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

Loss of microbial diversity increases methane emissions and arsenic release in paddy soils

Microorganisms are vital to the emission of greenhouse gases and transforming pollutants in paddy soils. However, the impact of microbial diversity loss on anaerobic methane (CH4) oxidation and arsenic (As) reduction under flooded conditions remains unclear. In this study, we inoculated microbial suspensions into natural As-contaminated paddy soils using a dilution approach (untreated, 10-2, 10-4, 10-6, 10-8 dilutions) to manipulate microbial diversity levels. The results revealed that the 10-4 and 10-6 dilutions resulted in the highest CH4 emissions (97.0 μmol and 102.3 μmol) compared to untreated groups (27.6 μmol). However, anaerobic CH4 oxidation was not observed in 10-4 dilution groups and higher dilutions, suggesting the loss of diversity inhibited the natural reduction of CH4. Moreover, the porewater As concentration in the dilution groups was 1.8-8.2 times greater than in the untreated groups. The loss of microbial diversity promoted the reductive dissolution of iron (Fe) minerals bearing As, leading to increased concentrations of Fe(II) and dissolved organic carbon (DOC), which further enhanced As release (Fe(II), R = 0.9, p < 0.001) (DOC, R = 0.8, p < 0.001) from soil to porewater. However, CH4-dependent As(V) reduction was almost entirely inhibited under diversity loss. The decline in microbial diversity increased the relative abundances of methanogens (e.g., Methanobacterium and Methanomassiliicoccus), Fe(III)/As(V)-reducing bacteria (e.g., Bacillus, Clostridium_sensu_stricto_10, and Geobacter), and the related functional genes (i.e., mcrA and Geo). These findings suggest that microbial diversity is critical for specialized soil processes, highlighting the detrimental effects of biodiversity loss on CH4 emissions and As release in As-contaminated paddies.

Water-fertilizer regulation drives microorganisms to promote iron, nitrogen and manganese cycling: A solution for arsenic and cadmium pollution in paddy soils

The co-contamination of arsenic (As) and cadmium (Cd) in rice fields presents a global imperative for resolution. However, understanding the complex microbially driven geochemical processes and network connectivity crucial for As and Cd bioavailability under the frequent redox transitions in rice fields remains limited. Here, we conducted a series of microcosm experiments, using flooding and drainage, alongside fertilization treatments to emulate different redox environment in paddy soils. Soil As significantly reduced in drained conditions following applications of biochar or calcium-magnesium-phosphate (CMP) fertilizers by 26.3 % and 31.2 %, respectively, with concurrent decreases in Cd levels. Utilizing geochemical models, we identified the primary redox cycles dynamically altering during flooding (Fe and S cycles) and drainage (Fe, Mn, and N cycles). PLS-SEM elucidated 76 % and 61 % of the variation in Cd and As through Mn and N cycles. Functional genes implicated in multi-element cycles were analyzed, revealing a significantly higher abundance of assimilatory N reduction genes (nasA, nirA/B, narB) in drained soil, whereas an increase in ammonia-oxidizing genes (amoA/B) and a decrease in nitrate reduction to ammonium genes were observed after CMP fertilizer application. Biochar application led to significant enrichment of the substrate-binding protein of the Mn transport gene (mntC). Moreover, Fe transport genes were enriched after biochar or CMP application compared to drained soils. Among 40 high-quality metagenome-assembled genomes (MAGs), microbial predictors associated with low Cd and As contents across different treatments were examined. Bradyrhizobacea harbored abundant Mn and FeIII transport genes, while Nitrososphaeraceae carried nitrification-related genes. Two MAGs affiliated with Caulobacteraceae, carrying diverse Fe transport genes, were enriched in biochar-applied soils. Therefore, applying CMP fertilizer or biochar in aerobic rice fields can synergistically reduce the bioavailability of Cd and As by specifically enhancing the circulation of essential elements.

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.

Response of soil fungi to textile dye contamination

This study examines the impact of textile dye contamination on the structure of soil fungal communities near a Shaoxing textile dye factory. We quantified the concentrations of various textile dyes, including anthraquinone azodye and phthalocyanine, which ranged from 20.20 to 140.62 mg kg^-1, 102.01-698.12 mg kg^-1, and 7.78-42.65 mg kg^-1, respectively, within a 1000 m radius of the factory. Our findings indicate that as dye concentration increases, the biodiversity of soil fungi, as measured by the Chao1 index, decreases significantly, highlighting the profound influence of dye contamination on fungal community structure. Additionally, microbial correlation network analysis revealed a reduction in fungal interactions correlating with increased dye concentrations. We also observed that textile dyes suppressed carbon and nitrogen metabolism in fungi while elevating the transcription levels of antioxidant-related genes. Enzymes such as lignin peroxidase (LiP), manganese peroxidase (MnP), laccase (Lac), dye-decolorizing peroxidases (DyPs), and versatile peroxidase (VP) were upregulated in contaminated soils, underscoring the critical role of fungi in dye degradation. These insights contribute to the foundational knowledge required for developing in situ bioremediation technologies for contaminated farmlands.

Metal-Binding Protein TaGlo1 Improves Fungal Resistance to Arsenite (AsIII) and Methylarsenite (MAsIII) in Paddy Soil

Trivalent arsenicals such as arsenite (AsIII) and methylarsenite (MAsIII) are thought to be ubiquitous in flooded paddy soils and have higher toxicity than pentavalent forms. Fungi are widely prevalent in the rice rhizosphere, and the latter is considered a hotspot for As uptake. However, few studies have focused on alleviating As toxicity in paddy soils using fungi. In this study, we investigated the mechanism by which the protein TaGlo1, derived from the As-resistant fungal strain Trichoderma asperellum SM-12F1, mitigates AsIII and MAsIII toxicity in paddy soils. Taglo1 gene expression in Escherichia coli BL21 conferred strong resistance to AsIII and MAsIII, while purified TaGlo1 showed a high affinity for AsIII and MAsIII. Three cysteine residues (Cys13, Cys18, and Cys71) play crucial roles in binding with AsIII, while only two (Cys13 and Cys18) play crucial roles for MAsIII binding. TaGlo1 had a stronger binding strength for MAsIII than AsIII. Importantly, up to 90.2% of the homologous TaGlo1 proteins originate from fungi by GenBank searching. In the rhizospheres of 14 Chinese paddy soils, Taglo1 was widely distributed and its gene abundance increased with porewater As. This study highlights the potential of fungi to mitigate As toxicity and availability in the soil-rice continuum and suggests future microbial strategies for bioremediation.

Fundamentals and application in phytoremediation of an efficient arsenate reducing bacterium Pseudomonas putida ARS1

Arsenic is a ubiquitous environmental pollutant. Microbe-mediated arsenic bio-transformations significantly influence arsenic mobility and toxicity. Arsenic transformations by soil and aquatic organisms have been well documented, while little is known regarding effects due to endophytic bacteria. An endophyte Pseudomonas putida ARS1 was isolated from rice grown in arsenic contaminated soil. P. putida ARS1 shows high tolerance to arsenite (As(III)) and arsenate (As(V)), and exhibits efficient As(V) reduction and As(III) efflux activities. When exposed to 0.6 mg/L As(V), As(V) in the medium was completely converted to As(III) by P. putida ARS1 within 4 hr. Genome sequencing showed that P. putida ARS1 has two chromosomal arsenic resistance gene clusters (arsRCBH) that contribute to efficient As(V) reduction and As(III) efflux, and result in high resistance to arsenicals. Wolffia globosa is a strong arsenic accumulator with high potential for arsenic phytoremediation, which takes up As(III) more efficiently than As(V). Co-culture of P. putida ARS1 and W. globosa enhanced arsenic accumulation in W. globosa by 69%, and resulted in 91% removal of arsenic (at initial concentration of 0.6 mg/L As(V)) from water within 3 days. This study provides a promising strategy for in situ arsenic phytoremediation through the cooperation of plant and endophytic bacterium.

Dietary Galactooligosaccharides Supplementation as a Gut Microbiota-Regulating Approach to Lower Early Life Arsenic Exposure

Prebiotics may stimulate beneficial gut microorganisms. However, it remains unclear whether they can lower the oral bioavailability of early life arsenic (As) exposure via regulating gut microbiota and altering As biotransformation along the gastrointestinal (GI) tract. In this study, weanling mice were exposed to arsenate (iAsV) via diet (7.5 μg As g-1) amended with fructooligosaccharides (FOS), galactooligosaccharides (GOS), and inulin individually at 1% and 5% (w/w). Compared to As exposure control mice, As concentrations in mouse blood, liver, and kidneys and As urinary excretion factor (UEF) were reduced by 43.7%-74.1% when treated with 5% GOS. The decrease corresponded to a significant proliferation of Akkermansia and Psychrobacter, reduced percentage of inorganic arsenite (iAsIII) and iAsV by 47.4% and 65.4%, and increased proportion of DMAV in intestinal contents by 101% in the guts of mice treated with 5% GOS compared to the As control group. In contrast, FOS and inulin either at l% or 5% did not reduce As concentration in mouse blood, liver, and kidneys or As UEF. These results suggest that GOS supplementation may be a gut microbiota-regulating approach to lower early life As exposure via stimulating the growth of Akkermansia and Psychrobacter and enhancing As methylation in the GI tract.

Phosphate-solubilizing fungi enhances the growth of Brassica chinensis L. and reduces arsenic uptake by reshaping the rhizosphere microbial community

High concentrations of arsenic in soil and plant systems are a threat to human health and ecosystems. The levels of phosphate ions in the soil strongly influence the soil efficacy and arsenic absorption by plants. This study investigated the effects of phosphate-solubilizing fungi (PSF) on environmental factors and structural changes in microbial community in soils contaminated with arsenic. Four experimental groups were created: control (CK), Penicillium GYAHH-CCT186 (W186), Aspergillus AHBB-CT196 (W196), and Penicillium GYAHH-CCT186 + Aspergillus AHBB-CT196 (W186 + W196), with Pakchoi (Brassica chinensis L.) as the test plant. Analysis of altered nutrient levels, enzyme activities and microbial community structure in the soil as well as the growth and physiological characteristics of Pakchoi, revealed a significant increase in the available phosphorus (AP), organic matter (OM), cation exchange capacity (CEC) and available arsenic (AAs) content of the soil following W186 + W196, W196 and W186 treatments. All experimental treatments enhanced the activity of soil β-glucosidase (β-GC) and soil catalase (S-CAT). W186 + W196 and W196 treatments significantly enhanced soil acid phosphatase (S-ACP) activity. Besides, W186 + W196 treatment significantly induced dehydrogenase (S-DHA) activity. Further, of the treatment with PSF increased the fresh weight, root length, plant height and chlorophyll levels while decreasing the arsenic accumulation in Pakchoi. Exposure to PSF also increased the activity of Ascomycota, Basidiomycota, Chytridiomycota, unclassified_Fungi, Mortierellomycota, Cryptomycota and Rozellomycota in the soil. The relative abundance of Ascomycota, Basidiomycota, and Mortierellomycota was positively correlated with the available nutrients (except iron) in the soil as well as enzyme activities. Consequently, the PSF improved the quality of soil and the safety of Pakchoi, suggesting that PSF can be utilized for the remediation of arsenic-contaminated soil.

Coal gangue-based magnetic porous material for simultaneous remediation of arsenic and cadmium in contaminated soils: Performance and mechanisms

Remediation of arsenic (As) and cadmium (Cd) co-contaminated soil is a challenge in environmental remediation. In this study, coal gangue-based magnetic porous material (MPCG) was designed for simultaneous immobilization of As and Cd in contaminated soil. After the incubation experiment, the effects of CG and MPCG on the availability and fractions of As and Cd and the related microbial functional genes were analyzed to explore the potential remediation mechanisms of MPCG for As and Cd in contaminated soil. The results showed that the stabilization effect of MPCG on As and Cd was significantly higher than that of coal gangue. It reduced the available As and Cd by 17.94-29.81% and 14.22-30.41%, respectively, and transformed unstable As/Cd to stable. The remediation mechanisms of MPCG on As included adsorption, oxidation, complexation and precipitation/co-precipitation. Meanwhile, the remediation mechanisms of MPCG for Cd included adsorption, ion exchange, complexation and precipitation. In addition, MPCG increases the abundance of sulfate-reducing bacteria (dsrA) by 43.39-381.28%, which can promote sulfate reduction. The sulfide can precipitate with As and Cd to reduce the availability of As and Cd in soil. Thus, MPCG is a promising amendment for achieving the remediation of As and Cd co-contaminated soil.

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.

Microbial community composition and cooccurrence patterns driven by co-contamination of arsenic and antimony in antimony-mining area

In the current study, a typical Sb mine was selected to explore the microbial community composition and assembly driven by the cocontamination of As/Sb with geographic distance. Our results showed that environmental parameters, especially pH, TOC, nitrate, total and bioavailable As/Sb contents largely affected the microbial community diversity and composition. The total and bioavailable As/Sb levels were significantly positively correlated with the relative abundance of Zavarzinella, Thermosporothrix and Holophaga, while the pH presented a significant negative correlation with the three genera, potentially implying they are important taxonomic groups in acid-mining soils. The cooccurrence network analysis indicated the environmental stress dominated by pH and As/Sb co-contamination affected the microbial modularity and interaction. Meanwhile, Homogeneous selection (HoS, 26.4-49.3%), and drift and others (DR, 27.1∼40.2%) were the most important assembly processes for soil bacterial, and the importance of HoS decreased and the DR increased with geographic distance to the contamination source respectively. Soil pH, nutrient availability, total and bioavailable As/Sb contents significantly affected the HoS and DR processes. This study provides theoretical support for microbial remediation in metal(loid)-contaminated soils.

Soil particle size fractions affect arsenic (As) release and speciation: Insights into dissolved organic matter and functional genes

Soil particle size fractions (PSFs) are important for arsenic (As) partitioning, migration, and speciation transformation. However, information is lacking about the environmental fate of As and its distribution on different PSFs. In the present study, two types of soils from mining areas were divided into four PSFs, including coarse sand (2-0.25 mm), fine sand (0.25-0.05 mm), silt (0.05-0.002 mm), and clay (< 0.002 mm) fractions. The results showed that As was enriched in the coarse sand, which was primarily affected by the content of organic carbon (OC), followed by iron (Fe), aluminum (Al), and manganese (Mn) (hydr)oxides. The elevated total As (TAs), As(III), organic As, Fe(II), and dissolved organic carbon (DOC) concentrations were mainly originated from the clay fraction. The intensified humification degree of DOM and promoted bacterial metabolism related to As/iron bioreduction were also exhibited in the clay fractions. The dynamics of As fractions in soils indicated the potential formation of secondary minerals and re-adsorption of As in the PSFs. The highest abundances of arrA, arsC, arsM, and Geo genes were found in the clay fraction, implying that the clay fraction potentially released more As, including As(III) and organic As. Results from the correlation analysis showed that elevated DOC concentrations promoted the catabolic responses of iron-reducing microorganisms and triggered microbial As detoxification. Overall, this study provides valuable information and guidance for the remediation of As-contaminated soils.

Anaerobic methane oxidation coupled to arsenate reduction in paddy soils: Insights from laboratory and field studies

Anaerobic methane oxidation (AOM) coupled to nitrate, sulfate and iron has been most extensively studied. Recently, AOM coupled with arsenate reduction (AOM-AsR) was demonstrated in laboratory microcosm incubation, however whether AOM-AsR is active in the field conditions remains elusive. Here, we used 13C-labeled methane (13CH4) to investigate the AOM-AsR process in both anaerobic microcosms and field conditions with identical soils. Our results revealed the occurrence of AOM-AsR in the field, but AOM-AsR in the field was not as active as that which occurred in the laboratory (AOM-AsR contributed approximately 33.87% and 80.76% of total As release in the field and laboratory studies, respectively). This occurred because the laboratory setting provided a more suitable condition for the AOM-AsR process. Moreover, the results suggested that the relative abundance of mcrA from the ANME-2d was the most abundant. Our results clearly demonstrate that the AOM-AsR is active in both the laboratory and field conditions. Moreover, the results highlight the potential risk the AOM-AsR for pose for As contamination in rice paddies.

Rhizosphere bacteria regulated arsenic bioavailability and accumulation in the soil-Chinese cabbage system

The accumulation of arsenic (As) in Chinese cabbage (Brassica rapa ssp. pekinensis) has recently been a source of concern for a potential risk to human health. It is unknown whether natural variations of As accumulation in different genotypes of Chinese cabbage are related to rhizobacterial characteristics. Experiments were conducted to investigate the mechanisms of rhizobacteria involving in As fates in a soil-Chinese cabbage system using various genotypes using high-throughput sequencing and quantitative PCR. There were significant differences in As accumulation in cabbage leaves between 32 genotypes, and genotypes of low-As-accumulation (LSA) and high-As-accumulation (HSA) were identified. The As concentrations in the shoots of LSA were 23.25 %, 24.19 %, 15.05 %, and 70.69 % lower than those of HSA in seedling stage (SS), rosette stage (RS), heading stage (HS), and mature stage (MS), respectively. Meanwhile, the relative abundances of phyla Patescibacteria (in RS), Acidobacteria and Rokubacteria (in HS) in the rhizosphere of LSA were 60.18 %, 28.19 %, and 45.38 % less than those of HSA, respectively. Additionally, both shoot-As and As translocation factor had significantly positive or negative correlations with the relative abundances of Rokubacteria or Actinobacteria. In LSA rhizosphere, the relative abundances of genera Flavobacterium (in SS), Ellin6055 and Sphingomonas (in HS) were 128.12 %, 83.69 % and 79.50 % higher than those of HSA, respectively. This demonstrated that rhizobacteria contribute to the accumulation and translocation of As in HSA and LSA. Furthermore, the gene copies of aioA and arsM in LSA rhizosphere were 25.54 % and 16.13 % higher than those of HSA, respectively, whereas the gene copies of arsC in LSA rhizosphere were 26.36 % less than those of HSA in MS, indicating that rhizobacteria are involved in As biotransformation in the soil. These results provide a comprehensive understanding of the relationship between characteristics of rhizobacterial communities and As variations in Chinese cabbage genotypes.

Distinct arsenic uptake feature in rice reveals the importance of N fertilization strategies

The environmental behavior of arsenic (As) is commonly affected by the biogeochemical processes of iron (Fe) and nitrogen (N). In this study, field experiments were conducted to explore As uptake in rice and As translation and distribution in As-contaminated iron-rich paddy soils after applying different forms of N fertilizers, including urea (CO(NH2)2), ammonium bicarbonate (NH4HCO3), nitrate of potash (KNO3), and ammonium bicarbonate + nitrate of potash (NH4HCO3 + KNO3). The results indicated that applying nitrate N fertilizer inhibited the reduction and dissolution of As-bearing iron minerals and promoted microbial-mediated As(III) oxidation in flooded soil, thus reducing the soil As bioavailability. The concentrations of total As and inorganic As ratio (iAs/TAs) in rice grain decreased by 32.4 % and 15.4 %, respectively. However, the application of ammonium nitrogen promoted the reductive dissolution of As-bearing iron minerals and stimulated microbial As(V) reduction in flooded soil, leading to the release of As from soil to porewater. The total As concentration and inorganic As uptake ratio in rice grain increased by 20.1 % and 6.2 %, respectively, when urea was applied, and by 29.6 % and 10.5 %, respectively, when ammonium bicarbonate was applied. However, the simultaneous application of NH4+ and NO3- had no significant effect on As concentration in rice grain and its transformation in paddy soils. Ammonium nitrogen enhanced the organic As concentration in rice grain because the increased As(III) promoted As methylation in soil. In contrast, nitrate decreased the organic As uptake by rice grain because the decreased As(III) diminished As methylation in soil. The results provide reasonable N fertilization strategies for regulating the As biogeochemical process and reducing the risk of As contamination in rice.

Arsenic biotransformation genes and As transportation in soil-rice system affected by iron-oxidizing strain (Ochrobactrum sp.)

Arsenic (As) biotransformation in soil affects As biogeochemical cycling and is associated with As accumulation in rice. After inoculation with 1% iron-oxidizing bacteria (FeOB) in paddy soil, As speciation, As biotransformation genes in soil, As/Fe in Fe plaques, and As accumulation in rice were characterized. Compared with the control, the available As concentrations in soils decreased while amorphous and poorly crystalline Fe-Al oxidized As and crystalline Fe-Al oxidized As fractions increased of F (FeOB) and RF (rice and FeOB) treatments. Fe concentrations increased and positively correlated with As concentrations in Fe plaques on the rice root surface (***P < 0.001). Compared with R (rice), Monomethyl As (MMA), dimethyl As (DMA), arsenate (As(V)), and arsenite (As(III)) concentrations in rice plants showed a downwards trend of RF treatment. The As concentration in grains was below the National Standard for Food Safety (GB 2762-2017). A total of 16 As biotransformation genes in rhizosphere soils of different treatments (CK, F, R and RF were quantified by high-throughput qPCR (HT-qPCR). Compared with the control, the As(V) reduction and As transport genes abundance in other treatments increased respectively by 54.54%-69.17% and 54.63%-73.71%; the As(III) oxidation and As (de) methylation genes did not change significantly; however, several As(III) oxidation genes (aoxA, aoxB, aoxS, and arsH) increased. These results revealed that FeOB could reduce, transport As, and maybe also oxidize As. In addition, As(III) oxidation gene (aoxC) in rhizosphere soil was more abundant than in non-rhizosphere soil. It indicated that radial oxygen loss (ROL) promoted As(III) oxidation in rhizosphere soils. The results provide evidence for As biotransformation by ROL and FeOB in soil-rice system. ROL affects As oxidation and immobilization, and FeOB affects As reduction, transportation and may also affect As oxidation.

Iron-based passivator mitigates the coupling process of anaerobic methane oxidation and arsenate reduction in paddy soils

Arsenic (As) is a toxic metalloid that is ubiquitous in paddy soils, where passivation is the most widely used method for remediating As contamination. Recently, anaerobic methane oxidation coupled with arsenate (As(V)) reduction (AOM-AsR) has been shown to act as a critical driver for As release in paddy fields. However, the effect and mechanism of the passivators on the AOM-AsR process remain unclear. In this study, we incubated arsenate-contaminated paddy soils under anaerobic conditions. Using isotopically labelled methane and different passivators, we found that an iron-based passivator containing calcium sulfate and iron oxide (9:1, m/m) named IBP showed a much better performance than the other passivators. Adding IBP decreased the arsenite (As(III)) concentration in the soil solution by 78% and increased the AOM rate by 55%. Furthermore, we employed high-throughput sequencing and real-time quantitative polymerase chain reaction (qPCR) to investigate the ability of IBP to control As release mediated by AOM-AsR in paddy fields, as well as its underlying mechanism. Our results showed that IBP addition significantly increased anaerobic methanotrophic (ANME) archaea (ANME-2a-c, ANME-2d, and ANME-3) by 91%, and increased the methane-oxidizing bacterium Methylobacter by 262%. Similarly, IBP addition significantly increased the Fe(III) concentration in soil solution by 39% and increased the absolute abundance of Fe(III)-reducing bacteria (Geobacteraceae) by 21 times in soil. Adding IBP may significantly promote AOM coupled with Fe(III) reduction, significantly reducing electron transfer from AOM to As(V) reduction. Hence, IBP may be used as an efficient passivator to remediate As-contaminated soil using an active AOM-AsR process. These results provide a novel insight into controlling soil As release by regulating an active and critical As mobilization pathway in the environment.

Effect of applying persulfate on the accumulation of arsenic in rice plants grown in arsenic-contaminated paddy soil

Arsenic is known to be a notorious human carcinogen and rice consumption is becoming the primary human exposure route for As, especially in many Asian countries. As one of redox-sensitive elements in soil, sulfur plays an indisputable role in controlling As behaviors. However, information on the effects of persulfe (PS) on the toxicity and accumulation of As in rice plant under flooded conditions is limited. Therefore, a pot experiment was conducted to investigate the effects of PS amendment on the growth and accumulation of As species in rice plants grown in As-contaminated paddy soil. Results revealed that PS application increased the As, Fe, and Mn in porewater at the early stage, and then declined. Application of PS increased the biomass of stem and root, while inhibited the formation of iron plaque on the root surface. The As translocation from root to rice above tissues and accumulation of As species in brown rice were declined by amendment with PS. The inorganic arsenic (iAs) and DMA were the two main species in brown rice, and decreased by 13~26% and 40~60% respectively upon PS application. The results suggested that amendment with PS might be feasible for reducing the accumulation of As in rice grains grown in As-contaminated paddy soil. However, further detailed studies on the potential soil biogeochemical and physiological mechanisms are recommended.

Distribution Pattern and Influencing Factors of Heavy Metal Resistance Genes in the Yellow River Sediments of Henan Section

The transformation of heavy metal resistance genes (MRGs) in the environment has attracted increasing attention in recent years. However, few studies have reported the MRG content in the Yellow River, one of the main irrigation water sources in the North China Plain. In this study, we quantified MRG abundance by a metagenomic approach, and assessed the influence on MRGs of both bioavailable and total heavy metal (HM) content. The results indicate that Cu-resistant genes are the most common genes, and the prevalence of arsM needs more attention. Comamonadaceae is the dominant family in the Yellow River, and the presence of organic pollutants may contribute to the prevalence of Vicinamibacteraceae, Nocardioidaceae, and Flavobacteriacea. The results of the Mantel test and Spearman analysis indicate that both the bioavailable fractions and total content of HMs could have little influence on MRGs. Network analysis results indicate that some dominant bacteria could be the potential hosts of some prevalent MRGs, which may exert an adverse impact on human health.

Arsenic and nitrate remediation by isolated FeOB strains coupled with additional ferrous iron in the iron-deficient arid soils

Remediation of As(III) by use of Fe(II) oxidation bacteria (FeOB) in iron-rich soils has been reported, but seldom used in the iron-deficient soil of arid areas. This study was aimed at selecting native bacterial strains to remediate As pollution in arid soils, coupled with the addition of Fe(II). The used methods included: The selection of two FeOB strains; XRD for solid phase identification based on peaks; SEM with EDS for morphology identification of newly formed minerals with chemical compositions; XPS for surface chemistry of the minerals; FTIR for functional groups of precipitates and 3DEEM for EPS determination, etc. The results were as follows: Sharp decrement curves of As(III) and NO₃^- with Fe(II) and total Fe contents and increment of NO₂^-; NH₄⁺ fluctuating during the experimental period of 11 days; and precipitation of Fe(III) hydroxides together with As(III) with broken FeOBs due to encrustation in the SEM scan. It was concluded that two selected Pseudomonas strains have NAFO functionality by addition of iron as iron reduction-oxidation pair in the arid soil, further potentially fixing NH₄⁺ while As(III) can be effectively remediated through the FeOB participation in forms of adsorption and co-precipitation of Fe(OH)₃ through an oxidation of Fe(II) process.

Remediation of arsenic-contaminated paddy field by a new iron oxidizing strain (Ochrobactrum sp.) and iron-modified biochar

Iron-oxidizing strain (FeOB) and iron modified biochars have been shown arsenic (As) remediation ability in the environment. However, due to the complicated soil environment, few field experiment has been conducted. The study was conducted to investigate the potential of iron modified biochar (BC-FeOS) and biomineralization by a new found FeOB to remediate As-contaminated paddy field. Compared with the control, the As contents of G_B (BC-FeOS), G_F (FeOB), G_FN (FeOB and nitrogen fertilizer), G_BF (BC-FeOS and FeOB) and G_BFN (BC-FeOS, FeOB and nitrogen fertilizer) treatments in pore water decreased by 36.53%-80.03% and the microbial richness of iron-oxidizing bacteria in these treatments increased in soils at the rice maturation stage. The concentrations of available As of G_B, G_F, G_FN, G_BF and G_BFN at the tillering stage were significantly decreased by 10.78%-55.48%. The concentrations of nonspecifically absorbed and specifically absorbed As fractions of G_B, G_F, G_FN, G_BF and G_BFN in soils were decreased and the amorphous and poorly crystalline hydrated Fe and Al oxide-bound fraction was increased. Moreover, the As contents of G_B, G_F, G_FN, G_BF and G_BFN in rice grains were significantly decreased (*P < 0.05) and the total As contents of G_FN, G_BF and G_BFN were lower than the standard limit of the National Standard for Food Safety (GB 2762-2017). Compared with the other treatments, G_BFN showed the greatest potential for the effective remediation of As-contaminated paddy fields.

Endophytic fungus Serendipita indica reduces arsenic mobilization from root to fruit in colonized tomato plant

The accumulation of arsenic in crop plants has become a worldwide concern that affects millions of people. The major source of arsenic in crop plants is irrigation water and soil. In this study, Serendipita indica, an endophytic fungus, was used to investigate the protection against arsenic and its accumulation in the tomato plant. We found that inoculation of S. indica recovers seed germination, plant growth and improves overall plant health under arsenic stress. A hyper-colonization of fungus in the plant root was observed under arsenic stress, which results in reduced oxidative stress via modulation of antioxidative enzymes, glutathione, and proline levels. Furthermore, fungal colonization restricts arsenic mobilization from root to shoot and fruit by accumulating it exclusively in the root. We observed that fungal colonization enhances the arsenic bioaccumulation factor 1.48 times in root and reduces the arsenic translocation factor by 2.96 times from root to shoot and 13.6 times from root to fruit compared to non colonized plants. Further, investigation suggests that S. indica can tolerate arsenic by immobilizing it on the cell wall and accumulating it in the vacuole. This study shows that S. indica may be helpful for the reduction of arsenic accumulation in crops grown in arsenic-contaminated agriculture fields.

Influence of tetracycline on arsenic mobilization and biotransformation in flooded soils

This study examined the effect of tetracycline addition on arsenic (As) mobilization and biotransformation in two contrasting soils (upland soil and paddy soil) under flooded conditions. The soils with added tetracycline (0-50 mg kg^-1) were incubated for 30 days, and soil properties and microbial functional genes over time were quantified. Tetracycline significantly promoted As reduction and As release into porewater in both soils. The enhancement had resulted from an increase in the concentration of dissolved organic carbon and a decrease in soil redox potential. Tetracycline also increased the abundances of As-reducing genes (arsC and arrA) and the relative abundances of As-reducing bacteria Streptomyces, Bacillus, Burkholderia, Clostridium and Rhodococcus, all of which have been found resistant to tetracycline. These genera play a key part in stimulating As reduction in the presence of tetracycline. The study indicated the significance of tetracycline in the biochemical behavior of As in flooded soils and provided new insights into the potential effects of tetracycline on the quality and safety of agricultural products in the future.

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.

Variations of arsenic forms and the role of arsenate reductase in three hydrophytes exposed to different arsenic species

In order to understand the mechanisms of arsenic (As) accumulation and detoxification in aquatic plants exposed to different As species, a hydroponic experiment was conducted and the three aquatic plants (Hydrilla verticillata, Pistia stratiotes and Eichhornia crassipes) were exposed to different concentrations of As(III), As(V) and dimethylarsinate (DMA) for 10 days. The biomass, the surface As adsorption and total As adsorption of three plants were determined. Furthermore, As speciation in the culture solution and plant body, as well as the arsenate reductase (AR) activities of roots and shoots, were also analyzed. The results showed that the surface As adsorption of plants was far less than total As absorption. Compared to As(V), the plants showed a lower DMA accumulation. P. stratiotes showed the highest accumulation of inorganic arsenic but E. crassipes showed the lowest at the same As treatment. E. crassipes showed a strong ability to accumulate DMA. Results from As speciation analysis in culture solution showed that As(III) was transformed to As(V) in all As(III) treatments, and the oxidation rates followed as the sequence of H. verticillata>P. stratiotes>E. crassipes>no plant. As(III) was the predominant species in both roots (39.4-88.3%) and shoots (39-86%) of As(III)-exposed plants. As(V) and As(III) were the predominant species in roots (37-94%) and shoots (31.1-85.6%) in As(V)-exposed plants, respectively. DMA was the predominant species in both roots (23.46-100%) and shoots (72.6-100%) in DMA-exposed plants. The As(III) contents and AR activities in the roots of P. stratiotes and in the shoots of H. verticillata were significantly increased when exposed to 1 mg·L^-1 or 3 mg·L^-1 As(V). Therefore, As accumulation mainly occurred via biological uptake rather than physicochemical adsorption, and AR played an important role in As detoxification in aquatic plants. In the case of As(V)-exposed plants, their As tolerance was attributed to the increase of AR activities.

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.

Variations in root morphological indices of rice (Oryza sativa L.) induced by seedling establishment methods and their relation to arsenic accumulation in plant tissues

Understanding how the seedling establishment method affects arsenic (As) accumulation in rice is important for safe agricultural production. In a field experiment with three seedling establishment methods and two rice cultivars, the effects of direct seeding (DS), manual transplanting (MT), and seedling throwing (ST) on root morphological indices and the distribution, translocation, and accumulation of As in rice tissues across growth stages were compared. DS method resulted in the greatest accumulation of As in the two rice cultivars and led to more As distributed in aboveground tissues during the entire growth period. Especially in DS brown rice, the concentration of total As increased by 24.0%-40.8%, and that of inorganic As increased by 24.4%-40.0%, compared with the concentrations in MT and ST rice. A multiple regression model was developed with root morphological indices and the total As concentration in brown rice, and the R² value of the model was 0.819, which was significant at the 1% level. Compared with the other establishment methods, the thinner diameters, smaller volumes, larger specific surface areas, and greater numbers of root tips in DS rice roots across growth stages promoted As uptake. The concentrations of As in root tips were approximately five times greater than those in the root base, and root tips were the key factor determining the difference in As accumulation in rice roots under the different seedling establishment methods. The results of this study demonstrate that the choice of an appropriate rice seedling establishment method is important to avoid the environmental consequences of As contamination and safely produce rice grain. Therefore, despite the current trend of increased use of DS, transplantation is recommended as a safer pattern of rice seedling establishment in As-contaminated areas.

Arsenic biogeochemical cycling in paddy soil-rice system: Interaction with various factors, amendments and mineral nutrients

Arsenic (As) contamination is a well-recognized environmental and health issue, threatening over 200 million people worldwide with the prime cases in South and Southeast Asian and Latin American countries. Rice is mostly cultivated under flooded paddy soil conditions, where As speciation and accumulation by rice plants is controlled by various geo-environmental (biotic and abiotic) factors. In contrast to other food crops, As uptake in rice has been found to be substantially higher due to the prevalence of highly mobile and toxic As species, arsenite (As(III)), under paddy soil conditions. In this review, we discussed the biogeochemical cycling of As in paddy soil-rice system, described the influence of critical factors such as pH, iron oxides, organic matter, microbial species, and pathways affecting As transformation and accumulation by rice. Moreover, we elucidated As interaction with organic and inorganic amendments and mineral nutrients. The review also elaborates on As (im)mobilization processes and As uptake by rice under the influence of different mineral nutrients and amendments in paddy soil conditions, as well as their role in mitigating As transfer to rice grain. This review article provides critical information on As contamination in paddy soil-rice system, which is important to develop suitable strategies and mitigation programs for limiting As exposure via rice crop, and meet the UN's key Sustainable Development Goals (SDGs: 2 (zero hunger), 3 (good health and well-being), 12 (responsible consumption and production), and 13 (climate action)).

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.

Altered arsenic availability, uptake, and allocation in rice under elevated temperature

Climate change is expected to increase growing temperatures in rice cultivating regions worldwide. Recent research demonstrates that elevated temperature can increase arsenic concentrations in rice tissue, exacerbating an existing threat to rice quality and human health. However, the specific temperature-induced changes in the plant-soil system responsible for increased arsenic concentrations remain unclear and such knowledge is necessary to manage human dietary arsenic exposure in a warmer future. To elucidate these changes, we established four temperature treatments in climate-controlled growth chambers and grew rice plants (Oryza sativa cv. M206) in pots filled with Californian paddy soil with arsenic concentrations of 7.7 mg kg^-1. The four chosen temperatures mimicked IPCC forecasting for Northern California, with a roughly 2.5 °C increase between treatments (nighttime temperatures ~2 °C cooler). We observed that arsenic concentrations in porewater, root iron plaque, and plant tissue increased in response to elevated temperature. There was a positive linear relationship between temperature and rice grain arsenic, almost all of which was present as inorganic As (III). Above-ground allocation patterns were consistent across treatments. We found no upregulation in the gene encoding the OsABCC1 transporter, believed to be important for arsenic sequestration in vacuoles and thereby preventing arsenic transfer to grain. Rice plants grown at higher temperatures had more adsorbed arsenic per unit of iron plaque (measured as [As]/[Fe]), indicating temperature may impact arsenic sorption to root plaque. We present evidence that increased soil mobilization of arsenic was the driving factor responsible for increased arsenic uptake into rice grain. Transpiration, which can increase arsenic transport to roots, was also heightened with elevated temperature but appeared to play a secondary role. Our system had low soil arsenic concentrations typical for California. Our findings highlight that elevated growing temperatures may increase the risk of dietary arsenic exposure in rice systems that were previously considered low risk.

Effects of Dissolved Organic Matter on the Bioavailability of Heavy Metals During Microbial Dissimilatory Iron Reduction: A Review

Dissolved organic matter (DOM), a type of mixture containing complex structures and interactions, has important effects on environmental processes such as the complexation and interface reactions of soil heavy metals. Furthermore, microbial dissimilatory iron reduction (DIR), a key process of soil biogeochemical cycle, is closely related to the migration and transformation of heavy metals and causes the release of DOM by carbon-ferrihydrite associations. This chapter considers the structural properties and characterization techniques of DOM and its interaction with microbial dissimilated iron. The effect of DOM on microbial DIR is specifically manifested as driving force properties, coprecipitation, complexation, and electronic shuttle properties. The study, in addition, further explored the influence of pH, microorganisms, salinity, and light conditions, mechanism of DOM and microbial DIR on the toxicity and bioavailability of different heavy metals. The action mechanism of these factors on heavy metals can be summarized as adsorption coprecipitation, methylation, and redox. Based on the findings of the review, future research is expected to focus on: (1) The combination of DOM functional group structure analysis with high-resolution mass spectrometry technology and electrochemical methods to determine the electron supply in the mechanism of DOM action on DIR; (2) Impact of DOM on differences in structure and functions of plant rhizosphere in heavy metal contaminated soil; and (3) Bioavailability of DOM-dissociative iron-reducing bacteria-heavy metal ternary binding on rhizosphere heavy metals under dynamic changes of water level from the perspective of the differences in DOM properties, such as polarity, molecular weight, and functional group.

Iron Stable Isotopes in Bulk Soil and Sequential Extracted Fractions Trace Fe Redox Cycling in Paddy Soils

In paddy soils, iron (Fe) forms are highly influenced by the seasonal redox changes and leave detectable isotope signals because of fractionation between different Fe forms. Here, we present Fe concentrations and Fe isotope compositions (expressed as δ⁵⁶Fe values) in a paddy soil profile from Suzhou, China. Light Fe isotopes were enriched in two iron-accumulation layers (Br3 and G1) with high Fe concentrations. In particular, large shifts in both Fe concentrations and δ⁵⁶Fe values were found at the Br2 and Br3 boundaries, showing fast and efficient transformation between these horizons. With sequential extraction, we show that Fe isotopes in the short-range-ordered Fe minerals and crystalline Fe oxides were lighter than those in the residual silicate minerals. Iron enriched in light isotopes was leached from the Ap horizon and subsequently moved to Br horizon, quickly precipitating there as Fe oxides.