reduction in macro- and micronutrient content. The provided data highlight the high-impact of nanomaterials on the environmental risk of As in agricultural systems.

Impact of Water Regimes and Amendments on Inorganic Arsenic Exposure to Rice

Rice-based diet faces an important public health concern due to arsenic (As) accumulation in rice grain, which is toxic to humans. Rice crops are prone to assimilate As due to continuously flooded cultivation. In this study, the objective was to determine how water regimes (flooded and aerobic) in rice cultivation impact total As and inorganic As speciation in rice on the basis of a field-scale trial in the post-monsoon season. Iron and silicon with NPK/organic manure were amended in each regime. We hypothesised that aerobic practice receiving amendments would reduce As uptake in rice grain with a subsequent decrease in accumulation of inorganic As species relative to flooded conditions (control). Continuously flooded conditions enhanced soil As availability by 32% compared to aerobic conditions. Under aerobic conditions, total As concentrations in rice decreased by 62% compared to flooded conditions. Speciation analyses revealed that aerobic conditions significantly reduced (p < 0.05) arsenite (68%) and arsenate (61%) accumulation in rice grains. Iron and silicon exhibited significant impact on reducing arsenate and arsenite uptake in rice, respectively. The study indicates that aerobic rice cultivation with minimum use of irrigation water can lead to lower risk of inorganic As exposure to rice relative to flooded practice.

Warming facilitates microbial reduction and release of arsenic in flooded paddy soil and arsenic accumulation in rice grains

Global warming severely hinders both rice (Oryza sativa L.) quality and yield by increasing arsenic (As) bioavailability in paddy soils. However, details regarding As biotransformation and migration in the rice-soil system at elevated temperatures remain unclear. This study investigated the effects of increasing temperature on As behavior and translocation in rice grown in As-contaminated paddy soil at two temperature treatments (33 °C warmer temperature and 28 °C as control). The results showed that increasing temperature from 28 °C to 33 °C significantly favored total As, arsenite (As(III)) and arsenate (As(Ⅴ)) release into the soil pore-water. This increase in As bioavailability resulted in significantly higher As(III) accumulation in the whole grains at warmer treatment relative to the control. Moreover, the results suggest that increasing temperature to 33 °C promoted As(III) migration from the roots to the whole grains. Furthermore, the As(V)-reducing Xanthomonadales order and Alcaligenaceae family, and As(V) reductase-encoding arsC gene were enriched in the rhizosphere soils incubated at 33 °C. This suggests that the increase in As bioavailability in that treatment was due to enhanced As(V) reductive dissolution into the soil pore-water. Overall, this study provides new insights on how warmer future temperatures will exacerbate As accumulation in rice grains.

Inorganic arsenic toxicity and alleviation strategies in rice

Direct or indirect exposure to inorganic arsenic (iAs) in the forms of AsIII (arsenite) and AsV (arsenate) through consumption of As-contaminated food materials and drinking water leads to arsenic poisoning. Rice (Oryza sativa L.) plant potentially accumulates a high amount of iAs from paddy fields than any other cereal crops. This makes it to be a major source of iAs especially among the population that uses it as their dominant source of diet. The accumulation of As in human bodies poses a serious global health risk to the human population. Various conventional methods have been applied to reduce the arsenic accumulation in rice plant. However, the success rate of these techniques is low. Therefore, the development of efficient and effective methods aimed at lowering iAs toxicity is a very crucial public concern. With the current advancement in technology, new strategies aimed at addressing this concern are being developed and utilized in various parts of the world. In this review, we discuss the recent advances in the management of iAs in rice plants emphasizing the use of nanotechnology and biotechnology approaches. Also, the prospects and challenges facing these approaches are described.

Root microbiome assembly of As-hyperaccumulator Pteris vittata and its efficacy in arsenic requisition

The assemblage of root-associated microorganisms plays important roles in improving their capability to adapt to environmental stress. Metal(loid) hyperaccumulators exhibit disparate adaptive capability compared to that of non-hyperaccumulators when faced with elevated contents of metal(loid)s. However, knowledge of the assemblage of root microbes of hyperaccumulators and their ecological roles in plant growth is still scarce. The present study used Pteris vittata as a model plant to study the microbial assemblage and its beneficial role in plant growth. We demonstrated that the assemblage of microbes from the associated bulk soil to the root compartment was based on their lifestyles. We used metagenomic analysis and identified that the assembled microbes were primarily involved in root-microbe interactions in P. vittata root. Notably, we identified that the assembled root microbiome played an important role in As requisition, which promoted the fitness and growth of P. vittata. This study provides new insights into the root microbiome and potential valuable knowledge to understand how the root microbiome contributes to the fitness of its host.

Long-Term Manure Application Changes Bacterial Communities in Rice Rhizosphere and Arsenic Speciation in Rice Grains

Bioavailability and speciation of arsenic (As) are impacted by fertilization and bacteria in the rice rhizosphere. In this study, we investigated the effects of long-term manure application on As bioavailability, microbial community structure, and functional genes in a rice paddy field. The results showed that manure application did not affect total As in the soil but increased soluble As forms by 19%, increasing arsenite (As(III)) accumulation in rice grains and roots by 34 and 64% compared to a control. A real-time quantitative polymerase chain reaction (qPCR) and high-throughput sequencing analysis demonstrated that manure application increased the relative abundance of Rhizobium, Burkholderia, Sphingobium, and Sphingomonas containing arsenate reductase genes (arsC) in the rhizosphere soil, consistent with the 529% increase in arsC, which may have promoted arsenate (As(V)) reduction and increased As availability in pore water. In addition, manure application significantly altered the iron (Fe)-plaque microbial community structure and diversity. The microbes, particularly, Bradyrhizobium, Burkholderia, and Ralstonia, were mostly associated with As, Fe, and sulfur (S) cycles. This result was consistent with changes in the functional genes related to As, Fe, and S transformation. Although manure application promoted As(V) reduction (arsC) in Fe-plaque by 682%, it inhibited Fe and S reduction by decreasing Fe^III reduction bacteria (Geobacteraceae) and the sulfate-reducing gene (dsrA) abundance. Further, manure application changed the composition of the microbial community that contained the arsC gene. In short, caution needs to be excised even in the soil with a low As concentration as manure application increased As(III) accumulation in rice grains.

Grain Inorganic Arsenic Content in Rice Managed Through Targeted Introgressions and Irrigation Management

Arsenic (As) accumulation in rice grain is a significant public health concern. Inorganic As (iAs) is of particular concern because it has increased toxicity as compared to organic As. Irrigation management practices, such as alternate wetting and drying (AWD), as well as genotypic differences between cultivars, have been shown to influence As accumulation in rice grain. A 2 year field study using a Lemont × TeQing backcross introgression line (TIL) mapping population examined the impact of genotype and AWD severity on iAs grain concentrations. The "Safe"-AWD [35-40% soil volumetric water content (VWC)] treatment did not reduce grain iAs levels, whereas the more severe AWD30 (25-30% VWC) consistently reduced iAs concentrations across all genotypes. The TILs displayed a range of iAs concentrations by genotype, from less than 10 to up to 46 μg kg-1 under AWD30 and from 28 to 104 μg kg-1 under Safe-AWD. TIL grain iAs concentrations for flood treatments across both years ranged from 26 to 127 μg kg-1. Additionally, seven quantitative trait loci (QTLs) were identified in the mapping population associated with grain iAs. A subset of eight TILs and their parents were grown to confirm field-identified grain iAs QTLs in a controlled greenhouse environment. Greenhouse results confirmed the genotypic grain iAs patterns observed in the field; however, iAs concentrations were higher under greenhouse conditions as compared to the field. In the greenhouse, the number of days under AWD was negatively correlated with grain iAs concentrations. Thus, longer drying periods to meet the same soil VWC resulted in lower grain iAs levels. Both the number and combinations of iAs-affecting QTLs significantly impacted grain iAs concentrations. Therefore, identifying more grain iAs-affecting QTLs could be important to inform future breeding efforts for low iAs rice varieties. Our study suggests that coupling AWD practices targeting a soil VWC of less than or equal to 30% coupled with the use of cultivars developed to possess multiple QTLs that negatively regulate grain iAs concentrations will be helpful in mitigating exposure of iAs from rice consumption.

Improved grain yield and lowered arsenic accumulation in rice plants by inoculation with arsenite-oxidizing Achromobacter xylosoxidans GD03

Arsenite is the predominant arsenic species in flooded paddy soil, and arsenite bioaccumulation in rice grains has been identified as a major problem in many Asian countries. Lowering arsenite level in rice plants and grain via accelerating arsenite oxidation is a potential strategy to help populations, who depended on rice consumption, to reduce the internal exposure level of arsenic. We herein isolated a strain, Achromobacter xylosoxidans GD03, with the high arsenite-oxidizing ability and plant growth-promoting traits. We observed that arsenite exposure could promote A. xylosoxidans GD03 to excrete indole-3-acetic acid and thus promoted rice growth. The pot culture experiments of Indica rice cultivar Guang You Ming 118 (GYM118) demonstrated that A. xylosoxidans GD03 inoculation of paddy soil (4.5-180 × 10⁸ CFU GD03/kg soil) significantly accelerated arsenite oxidation in flooded soil. The daily arsenic oxidation rate with GD03 inoculation was 1.5-3.3 times as that without strain GD03 inoculation within the whole growth period of Indica GYM118 in the presence of the native microflora. It thus led to a 34-69%, 43-74%, 24-76% and 35-57% decrease in arsenite concentration of the stems, leaves, bran and grain of Indica GYM118 respectively and a 59-96% increase in rice grain yield. The paddy soil inoculated with 40.0 mL/kg of A. xylosoxidans GD03 resulted in a lowest As(III) concentrations in all rice organs of Indica GYM118, which equivalent to only 24-50% of the As(III) concentrations in the group without GD03 inoculation. The results highlight that a highly arsenite-oxidizing bacterium could accelerate arsenite oxidation of paddy soil when facing competition with the native microflora, thus decrease arsenic toxicity and bioavailable soil arsenic.

Water management affects arsenic uptake and translocation by regulating arsenic bioavailability, transporter expression and thiol metabolism in rice (Oryza sativa L.)

Water management is an economic and effective strategy to reduce arsenic (As) accumulation in rice grains, but little is known about the effect of water management on the migration and transformation of As in the soil-rice system. In this study, the effect of the continually (CF) and intermittent flooding (IF) treatments on the dynamic change of As in the rhizosphere soil-pore water-iron plaque-rice system was systematically investigated using pot experiments. The expressions of genes involved in As uptake and translocation in rice plants under different water management treatments were further examined. Results showed that the total As concentration in brown rice was increased by 50.8% in the CF treatment compared to the IF treatment, and dimethylarsinic acid (DMA) made greater contribution (from 15.5% to 29.2%) to total As increase in brown rice under the CF treatment. The CF treatment increased As bioavailability in the rhizosphere soil and soil pore water, which enhanced As uptake and transport to the xylem in rice plants by inducing the expressions of silicon transporter genes (OsLsi1 and OsLsi2) compared to the IF treatment. Moreover, the CF treatment increased As translocation from roots to shoots by reducing soil available sulfur and phytochelatins (PCs) biosynthesis and vacuolar sequestration in rice roots compared with the IF treatment. The study provides insight into the physiological and molecular mechanisms underlying As uptake and translocation in rice plants under different water regimes, which will be helpful for adopting the irrigation technique to mitigate excessive As accumulation in rice grains and associated health risk to humans.

Epiphytic bacterial community enhances arsenic uptake and reduction by Myriophyllum verticillatum

Microbes play an important role in the biotransformation of arsenic (As) speciation in various environments. Nevertheless, whether epiphytic bacteria that attached on submerged macrophytes have the potential to influence As speciation still remains unclear. In this study, sterile or nonsterile Myriophyllum verticillatum was cultured with arsenite (As(III)) or arsenate (As(V)) to investigate the impact of epiphytic bacterial community on As uptake, transformation, and efflux. Results showed that both sterile and nonsterile M. verticillatum did not display substantial As(III) oxidation, suggesting that neither M. verticillatum nor epiphytic bacterial community has the capacities of As(III) oxidation. However, sterile M. verticillatum exhibited capacity for As(V) reduction, and the presence of epiphytic bacterial community substantially enhanced the proportions of As(III) in the medium (from 39.91 to 98.44%), indicating that epiphytic bacterial community contributes significantly to As(V) reduction in the medium. The presence of epiphytic bacterial community elevated As accumulation (by up to 2.06-fold) in plants when exposed to As(V). Results also showed that epiphytic bacterial community contributed little to As(III) efflux. Quantitative PCR of As metabolism genes revealed the dominance of the respiratory As(V) reductase genes (arrA) in epiphytic bacterial community, which might play a significant role in As(V) reduction in aquatic environments. Phylogenetic analysis of the arrA genes revealed the widely distribution and diversity of As(V)-respiring bacteria. These results highlighted the substantial impact of the epiphytic bacterial community associated with submerged aquatic macrophytes on As biogeochemistry in wetland and water environments.

Microbe mediated immobilization of arsenic in the rice rhizosphere after incorporation of silica impregnated biochar composites

This study mechanistically addressed for the first time, the contradiction between the application of many biochars to paddy soil and increased arsenic (As) release as employed by most of previous studies. Three types of biochar containing natural and chemical forms of Si: (i) unmodified rice husk biochar (RHBC), (ii) RHBC modified with Si fertilizer (Si-RHBC), and (iii) RHBC modified with nanoparticles of montmorillonite clay (NM-RHBC) were applied in As-contaminated paddy soil to examine their potential to control the mobility of As in the soil-microbe-rice system. Both Si-RHBC and NM-RHBC decreased As concentration in porewater by 40-65 %, while RHBC decreased by 30-44 % compared to biochar unamended soil from tillering to maturing stage. At tillering stage, RHBC, Si-RHBC and NM-RHBC amendments significantly decreased As(III) concentration in the rice rhizosphere by 57, 76 and 73 %, respectively compared to the control soil. The immobilization of As is due to: (i) lowering of microbe mediated As release from iron minerals, (ii) oxidation of As(III) to As(V) by aioA gene, and (iii) adsorption on a Si-ferrihydrite complex. The decrease of more toxic As(III) and its oxidation to less mobile As(V) by Si-rich biochar amendments is a promising As detoxification phenomenon in the rice rhizosphere.

Minerals loaded with oxygen nanobubbles mitigate arsenic translocation from paddy soils to rice

Inhibiting reductive transformation of arsenic (As) in flooded paddy soils is fundamentally important for mitigating As transfer into the food chain. In this study, oxygen-nanobubble-loaded-zeolites (ZON) and -vermiculites (VON) were tested as a novel approach for supplying oxygen to paddy soils to inhibit As influx into rice. The dynamic physio- and bio-chemical variations in the rhizosphere and bulk soil were profiled in a rhizobox experiment. Upon adding ZON and VON, the redox potential and dissolved oxygen consistently increased throughout the cultivation period. The improved redox environment inhibited As(III) release into porewater and increased As(V) adsorbed on crystalline Fe (hydr)oxides, following the reduction of arsC and arrA gene abundances and enhancement of the aioA gene. Moreover, adding ZON and VON promoted root iron plaque formation, which increased As retention on iron plaque. Both ZON and VON treatments mitigated As translocation from soil to rice, meanwhile increasing root and shoot biomass. ZON was superior to VON in repressing As transfer and promoting rice growth due to its higher oxygen loading capacity. This study provides a novel and environment-friendly material to both mitigate the As translocation from paddy soil to rice and improve rice growth.

Phosphorus regulates As uptake by rice via releasing As into soil porewater and sequestrating it on Fe plaque

Phosphorus (P) application rate can affect the As uptake by rice, but its mechanism lacks systematic studies. In this study, P fertilizers with different dosages (0, 75, 150, and 300 mg P₂O₅ kg^-1 soil) were used to investigate the effects of P on As release in soil porewater, As sequestration on Fe plaque and the change of abundance and communities of aioA and arsC genes in rhizosphere, and then explore its effect on As uptake by rice. Our results indicated that As content in brown rice under P0 and P75 treatments was 14.3-28.6% lower than that under P150 treatment. The total accumulation of As in brown rice under P0 treatment (1.51 μg plant^-1) was significantly lower than that under P150 treatment (2.17 μg plant^-1). Compared to P150 treatment, P0 treatment decreased the total As content in porewater but increased the proportion of As(V) to total As in porewater. The activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) in rice roots and the Fe and As contents in Fe plaque were significantly higher under P0 treatment than under P150 treatment. Most of As (80.3-82.9%) sequestered by Fe plaque was in the form of arsenate (As(V)), and the associated As(V) on Fe plaque was 11.0% higher under P0 treatment than under P150 treatment. In addition, the abundance of aioA gene was 73.5% higher under P0 treatment than under P150 treatment, and the dominant aioA at genus level was Rhizobium and Rhodoferax. In general, P0 treatment led to higher root oxidation activity, which improved the formation of Fe plaque; and P0 treatment also improved the abundance of aioA gene in rhizosphere, thus increased the oxidation of As; so, P0 treatment indirectly enhanced As sequestration on Fe plaque, and that in turn reduced As accumulation in brown rice.

Microbial adaptation in vertical soil profiles contaminated by an antimony smelting plant

Antimony mining has resulted in considerable pollution to the soil environment. Although studies on antinomy contamination have been conducted, its effects on vertical soil profiles and depth-resolved microbial communities remain unknown. The current study selected three vertical soil profiles (0–2 m) from the world's largest antimony mining area to characterize the depth-resolved soil microbiota and investigate the effects of mining contamination on microbial adaptation. Results demonstrated that contaminated soil profiles showed distinct depth-resolved effects when compared to uncontaminated soil profiles. As soil depth increased, the concentrations of antimony and arsenic gradually declined in the contaminated soil profiles. Acidobacteria, Chloroflexi, Proteobacteria and Thaumarchaeota were the most variable phyla from surface to deep soil. The co-occurrence networks were loosely connected in surface soil, but obviously recovered and were well-connected in deep soil. The metagenomic results indicated that microbial metabolic potential also changed with soil depth. Genes encoding C metabolism pathways were negatively correlated with antimony and arsenic concentrations. Abundances of arsenic-related genes were enriched by severe contamination, but reduced with soil depth. Overall, soil depth-resolved characteristics are often many meters deep and such effects affected the indigenous microbial communities, as well as their metabolic potential due to different contaminants along vertical depths.

Increased arsenic mobilization in the rice rhizosphere is mediated by iron-reducing bacteria

Rice (Oryza sativa) tends to accumulate elevated levels of arsenic (As) in grain, threatening food safety and human health. The rice rhizosphere has a micro-environment that differs markedly from the bulk soil. Yet, little is known about how this micro-environment influences the mobility of As in the rhizosphere. Using rhizoboxes with two rice cultivars (cv. Shenyou 957 and Yangdao 6) differing in their radial oxygen loss (ROL), we investigated the in situ transformation of As in the rhizosphere associated with changes in microbial communities and As-related functional genes. Contrary to expectation, dissolved (porewater) As concentrations within the rhizosphere increased by 1.3-2.4 fold compared to the bulk soil during the seedling stage, with the magnitude of this difference gradually decreasing over time. The increased As mobilization in the rhizosphere was associated with increased soluble Fe. This increasing trend was associated with the increased abundance of both Fe-reducing bacteria (FeRB) and As-related functional genes within the rhizosphere. Furthermore, bacterial 16S rRNA gene sequencing data showed that the abundances of Geobacter and Clostridium were 3.1 times and 12.4 times higher in the rhizosphere, respectively. The importance of FeRB was also suggested by the fact that dissolved As concentrations were highly correlated with dissolved Fe concentrations (r² = 0.83) and also with the relative abundance of genus Clostridium_sensu_stricto_10 (r² = 0.85). This study highlights that although the rice rhizosphere favors a more aerobic condition compared to the bulk soil, As is more mobilized in the rhizosphere, and that Geobacter and some species of Clostridium play a critical role in controlling As mobilization in the rhizosphere.

Using rice as a remediating plant to deplete bioavailable arsenic from paddy soils

Rice plant is efficient in arsenic (As) accumulation due to enhanced soil As release under flooded condition and its effective As uptake. Therefore, rice plant can be used to remove bioavailable As from paddy soil. In this study, the depleting dynamics of soil As with rice growth was mapped two-dimensionally with the zirconium-oxide diffusive gradients in thin films (DGT) technique. Further, the key biochemistry promoting soil As bioavailability was studied to better understand the underlying processes. Results revealed that the average DGT-As encompassing the root zone decreased steeply from 331 in the seedling stage to 136 in the heading & flowering stage and further to 118 μg l^-1 at harvest, which was 26% lower than that of the control at 160 μg l^-1. During this process, rhizosphere porewater As developed a dynamic profile similar to Fe and dissolved organic carbon, with the diversity of arrA gene peaking at heading & flowering stage. The data support soil As release from microbial reduction of Fe hydroxides fueled by root exudation as carbon source. Arsenic was mainly accumulated in the roots, accounting for up to 95% of total As in rice plants. Removal of rice roots resulted in ~19% lower DGT-As in post-harvest soil compared to without removing the roots. As a result, a sharp decline in As accumulation in rice plants was obtained in the second planting after removing one crop of rice roots. The results highlight that rice, as a paddy-adapted plant, is effective in As uptake in the roots, and thereby removing rice roots efficiently depletes bioavailable As from paddy soils.

Arsenic phytovolatilization and epigenetic modifications in Arundo donax L. assisted by a PGPR consortium

Arsenic-(As) pollution is an increasing threat across the globe and it is reaching harmful values in several areas of the world. In this perspective, we assayed bio-phyto-remediation technology using Arundo donax L., assisted by Plant Growth Promoting Bacteria (PGPB) consortium (BC) constituted of two strains of Stenotrophomonas maltophilia sp. and one of Agrobacterium sp.; furthermore, we assayed the epigenetic response to As pollution. The three bacterial strains initially evaluated for their As tolerance, revealed different resistance to both forms of As[As(III) and As(V)] however at concentration greater than those foreseen in the phytoremediation experiment (2.0, 10.0, 20.0 mgL^-1 of NaAsO₂). At the end of the trial plant biomass and As concentration were measured. Plants did not show any visible signs of toxicity, rather the leaf and stem biomass slightly increased in the presence of As and/or PGPBs; moreover, although the Bioaccumulation Factor was double in the presence of BC, the absolute values of As accumulation in the Arundo plants were very low, both in the presence or absence of BC and only detectable in the presence of the highest As dose (20 mgL^-1 As). In this case, regardless the presence of PGPB, ≈25% of As remained in the sand and ≈0.15% was accumulated in the plant, whilst the remaining 75% was volatilized by transpiration. Finally, the methylation sensitive amplified polymorphisms (MSAP) of leaves were analyzed in order to investigate their epigenetic response to As and/or BC. Our results suggest that epigenetic modifications are involved in stress response and As detoxification.

Influence of epiphytic bacteria on arsenic metabolism in Hydrilla verticillata

Microbial assemblages such as biofilms around aquatic plants play a major role in arsenic (As) cycling, which has often been overlooked in previous studies. In this study, arsenite (As(III))-oxidizing, arsenate (As(V))-reducing and As(III)-methylating bacteria were found to coexist in the phyllosphere of Hydrilla verticillata, and their relative activities were shown to determine As speciation, accumulation and efflux. When exposed to As(III), As(III) oxidation was not observed in treatment H(III)-B, whereas treatment H(III)+B showed a significant As(III) oxidation ability, thereby indicating that epiphytic bacteria displayed a substantial As(III) oxidation ability. When exposed to As(V), the medium only contained 5.89% As(III) after 48 h of treatment H(V)-B, while an As(III) content of 86.72% was observed after treatment H(V)+B, thereby indicating that the elevated As(III) in the medium probably originated from As(V) reduction by epiphytic bacteria. Our data also indicated that oxidizing bacteria decreased the As accumulation (by approximately 64.44% compared with that of treatment H(III)-B) in plants, while reducing bacteria played a critical role in increasing As accumulation (by approximately 3.31-fold compared with that of treatment H(V)-B) in plants. Regardless of whether As(III) or As(V) was supplied, As(III) was dominant in the plant tissue (over 75%). Furthermore, the presence of epiphytic bacteria enhanced As efflux by approximately 9-fold. Metagenomic analysis revealed highly diverse As metabolism genes in epiphytic bacterial community, particularly those related to energetic metabolism (aioAB), and As resistance (arsABCR, acr3, arsM). Phylogenetic analysis of As metabolism genes revealed evidence of both vertical inheritance and horizontal gene transfer, which might have contributed to the evolution of the As metabolism genes. Taken together, our research suggested that the diversity of As metabolism genes in epiphytic bacterial community is associated with aquatic submerged macrophytes which may play an important role in As biogeochemistry in aquatic environments.

The effects of biochar as the electron shuttle on the ferrihydrite reduction and related arsenic (As) fate

The effects of electron shuttles (biochar/anthraquinone-2,6-disulphonate (AQDS)) on the process of the Shewanella oneidensis MR-1-induced As(V)-adsorbed ferrihydrite reduction were studied. The results showed that biochar could stimulate Fe(Ⅱ) and As release during the ferrihydrite bioreduction. After the addition of biochar, more dissolved organic matter (DOM) can be consumed as an electron donor to promote the metabolism of microorganisms by the fluorescence excitation-emission matrix spectra analysis. After microbial treatment, cyclic voltammetry (CV) showed that a unique cathodic peak and a distinct anodic peak appeared, which may represent the reduction of Fe(OH)3 to Fe(OH)2 and the complexed oxidation of Fe2+ to Fe3+. No characteristic peak was associated with arsenate reduction or arsenite oxidation. The mineralogical characterization of the final products indicated that AQDS can promote solid-state conversion from ferrihydrite to vivianite (Fe3(PO4)2·8H2O). However, the addition of biochar inhibited solid-state conversion of ferrihydrite. It was shown that after 6 d, the secondary mineral vivianite production in the bacteria alone and AQDS treatments was 8.12% and 15.6% respectively by mössbauer spectroscopy analysis. Moreover, the XPS indicated that As(V) has no species transformation. It provided new data for understanding the iron-reducing bacteria induced mineralization process and related biogeochemical cycles of Fe and As.

Arsenic and cadmium as predominant factors shaping the distribution patterns of antibiotic resistance genes in polluted paddy soils

Heavy metals have been recognized as potential factors driving the evolution and development of antibiotic resistance. However, the relative effects of cadmium (Cd) and arsenic (As) on the prevalence and distribution of antibiotic resistance genes (ARGs) remain unclear. We investigated the co-selection effects of Cd and As on ARGs in 45 paddy soils polluted by heavy metals, using high-throughput quantitative PCR. A total of 119 ARGs and 9 mobile genetic elements (MGEs) were detected in all samples. Regression analysis showed that the single pollution index (PI_As and PI_Cd) and Nemerow integrated pollution index (NIPI) both had significant and positive correlations with ARGs (P <  0.05), indicating the co-selective effects of Cd and As on ARGs distribution. The significant correlations between bacterial taxa and different ARGs in network analysis revealed potential hosts of ARGs. Structural equation models indicated that the effects of As on ARGs were stronger than that of Cd. The profile of ARGs could be impacted by Cd and As indirectly by strongly affecting the bacterial abundance. Overall, this study extended our knowledge about the co-selection of Cd and As on ARGs in paddy soil, and had important implications for assessing the potential risks of ARGs in paddy soils.

Microbial driven iron reduction affects arsenic transformation and transportation in soil-rice system

The microbe-driven iron cycle plays an important role in speciation transformation and migration of arsenic (As) in soil-rice systems. In this study, pot experiments were used to investigate the effect of bacterial iron (Fe) reduction processes in soils on As speciation and migration, as well as on As uptake in soil-rice system. During the rice growth period, pH and electrical conductivity (EC) in soil solutions initially increased and then decreased, with the ranges of 7.4-8.8 and 116.3-820 mS cm-1, respectively. The concentrations of Fe, total As and As(III) showed an increasing trend in the rhizosphere and non-rhizosphere soil solutions with the increasing time. Fe concentrations were significantly positively correlated with total As and As(III) concentrations (***p < 0.001) in the soil solutions. The abundances of the arsenate reductase gene (arsC) and the As(III) S-adenosylmethionine methyltransferase gene (arsM) in rhizosphere soils were higher than those in non-rhizosphere soils, while the abundance of the Fe-reducing bacteria (Geo) showed an opposite trend. Moreover, it showed that the Geo abundance was significantly positively correlated with that of the arsC (***p < 0.001) and arsM (**p < 0.01) genes, respectively. The abundances of Geo, arsC and arsM genes were significantly positively correlated with the concentrations of Fe, total As and As(III) in the soil solutions (*p < 0.05). Moreover, the abundances of arsC and arsM genes were significantly negatively correlated with total As and As(III) in rice grains (*P < 0.05). These results showed that the interaction of bacterial Fe reduction process and radial oxygen loss from roots promoted the reduction and methylation of As, and then decreased As uptake by rice, which provided a theoretical basis for alleviating As pollution in paddy soils.

Metagenomic insights into microbial arsenic metabolism in shallow groundwater of Datong basin, China

Elevated arsenic (As) in groundwater is an urgent environmental problem that has caused serious endemic diseases in Datong basin, China. The fate and toxicity of As are generally regulated by microbial As metabolic processes. However, little is known about the microbial community and As metabolism in Datong basin. Herein, the microbial community structure and As metabolism genes in four wells with different levels of As concentration in Shanyin county were investigated using metagenomics approach. The results showed that the presence of As influenced the microbial communities, and Rhodococcus genus was significantly enriched in elevated As wells. As resistance genes were dominant from low to high As containing wells, and As efflux genes such as arsB and acr3 were positively correlated with As concentrations, suggesting that microbes tend to pump As out of the cell as a strategy for As detoxification. Other environmental factors including oxidation-reduction potential (ORP), total organic carbon (TOC), sulfate, and temperature also played a role in shaping the microbial community structure and As metabolic processes.

Arsenic volatilization in roxarsone-loaded digester: Insight into the main factors and arsM genes

The extensive use of roxarsone (ROX) in livestock and poultry husbandry causes the production of arylarsenic-contaminated manure/wastewater. Anaerobic digestion is a conventional technique for livestock manure/wastewater treatment. However, the factors affecting arsenic volatilization are poorly understood in arylarsenic-loaded anaerobic reactors. The main factors such as ROX loading, exposure time of anaerobic granular sludge (AGS) to ROX, and volatile fatty acid (VFA) levels, affecting arsenic volatilization were investigated in this study. The results indicated that ROX loading of 5.70 mg-As·L^-1 triggered the maximum volatile arsenic yield of 6.78 ng-As·g^-1-VSS·d^-1, which was 4.95 times higher compared to the ROX-free assay. The conversion of ROX into inorganic arsenic was an essential step for arsenic volatilization. The 160-day and 270-day exposure of AGS to ROX caused 6-fold and 8-fold increase in volatile arsenic yield, respectively, compared to the 0-day exposure. With the longer-time exposure to ROX, AGS provided more available arsenic for volatilization and its arsenic-volatilizing capacity was significantly enhanced. VFA level was positively associated with arsenic volatilization (r = 0.832-0.950; p < 0.05). The abundance of arsM genes in AGS increased by 34.62-129.05% after the 100-day incubation, and was strongly correlated to arsenic volatilization. Based on these results, possible pathway of arsenic volatilization in ROX-loaded digesters were proposed. The result from this study improves a better understanding of the potential of arsenic volatilization in arylarsenic-contaminated environments.

Localized Intensification of Arsenic Release within the Emergent Rice Rhizosphere

Behavior of trace elements in flooded/lowland rice soils is controlled by root-zone iron oxidation. Insoluble iron species bind/capture toxic elements, i.e., arsenic. However, it was recently observed that within this territory of arsenic immobilization lies a zone of prolific iron release, accompanied by a significant flux of arsenic in close proximity to rice root apices. Questions still remain on how common this phenomenon is and whether the chemical imaging approaches or soils/cultivars used influence this event. Here, three types of ultrathin/high-resolution diffusive gradient in thin films (DGT) substrates were integrated with oxygen planar optodes in a multilayer system, providing two-dimensional mapping of solute fluxes. The three DGT approaches revealed a consistent/overlapping spatial distribution with localized flux maxima for arsenic, which occurred in all experiments, concomitant with iron mobilization. Soil/porewater microsampling within the rhizosphere revealed no significant elevation in the solid phase's total iron and arsenic concentrations between aerobic and anaerobic zones. Contrary to arsenic, phosphorus bioavailability was shown to decrease in the arsenic/iron flux maxima. Rice roots, in addition to their role in nutrient acquisition, also perform a key sensory function. Flux maxima represent a significant departure from the chemical conditions of the bulk/field environment, but our observations of a complete rhizosphere reveal a mixed mode of root-soil interactions.

Comparative effects on arsenic uptake between iron (hydro)oxides on root surface and rhizosphere of rice in an alkaline paddy soil

The iron (Fe) (hydro)oxides deposited around rice roots play an important role in arsenic (As) sequestration in paddy soils, but there is no systematic study on the relative importance of Fe (hydro)oxides on root surface and in rhizosphere soil in limiting As bioavailability. Twenty-seven rice genotypes were selected to investigate effects of Fe (hydro)oxides on As uptake by rice in an alkaline paddy soil. Results indicated that the As content was positively correlated with the Fe content on root surface, and most of As (88-97%) was sequestered by poorly crystalline and crystalline Fe (hydro)oxides in the alkaline paddy soil. The As sequestration by Fe (hydro)oxides on root surface (IAS_root 16.8-25.0 mg As/(g Fe)) was much higher than that in rhizosphere (IAS_rhizo 1.4-2.0 mg As/(g Fe)); therefore, in terms of As immobilization, the Fe (hydro)oxides on root surface were more important than that in rhizosphere. However, the As content in brown rice did not have significant correlation with the As content on root surface but was significantly correlated (R² = 0.43, P < 0.05) with the partition ratio (PR_As = IAS_root/IAS_rhizo) of As sequestration on root surface and in rhizosphere, which suggested that Fe (hydro)oxides on root surface did not play the controlling role in lowering As uptake, and the partition ratio PR_As would be a better indicator to evaluate effects of Fe (hydro)oxides around roots on As uptake by rice.

Root-induced changes in aggregation characteristics and potentially toxic elements (PTEs) speciation in a revegetated artificial zinc smelting waste slag site

Root-induced changes play a crucial role in influencing the fate and speciation of potentially toxic elements (PTEs) in contaminated soils, but their role in the phytostabilization of waste slag sites remain unclear. The aim of this study was to determine the effect of four phytostabilization plants, Broussonetia papyrifera, Arundo donax, Robinia pseudoacacia, and Cryptomeria fortunei, planted in a zinc smelting waste slag site for 5 years on PTEs speciation and the mineral and aggregation characteristics at the interface of the waste slag-plant system. The results showed that the presence of a higher content of oxalic acid in the rhizosphere slags of the four plant species than in the bare slag. Revegetation of the waste slag with the four plant species significantly changed the mineral composition and morphology of the waste slag. The mass percentage of large particles (1-5 mm) and small particles (0.5-1 mm, 0.25-0.5 mm, and <0.25 mm) in the rhizosphere slags decreased and increased, respectively. The PTEs (Cu, Pb, Zn, and Cd) in most of the rhizosphere slags were mainly distributed within the small particles, and the enrichment coefficients of PTEs in the large particles and small particles were less than and greater than 1, respectively. The bioavailability of the PTEs in the waste slag increased with decreasing particle size. Root-induced the transformation of acid-soluble PTEs into their reducible, oxidizable, and residual forms in the different waste slag particles weathered in the rhizosphere. These results suggested that there are root-induced changes in the aggregation characteristics and geochemical behaviours of PTEs in waste slag fractions during the phytoremediation of waste slag sites.

Safer food through plant science: reducing toxic element accumulation in crops

Natural processes and human activities have caused widespread background contamination with non-essential toxic elements. The uptake and accumulation of cadmium (Cd), arsenic (As), and lead (Pb) by crop plants results in chronic dietary exposure and is associated with various health risks. Current human intake levels are close to what is provisionally regarded as safe. This has recently triggered legislative actions to introduce or lower limits for toxic elements in food. Arguably, the most effective way to reduce the risk of slow poisoning is the breeding of crops with much lower accumulation of contaminants. The past years have seen tremendous progress in elucidating molecular mechanisms of toxic element transport. This was achieved in the model systems Arabidopsis thaliana and, most importantly, rice, the major source of exposure to As and Cd for a large fraction of the global population. Many components of entry and sequestration pathways have been identified. This knowledge can now be applied to engineer crops with reduced toxic element accumulation especially in edible organs. Most obvious in the case of Cd, it appears likely that subtle genetic intervention has the potential to reduce human exposure to non-essential toxic elements almost immediately. This review outlines the risks and discusses our current state of knowledge with emphasis on transgenic and gene editing approaches.

Variation in rhizosphere microbiota correlates with edaphic factor in an abandoned antimony tailing dump

The distribution pattern of root-associated bacteria in native plant growth in tailing dumps with extreme conditions remains poorly understood and largely unexplored. Herein we chose a native plant, Bidens bipinnata, growing on both an Sb tailing dump (WKA) and adjacent normal soils (WKC) to in-depth understand the distribution pattern of root-associated bacteria and their responses on environmental factors. We found that the rhizosphere microbial diversity indices in the tailing dump were significantly different from that in the adjacent soil, and that such variation was significantly related with soil nutrients (TC, TOC, TN) and metal(loid) concentrations (Sb and As). Some dominant genera were significant enriched in WKA, suggesting their adaption to harsh environments. Notably, these genera are proposed to be involved in nutrient and metal(liod) cycling, such as nitrogen fixing (Devosia, Cellvibrio, Lysobacter, and Cohnella), P solubilizing (Flavobacterium), and Sb and As oxidation (Paenibacillus, Bacillus, Pseudomonas, and Thiobacillus). Our results suggest that certain root-associated bacteria in tailing dump were governed by soil edaphic factors and play important ecological roles in nutrient amendments and metal cycling for the successful colonization of Bidens bipinnata in this tailing dump.

Expressing Arsenite Antiporter PvACR3;1 in Rice (Oryza sativa L.) Decreases Inorganic Arsenic Content in Rice Grains

Rice (Oryza sativa) is a major food crop in the world, feeding half of the world's population. However, rice is efficient in taking up toxic metalloid arsenic (As), adversely impacting human health. Among different As species, inorganic As is more toxic than organic As. Thus, it is important to decrease inorganic As in rice to reduce human exposure from the food chain. The arsenite (AsIII) antiporter gene PvACR3;1 from As-hyperaccumulator Pteris vittata decreases shoot As accumulation when heterologously expressed in plants. In this study, three homozygous transgenic lines (L2, L4, and L7) of T3 generation were obtained after transforming PvACR3;1 into rice. At 5 μM of AsIII, PvACR3;1 transgenic rice accumulated 127%-205% higher As in the roots, with lower As translocation than wild type (WT) plants. In addition, at 20 μM of AsV, the transgenic rice showed similar results, indicating that expressing PvACR3;1 increased As retention in the roots from both AsIII and AsV. Furthermore, PvACR3;1 transgenic rice plants were grown in As-contaminated soils under flooded conditions. PvACR3;1 decreased As accumulations in transgenic rice shoots by 72%-83% without impacting nutrient minerals (Mn, Zn, and Cu). In addition, not only total As in unhusked rice grain of PvACR3;1 transgenic lines were decreased by 28%-39%, but also inorganic As was 26%-46% lower. Taken together, the results showed that expressing PvACR3;1 effectively decreased both total As and inorganic As in rice grain, which is of significance to breed low-As rice for food safety and human health.

Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?

Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we found transfer-persistent arsenite oxidation activity under four conditions (aerobic/anaerobic; heterotrophic/autotrophic). This suggests that biological decontamination may help ameliorate the problem. The enriched microbial communities were phylogenetically at least as diverse as the unenriched communities: they contained a bonanza of 16S rRNA gene sequences. These related to Hydrogenophaga, Acinetobacter, Dechloromonas, Comamonas, and Rhizobium/Agrobacterium species. In addition, the enriched microbiomes contained genes highly similar to the arsenite oxidase (aioA) gene of chemolithoautotrophic (e.g., Paracoccus sp. SY) and heterotrophic arsenite-oxidizing strains. The enriched cultures also contained aioA phylotypes not detected in the previous survey of uncultivated samples from the same wells. Anaerobic enrichments disclosed a wider diversity of arsenite oxidizing aioA phylotypes than did aerobic enrichments. The cultivatable chemolithoautotrophic and heterotrophic arsenite oxidizers are of great interest for future in or ex-situ arsenic bioremediation technologies for the detoxification of drinking water by oxidizing arsenite to arsenate that should then precipitates with iron oxides. The microbial activities required for such a technology seem present, amplifiable, diverse and hence robust.

Microbial sulfate reduction decreases arsenic mobilization in flooded paddy soils with high potential for microbial Fe reduction

Arsenic (As) tends to mobilize in flooded paddy soil due to the reductive dissolution of the iron (oxyhydr)oxides to which As sorbs, resulting in elevated As accumulation in rice that poses a potential risk to the food safety and human health. Microbial sulfate reduction is an important biogeochemical process in paddy soils, but its impact on As mobilization remains poorly understood. In this study, we incubated eight As-contaminated paddy soils under flooded conditions to investigate the effect of sulfate addition on As mobility. Porewater Fe and As concentrations and As species were determined. Among the eight soils, an addition of 50 mg S kg^-1 as sodium sulfate decreased porewater arsenite only in two soils, which also showed a high mobilization of Fe²⁺. Further experiments showed that the addition of sulfate to these two soils stimulated microbial sulfate reduction but decreased porewater concentrations of both arsenite and Fe²⁺. Additionally, the supply of sulfate increased the fractions of As associated with acid volatile sulfides in the solid phase and decreased As uptake by rice in pot experiments under similar conditions. The effect of sulfate addition on porewater As was diminished by the addition of molybdate, an inhibitor of sulfate reducing bacteria. These results suggest the formation of secondary FeS minerals which co-precipitate or sorb arsenite as a likely mechanism of As immobilization, which was also supported by thermodynamic modeling of the pore water. Thus, sulfate additions can immobilize As and reduce its availability to rice plants in paddy soils containing a high potential for microbial Fe reduction, providing an efficient way to mitigate the As transfer to the food chain.

Inhibition of Microbial Methylation via arsM in the Rhizosphere: Arsenic Speciation in the Soil to Plant Continuum

The interplay between rice roots and manuring with respect to arsenic speciation, subsequent assimilation into roots, and translocation to shoots in paddy soil was investigated, alongside bacterial diversity characterization. Planting increased soil Eh and decreased soil solution arsenic species: inorganic arsenic, monomethylarsonic acid, trimethylarsenic oxide, and dimethylarsinic acid. Presence of plant roots increased the copy number of Clostridium and Tumebacillus 16S rRNA as well as Streptomyces arsenic methylating gene ( arsM), but decreased Acidobacteria_GP1 16S rRNA and Rhodopseudomonas. palustris BisB5 arsM. Sum of arsenic species decreased under root influence due to the interplay of inorganic arsenic mobilization in bulk soil under anaerobic and immobilization under oxygenated rhizospheric conditions. Manuring increased all soil solution arsenic species (>90%), shoot total arsenic (60%), copy number of Geobacter 16S rRNA, and R. palustris TIE-1 arsM, indicative of a shift towards microbes with iron reduction and oxidation as well as arsenic methylation capabilities.

Cr(VI) reduction by an extracellular polymeric substance (EPS) produced from a strain of Pseudochrobactrum saccharolyticum

A better understanding of the Cr(VI) reduction position and mechanisms by a Cr(VI)-reducing strain is important for the bioremediation of Cr pollution in the environment. In the present study, we were interested in figuring out the role of extracellular polymeric substances (EPS) as the main area for Cr(VI) reduction in the newly reported strain of Pseudochrobactrum saccharolyticum LY10. We investigated the subcellular distribution and reduction capability of each cellular component as the main area of Cr(VI) reduction by scanning electron microscopy and soft X-ray spectromicroscopy. The results suggested that most of Cr was presented in the supernatants as Cr(III) after reduction. In the cells, Cr was mostly distributed in the EPS and cell wall, while the EPS had the maximum Cr(VI) reduction rate (81.5%) as compared with the cell wall (30.1%). Soft X-ray spectromicroscopy analysis indicated that Cr accumulated more in the EPS. Therefore, the results suggested that the EPS were the main area for Cr(VI) reduction in the bacteria of P. saccharolyticum LY10.

Evaluation of uptake, translocation, and accumulation of arsenic species by six different Brazilian rice (Oryza sativa L.) cultivars

Rice is a significant source of arsenic (As) exposure. The accumulation of the plant depends on several factors, including environmental conditions and genetic factors. The differences in As uptake, translocation, and grains filling in different cultivars are a focus on studies to mitigate the grains contamination. This study assessed the pattern of As species accumulation in different Brazilian rice cultivars (Oryza sativa L.). Thus, pot experiments were conducted with 6 different cultivars (white rice: EPAGRI 109, EPAGRI 108, BRS Tiotaka SCS, and SCS 114 Andosan and red rice: Maranhão and Cáqui) cultivated in soils at low (As-) (0.65 mg kg^-1) and high (As+) (12.1 mg kg^-1) As levels. All cultivars in As+ group presented total As (t-As) in grains more elevated than the maximum limit of inorganic arsenic (i-As) recommended by Codex Alimentarius Commission. The As speciation disclose that Maranhão, Caqui, and SCS 114 Andosan cultivars presented the lowest % i-As (27%, 25% and 31%, respectively) at the highest As exposure condition. On the other hand, higher i-As concentration and % i-As (91%) were observed in EPAGRI 108. Moreover, EPAGRI 108 and EPAGRI 109 had the highest transference factor soil-to-grain (TFsoil-grain = 0.22 and 0.20, respectively). Interestingly, for the cultivars EPAGRI 108 and Maranhão, the levels of some essential elements (Co and Mn) in grains were modulated by the levels of As in the soil. This study shows that levels of i-As were modulated by the type of Brazilian rice cultivar, the range of As levels in soil, As phytotoxicity and the transference factor of As from soil to root straw and grains. Moreover, SCS 114 Andosan is the promising cultivar that exhibits low t-As and % i-As in grains and low TF soil-grain.

Arsenic contamination influences microbial community structure and putative arsenic metabolism gene abundance in iron plaque on paddy rice root

Iron (Fe) plaque on rice roots contains a unique microbiota that connects the root and rhizosphere environments. However, the factors controlling the microbial community structure and function in Fe plaque are unknown. We performed Illumina sequencing of 16S rRNA gene amplicons and of total community DNA to compare the microbial community structure and metabolic potential of Fe plaques derived from arsenic (As)- and non-contaminated sites. Geobacter and Hydrogenophaga were identified as the genera that differed significantly in abundance between As-contaminated and control samples (P < 0.05). Significant differences were found between contaminated and control samples in the relative abundances of predicted As functional genes of the microbial community in Fe plaque, in which the relative abundances of the arsC (encoding As(V) reductase) and arsB genes (encoding As(III) efflux membrane protein) in Fe plaque from contaminated sites (YH and TP samples) were significantly higher than those from the control samples (P < 0.05). In addition, the As concentration in Fe plaque contributed significantly to the relative abundance of genes related to As metabolism and correlated most strongly with the abundance of arrB genes (encoding respiratory arsenate reductase, FeS subunit). These results suggest that As contamination influences the community structure and metabolic potential of Fe plaque-associated microorganisms and may help in understanding the environmental behavior of As at the interface of Fe plaque.

Effects of Fe-Mn modified biochar composite treatment on the properties of As-polluted paddy soil

This study aimed to determine the effects of FeMn modified biochar composite (FMBC) treatment on the pH, redox properties, enzyme activities, and bacterial communities of As-polluted paddy soil. The two utilized FMBCs (FMBC₁ and FMBC₂) exhibited markedly different effects on soil pH, and treatment with biochar (BC) or FMBCs increased the soil redox potential and reduced the content of available As, facilitating the conversion of originally present non-specifically sorbed and specifically bound As forms to residual, amorphous hydrous oxide-bound, and crystalline hydrous oxide-bound ones. In general, the activities of soil enzymes increased after the above treatments, with the exception of that of alkaline phosphatase, which decreased upon supplementation with FMBC₂. Supplementation with BC or FMBCs increased the abundance of Proteobacteria and Firmicutes, decreasing that of Bacteroidetes. Notably, FMBC₁ and FMBC₂ affected soil properties in different ways, although the mechanisms of the corresponding influence were similar. Thus, treatment with BC-based materials changed the distribution of As and the activities of soil enzymes, additionally affecting a variety of other physicochemical soil properties to make it suitable for microbial growth.

Mitigation of arsenic toxicity and accumulation in hydroponically grown rice seedlings by co-inoculation with arsenite-oxidizing and cadmium-tolerant bacteria

Arsenic (As) contamination of rice grain is a serious problem worldwide. The objective of this study was to mitigate As toxicity and accumulation in hydroponically grown KDML105 rice seedlings using bacteria isolated from heavy metal-contaminated soils. Seven strains (KKU2500-1, -2, -3, -9, -12, -16 and -22) of 24 cadmium (Cd)-tolerant bacteria produced high levels of inorganic sulfide and thiol-rich compounds in As-supplemented media. The strains were allowed to colonize rice seedlings growing in arsenite [As(III)]- or arsenate [As(V)]-supplemented Hoagland's nutrient solutions. Colonization by strains KKU2500-3 and -12 led to increases in plant growth parameters and similarly reduced As translocation into shoots [translocation factor (TF) = 0.05] in the As(V)-supplemented solution. Strains KKU2500-1 and - 12 also greatly reduced As translocation into shoots (TF = 0.16-0.20) in As(III)-supplemented solution. KKU2500-3 and - 12 co-colonized onto seedlings with the As(III)-oxidizing isolates 4.25, 4.27, 4.40 and 4.44, and the strain combinations KKU2500-12/4.25, KKU2500-3/4.25, KKU2500-3/4.27 and KKU2500-3/4.44 resulted in higher growth parameters for plants grown in As [As(III)+As(V)]-supplemented solution than other combinations. Moreover, the combinations KKU2500-3/4.25 and KKU2500-3/4.44 greatly reduced As translocation (TF = 0.15 and 0.12, respectively), and this decreased As accumulation in shoots was significantly correlated with increased sulfide stimulation in roots and nutrient solution. These results indicate that these co-inoculated bacteria can mitigate As toxicity, translocation and accumulation in KDML105 seedlings and thus demonstrate synergistic activity in rice plants, and this effect can be further developed in field trials.

Elucidating the Effects of Cerium Oxide Nanoparticles and Zinc Oxide Nanoparticles on Arsenic Uptake and Speciation in Rice ( Oryza sativa) in a Hydroponic System

The accumulation of arsenic (As) in rice grains depends greatly on the redox chemistry in rice rhizosphere. Intentional or accidental introduction of strong oxidizing or reducing agents, such as metallic engineered nanoparticles (ENPs) into the plant-soil ecosystem, can change As speciation and plant uptake. However, investigation on the effects of ENPs on plant uptake of co-occurring redox sensitive heavy metals and their speciation in plant tissues is scarce. We investigated the mutual effects of two commonly encountered ENPs, cerium oxide nanoparticles (CeO₂ NPs) and zinc oxide nanoparticles (ZnO NPs), and two inorganic species of As on their uptake and accumulation in rice seedlings in a hydroponic system. Rice seedlings were exposed to different combinations of 1 mg/L of As(III) or As(V) and 100 mg/L of CeO₂ NPs and ZnO NPs for 6 days about 40 days after germination. ZnO NPs significantly reduced the accumulation of As(III) in rice roots by 88.1 and 96.7% and in rice shoots by 71.4 and 77.4% when the initial As was supplied as As(III) and As(V), respectively. ZnO NPs also reduced As(V) in rice roots by 68.3 and 52.3% when the As was provided as As(III) and As(V), respectively. However, the As(V) in rice shoots was unaffected by ZnO NPs regardless of the initial oxidation state of As. Neither the total As nor the individual species of As in rice tissues was significantly changed by CeO₂ NPs. The co-presence of As(III) and As(V) increased Ce in rice shoots by 6.5 and 2.3 times but did not affect plant uptake of Zn. The results confirmed the active interactions between ENPs and coexisting inorganic As species, and the extent of their interactions depends on the properties of ENPs as well as the initial oxidation state of As.

Effect of nanomaterials on arsenic volatilization and extraction from flooded soils

Herein, we utilize sequential extraction and high-throughput sequencing to investigate the effects of nanomaterial additives on As volatilization from flooded soils. We reveal that maximum volatilization is achieved in the fourth week and is followed by stabilization. The extent of volatilization decreased in the order of control > nano-zerovalent iron >40-nm hydroxyapatite > nano-Fe₃O₄ > 20-nm hydroxyapatite > multilayer graphene oxide > high-quality graphene oxide. The most abundant forms of As in soil corresponded to As-Fe and Al oxides. In soil with low levels of As pollution, the contents of these species increased after treatment with graphene oxides but decreased after treatment with other nanomaterials, with an opposite trend observed for soil with high levels of As pollution. The addition of nanomaterials influenced the activity of soil enzymes, e.g., hydroxyapatites affected the activities of urease and alkaline phosphatase, whereas graphene oxides significantly impacted that of peroxidase (P < 0.05). The addition of nanomaterials (which can potentially inhibit microbial growth) affected As levels by influencing the amount of As volatilized from polluted soil. Moreover, As volatilization, enzyme activity, and As speciation were observed to be mutually correlated (e.g., volatilization was negatively correlated to peroxidase activity and the contents of amorphous crystalline hydrous oxides of As-Fe and Al).

Effective rhizoinoculation and biofilm formation by arsenic immobilizing halophilic plant growth promoting bacteria (PGPB) isolated from mangrove rhizosphere: A step towards arsenic rhizoremediation

Arsenic (As) uptake by plants is largely influenced by the presence of microbial consortia and their interactions with As. In the coastal region of Bengal deltaic plain of Eastern India, the As-contaminated groundwater is frequently used for irrigation purposes resulting in an elevated level of soil As in agricultural lands. The health hazards associated with As necessitates development of cost-effective remediation strategies to reclaim contaminated agricultural lands. Among the available technologies developed in recent times, bioremediation using bacteria has been found to be the most propitious. In this study, two As-resistant halophilic bacterial strains Kocuria flava AB402 and Bacillus vietnamensis AB403 were isolated, identified and characterized from mangrove rhizosphere of Sundarban. The isolates, AB402 and AB403, could tolerate 35mM and 20mM of arsenite, respectively. The effect of As on the exopolysaccharide (EPS) synthesis, biofilm formation, and root association was evaluated for both the bacterial strains. Arsenic adsorption on the cell surfaces and intracellular accumulation in both the bacterial strains were promising under culture conditions. Moreover, both the strains when used as inoculum, not only promoted the growth of rice seedlings but also decreased As uptake and accumulation in plants.

Knocking Out OsPT4 Gene Decreases Arsenate Uptake by Rice Plants and Inorganic Arsenic Accumulation in Rice Grains

Arsenic (As) accumulation in rice grains poses health risk to humans. Plants including rice take up arsenate (AsV) by phosphate transporters. In this study, rice phosphate transporter OsPT4 (OsPht1;4) was investigated based on two independent T-DNA insertion mutants of OsPT4 (M1 and M2), which displayed stronger AsV resistance than wild types WT1 and WT2. When cultivated in medium (+P or -P) with AsV, ospt4 mutants accumulated 16-32% lower As in plants, suggesting that OsPT4 mediates AsV uptake. Analysis of the xylem sap showed that AsV concentrations in ospt4 mutants was 20-40% lower than WT controls under -P condition, indicating OsPT4 may also mediate AsV translocation. Moreover, kinetics analysis showed that ospt4 mutants had lower AsV uptake rates than the WT controls, further proving that OsPT4 functions as an AsV transporter in rice. When grown in flooded soils with As, AsV concentrations in rice grains of ospt4 mutants decreased by 50-55%. More importantly, knocking out OsPT4 in M1 and M2 reduced inorganic As accumulation in rice grains by 20-44%, significant for controlling As exposure risk from rice. Taken together, our findings revealed a critical role of OsPT4 in AsV uptake and translocation in rice. Knocking out OsPT4 effectively decreased inorganic As accumulation in rice grains, shedding light on engineering low-As rice to enhance food safety.