Water management impacts the soil microbial communities and total arsenic and methylated arsenicals in rice grains

Arsenic methylation and microbial communities in paddy soils under alternating anoxic and oxic conditions

Arsenic (As) methylation in soils affects the environmental behavior of As, excessive accumulation of dimethylarsenate (DMA) in rice plants leads to straighthead disease and a serious drop in crop yield. Understanding the mobility and transformation of methylated arsenic in redox-changing paddy fields is crucial for food security. Here, soils including un-arsenic contaminated (N-As), low-arsenic (L-As), medium-arsenic (M-As), and high-arsenic (H-As) soils were incubated under continuous anoxic, continuous oxic, and consecutive anoxic/oxic treatments respectively, to profile arsenic methylating process and microbial species involved in the As cycle. Under anoxic-oxic (A-O) treatment, methylated arsenic was significantly increased once oxygen was introduced into the incubation system. The methylated arsenic concentrations were up to 2-24 times higher than those in anoxic (A), oxic (O), and oxic-anoxic (O-A) treatments, under which arsenic was methylated slightly and then decreased in all four As concentration soils. In fact, the most plentiful arsenite S-adenosylmethionine methyltransferase genes (arsM) contributed to the increase in As methylation. Proteobacteria (40.8%-62.4%), Firmicutes (3.5%-15.7%), and Desulfobacterota (5.3%-13.3%) were the major microorganisms related to this process. These microbial increased markedly and played more important roles after oxygen was introduced, indicating that they were potential keystone microbial groups for As methylation in the alternating anoxic (flooding) and oxic (drainage) environment. The novel findings provided new insights into the reoxidation-driven arsenic methylation processes and the model could be used for further risk estimation in periodically flooded paddy fields.

Phase transformation of schwertmannite in paddy soil under different water management regimes and its impact on the migration of arsenic in soil

Schwertmannite (Sch) holds a great promise as an iron material for remediating Arsenic (As)-contaminated paddy soils, due to its extremely high immobilization capacities for both arsenate [As(V)] and arsenite [As(III)]. However, there is still limited knowledge on the mineral phase transformation of this metastable iron-oxyhydroxysulfate mineral in paddy soils, particularly under different water management regimes including aerobic, intermittent flooding, and continuous flooding, and how its phase transformation impacts the migration of As in paddy soils. In this study, a membrane coated with schwertmannite was first developed to directly reflect the phase transformation of bulk schwertmannite applied to paddy soils. A soil incubation experiment was then conducted to investigate the mineral phase transformation of schwertmannite in paddy soils under different water management regimes and its impact on the migration of As in paddy soil. Our findings revealed that schwertmannite can persist in the paddy soil for 90 days in the aerobic group, whereas in the continuous flooding and intermittent flooding groups, schwertmannite transformed into goethite, with the degree or rate of mineral phase transformation being 5% Sch >1% Sch > control. These results indicated that water management practices and the amount of schwertmannite applied were the primary factors determining the occurrence and degree of mineral transformation of schwertmannite in paddy soil. Moreover, despite undergoing phase transformation, schwertmannite still significantly reduced the porewater As (As(III) and As(V)), and facilitated the transfer of non-specifically adsorbed As (F1) and specifically adsorbed As (F2) to amorphous iron oxide-bound As (F3), effectively reducing the bioavailability of soil As. These findings contribute to a better understanding of the mineralogical transformation of schwertmannite in paddy soils and the impact of mineral phase transformation on the retention of As in soil, which carry important implications for the application of schwertmannite in remediating As-contaminated paddy soils.

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

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

Pathways and contributions of sulfate reducing-bacteria to arsenic cycling in landfills

Sulfate-reducing bacteria (SRB) are generally found in sanitary landfills and play a role in sulfur (S) and metal/metalloid geochemical cycling. In this study, we investigated the influence of SRB on arsenic (As) metabolic pathways in refuse-derived cultures. The results indicated that SRB promote As(III) methylation and are beneficial for controlling As levels. Heterotrophic and autotrophic SRB showed significant differences during As cycling. In heterotrophic SRB cultures, the As methylation rate increased with As(III) concentration in the medium and reached a peak (85.1%) in cultures containing 25 mg L-1 As(III). Moreover, 4.0-12.6% of SO42- was reduced to S2-, which then reacted with As(III) to form realgar (AsS). In contrast, autotrophic SRB oxidized As(III) to less toxic As(V) under anaerobic conditions. Heterotrophic arsM-harboring SRB, such as Desulfosporosinus, Desulfocurvibacter, and Desulfotomaculum, express As-related genes and are considered key genera for As methylation in landfills. Thiobacillus are the main autotrophic SRB in landfills and can derive energy by oxidizing sulfur compounds and metal(loid)s. These results suggest that different types of SRB drive As methylation, redox reaction, and mineral formation in landfills. These study findings have implications for the management of As pollutants in landfills and other contaminated environments.

Controlling factors of heavy metal(loid) accumulation in rice: Main and interactive effects

Identifying the key determinants of heavy metal(loid) accumulation in rice and quantifying their contributions are critical for precise prediction of heavy metal(loid) concentrations in rice and the formulation of effective pollution control strategies. The accumulation of heavy metal(loid)s in rice can be influenced by both natural and anthropogenic factors, which may interact with each other. However, distinguishing the independent roles (main effects) from interactive effects and quantifying their impacts separately pose challenges. To address this knowledge gap, we employed TreeExplainer-based SHAP and random forest algorithms in this study to quantitatively estimate the primary influencing factors and their main and interactive effects on heavy metal(loid)s in rice. Our findings reveal that soil cadmium (SCd) and rice cultivation time (C_TIME) were the primary contributors to rice cadmium (RCd) and rice arsenic (RAs), respectively. Soil lead (SPb) and sampling distances from roads significantly contributed to rice lead (RPb). Additionally, we identified significant interactive effects of SCd and C_TIME, C_TIME and RCd, and RCd and rice variety on RCd, RAs, and RPb, respectively, emphasizing their significance. These insights are pivotal in improving the accuracy of heavy metal(loid) concentration predictions in rice and offering theoretical guidance for the formulation of pollution control measures.

Exploring metal(loid)s dynamics and bacterial community shifts in contaminated paddy soil: Impact of MgO-laden biochar under different water conditions

In this study, a soil incubation experiment was conducted to explore the influence MgO-treated corn straw biochar (MCB) on the bioavailability and chemical forms of cadmium (Cd), lead (Pb), and arsenic (As), alongside the impact on the bacterial community within paddy soil subjected to both flooded and non-flooded conditions. Raw corn straw biochar (CB) served as the unmodified biochar control, aiding in the understanding of the biochar's role within the composite. The results showed that even at a minimal concentration of 0.5 %, MCB exhibited higher effectiveness in reducing the bioavailability of Pb and Cd compared to 1 % CB. In non-flooded conditions, 0.5 % MCB reduced the bioavailable Pb and Cd by 99.7 % and 87.4 %, respectively, while NaH2PO4-extracted As displayed a 14.5 % increase. With increasing MCB concentrations (from 0.5 % to 1.5 %), soil pH, DOC, EC, available phosphorus, and bioavailable As increased, while bioavailable Pb and Cd exhibited declining tendencies. Flooding did not notably alter MCB's role in reducing Pb and Cd bioavailability, yet it systematically amplified As release. Heavy metal fractions extracted by acetic acid increased in the MCB groups under flooding conditions, especially for As. The inclusion of 0.5 % MCB did not noticeably affect bacterial diversity, whereas higher doses led to reduced diversity and substantial changes in community composition. Specifically, the groups with MCB showed an increase in the Bacteroidetes and Proteobacteria phyla, accompanied by a decrease in Acidobacteria. These alterations were primarily attributed to the increased pH and EC resulting from MgO hydrolysis. Consequently, for Pb/Cd stabilization and soil bacterial diversity, a low dosage of MgO-treated biochar is recommended. However, caution is advised when employing MgO-treated biochar in soils with elevated arsenic levels, particularly under flooded conditions.

Evaluation of water management on arsenic methylation and volatilization in arsenic-contaminated soils strengthened by bioaugmentation and biostimulation

Arsenic (As) fate in paddy fields has been one of the most significant current issues due to the strong As accumulation potential of rice plants under flooded conditions. However, no attempt was done to explore As methylation and volatilization under non-flooded conditions. Herein, we investigated the effects of water management on As methylation and volatilization in three arsenic-contaminated soils enhanced by biostimulation with straw-derived organic matter and bioaugmentation with genetic engineered Pseudomonas putida KT2440 (GE P. putida). Under flooded conditions, the application of biochar (BC), rice straw (RS) and their combination (BC+RS) increased total As in porewater. However, these effects were greatly attenuated under non-flooded conditions. Compared with RS amendment alone, the combination of GE P. putida and RS further promoted the As methylation and volatilization, and the promotion percentage under non-flooded conditions were significantly higher than that under flooded conditions. The combined GE P. putida and RS showed the highest efficiency in As methylation (88 µg/L) and volatilization (415.4 µg/(kg·year)) in the non-flooded soil with moderate As contamination. Finally, stepwise multiple linear regression analysis presented that methylated As, DOC and pH in porewater were the most important factors contributing to As volatilization. Overall, our findings suggest that combination of bioaugmentation with GE P. putida and biostimulation with RS/BC+RS is a potential strategy for bioremediation of arsenic-contaminated soils by enhancing As methylation and volatilization under non-flooded conditions.

Arsenite S-Adenosylmethionine Methyltransferase Is Responsible for Antimony Biomethylation in Nostoc sp. PCC7120

Antimony (Sb) biomethylation is an important but uninformed process in Sb biogeochemical cycling. Methylated Sb species have been widely detected in the environment, but the gene and enzyme for Sb methylation remain unknown. Here, we found that arsenite S-adenosylmethionine methyltransferase (ArsM) is able to catalyze Sb(III) methylation. The stepwise methylation by ArsM forms mono-, di-, and trimethylated Sb species. Sb(III) is readily coordinated with glutathione, forming the preferred ArsM substrate which is anchored on three conserved cysteines. Overexpressing arsM in Escherichia coli AW3110 conferred resistance to Sb(III) by converting intracellular Sb(III) into gaseous methylated species, serving as a detoxification process. Methylated Sb species were detected in paddy soil cultures, and phylogenetic analysis of ArsM showed its great diversity in ecosystems, suggesting a high metabolic potential for Sb(III) methylation in the environment. This study shows an undiscovered microbial process methylating aqueous Sb(III) into the gaseous phase, mobilizing Sb on a regional and even global scale as a re-emerging contaminant.

Arbuscular mycorrhizal symbiosis alleviates arsenic phytotoxicity in flooded Iris tectorum Maxim. dependent on arsenic exposure levels

Arsenic (As) pollution in wetlands has emerged as a serious global concern, posing potential threat to the growth of wetland plants. Arbuscular mycorrhizal fungi (AMF) can alleviate As phytotoxicity to host plants, but their ecological functions in wetland plants under flooding conditions remain largely unknown. Thus, a pot experiment was conducted using Rhizophagus irregularis and Iris tectorum Maxim. exposed to light (15 and 30 mg/kg As) and high (75 and 100 mg/kg As) levels of As, to investigate the intrinsic mechanisms underlying the effects of mycorrhizal inoculation on plant As tolerance under flooding conditions. The mycorrhizal colonization rates ranged from 31.47 ± 3.92 % to 60.69 ± 5.58 %, which were higher than the colonization rate (29.55 ± 13.60%) before flooding. AMF significantly increased biomass of I. tectorum under light As levels, together with increased phosphorus (P) and As uptake. Moreover, expression of arsenate reductase gene RiarsC and a trace of dimethylarsenic (1.87 mg/kg in shoots) were detected in mycorrhizal plants, suggesting As transformation and detoxification by AMF exposed to light levels of As. However, under high As levels, AMF inhibited As translocation from roots to shoots, and facilitated the formation of iron plaque. The immobilized As concentrations in iron plaque of mycorrhizal plants were respectively 1133.68 ± 179.17 mg/kg and 869.11 ± 248.90 mg/kg at 75 and 100 mg/kg As addition level, both significantly higher than that in non-inoculated plants. Irrespective of As exposure levels, mycorrhizal symbiosis decreased soil As bioavailability. Overall, the study provides insights into the alleviation of As phytotoxicity in natural wetland plants through mycorrhizal symbiosis, and potentially indicates function diversity of AMF under flooding conditions and As stress, supporting the subsequent phytoremediation and restoration of As-contaminated wetlands.

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

IMPORTANCE

In waterlogged soils, iron plaque forms a reactive barrier between the root and soil, collecting phosphate and metals such as arsenic and cadmium. It is well established that iron-reducing bacteria solubilize iron, releasing these associated elements. In contrast, microbial roles in plaque formation have not been clear. Here, we show that there is a substantial population of iron oxidizers in plaque, and furthermore, that these organisms (Sideroxydans and Gallionella) are distinguished by genes for plant colonization and nutrient fixation. Our results suggest that iron-oxidizing and iron-reducing bacteria form and remodel iron plaque, making it a dynamic system that represents both a temporary sink for elements (P, As, Cd, C, etc.) as well as a source. In contrast to abiotic iron oxidation, microbial iron oxidation results in coupled Fe-C-N cycling, as well as microbe-microbe and microbe-plant ecological interactions that need to be considered in soil biogeochemistry, ecosystem dynamics, and crop management.

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.

Methylation of arsenic in rice: Mechanisms, factors, and mitigation strategies

Arsenic contamination in rice poses a significant health risk to rice consumers across the globe. This review examines the impact of water source and type on the speciation and methylation of arsenic in rice. The review highlights that groundwater used for irrigation in arsenic-affected regions can lead to higher total arsenic content in rice grains and lower proportions of methylated arsenic species. The methylation of As in rice is influenced by microbial activity in groundwater, which can methylate arsenic that is taken up by rice plants. Reclaimed water irrigation can also increase the risk of arsenic accumulation in rice crops, although the use of organic amendments and proper water management practices can reduce arsenic accumulation. Different water management regimes, such as continuous flooding irrigation, alternate wetting and drying, aerobic rice cultivation, and subsurface drip irrigation, can affect the speciation and methylation of As in rice. Continuous flooding irrigation reduces methylation of As due to anaerobic conditions, while alternate wetting and drying and aerobic rice cultivation promote methylation by creating aerobic conditions that stimulate the activity of arsenic-methylating microorganisms. Subsurface drip irrigation reduces total arsenic content in rice grains and increases the proportion of less toxic methylated arsenic species. The review also discusses the complex mechanisms of As-methylation and transport in rice, emphasizing the importance of understanding these mechanisms to develop strategies for reducing arsenic uptake in rice plants and mitigating health risks. The review addresses the impact of water source and type on arsenic speciation and methylation in rice and highlights the need for proper water management and treatment measures to ensure the safety of the food supply as well as aiding future research and policies to reduce health risks from rice consumption. The critical information gaps that this review addresses include the specific effects of different water management regimes on As-methylation, the role of microbial communities in groundwater in As-methylation, and the potential risks associated with the use of reclaimed water for irrigation.

l-Glutamate Seed Priming Enhances 2-Acetyl-1-pyrroline Formation in Fragrant Rice Seedlings in Response to Arsenite Stress

2-Acetyl-1-pyrroline (2-AP) is a fragrance compound and flavor in fragrant rice whose precursors are generally glutamate (Glu) and proline (Pro). Our previous study revealed that exogenous Glu enhanced the arsenic (As) tolerance in fragrant rice by improving the ascorbic acid-glutathione cycle and the Pro content in roots. However, less is known about how Glu is involved in 2-AP biosynthesis in fragrant rice under As stress. Herein, a hydroponic experiment of L-Glu seed priming with 0, 100, and 500 μM l-glutamic acid solutions was conducted with two fragrant rice varieties. After that, the 10-day-old seedlings were cultured under 0 and 100 μM arsenite stress for 10 d. Results showed that the 2-AP and Pro contents were increased by 18-30% and 21-78% under As100 μM-Glu100 μM treatment in comparison to the control As100 μM to Glu0 μM, while the activities of pyrroline-5-carboxylate synthetase (P5CS) and proline dehydrogenase (ProDH) were increased by 19-46% and 3-19%, respectively. Furthermore, the 2-AP, Pro contents, and P5CS activity were correlated positively. Correspondingly, a significant abundance of differential expressed metabolites (18) and differential expressed genes (26) was observed in amino acid metabolism and glutathione metabolism pathways. In addition, several essential genes were verified and grouped into the pathways of glutathione metabolism, proline, and arginine metabolism with antioxidant defense system to comodulate 2-AP biosynthesis and stress detoxification. Therefore, the Glu seed priming treatment had a positive impact on the 2-AP biosynthesis of fragrant rice under 100 μM arsenite toxicity.

Alternate wetting and drying water management can reduce phosphorus availability under lowland rice cultivation irrespective of nitrogen level

The limited availability of phosphorus (P) in the soil, which is affected by soil moisture, has a significant impact on crop production. However, we still do not fully understand how water management and nitrogen (N) addition affect the availability of P in paddy soil. An evaluation of the effects of two water management strategies that is continuous flooding (CF) and alternate wetting and drying (AWD) irrigation along with various nitrogenous fertilizer addition rates (equivalent to 0, 100%, 133%, and 166% recommended dose of N addition) on P availability in paddy soil took place over the course of a 2-year field experiment. The results showed that water management had a significant influence on ferrous iron, microbial biomass P, and soil-available P. However, the addition of N did not affect the availability of P in the soil. When N was added at various rates, AWD consistently reduced the amount of soil-available P compared to CF. This was primarily because AWD increased microbial biomass, which immobilized P and decreased the content of ferrous iron. As a result, the soil's ability to absorb P increased, leading to a decrease in the amount of P available. In conclusion, AWD decreases the amount of available P in paddy soil compared to CF.

A combination of organic fertilizers partially substitution with alternate wet and dry irrigation could further reduce greenhouse gases emission in rice field

Alternate wet and dry (AWD) irrigation and organic fertilizers substitution (OFS) have contrasting effects on CH4 and N2O emissions in rice cultivation. Combining these two practices may be feasible for simultaneous reduction of CH4 and N2O emission from paddy. Hence, we conducted a two-year field experiment to explore the reduction of greenhouse gases under the combination of AWD and OFS. The field experiment which was designed with two irrigation methods (continuous flooding (CF) irrigation and AWD irrigation), and five nitrogen regimes (N0, N135, and N180 represent 0, 135, and 180 kg N ha-1, respectively, ON25 and ON50 represent 25% and 50% OFS for inorganic fertilizer, respectively). The results showed a single-peak emission for CH4 fluxes during the whole rice growing season in all water and nitrogen treatments while the N2O fluxes peak only observed during tillering period with AWD irrigation. AWD irrigation and OFS showed a limited reduction in global warming potential (GWP). These were owing to that AWD irrigation reduced 38.3% CH4 emissions while increase 145.9% N2O emissions when compared to CF irrigation, and the low rate (25%) OFS only reduced CH4 emission by 29.4% while high rate (50%) only reduce N2O emission by 38.8% when compared to conventional inorganic nitrogen fertilizer (N180). Combined AWD and ON25 could maximize the reduction in GWP and yield-scaled GWP, which were reduce 58.0% and 52.5%, respectively, compare to the conventional water and nitrogen management (CF and N180). Furthermore, the structural equation modelling (SEM) indicated that the soil dissolved organic carbon (DOC) and rice aboveground biomass showed a significant positive effect on CH4 fluxes while soil NH4+ with a negative effect, and the soil NH4+, nitrification potential, denitrification potential significant affected N2O fluxes with a positive effect while DOC with a negative effect. These results investigated that 25% OFS rate for inorganic fertilizer could further reduce warming potential in AWD irrigation rice field.

Nano zero-valent iron enhances the absorption and transport of chromium in rice (Oryza sativa L.): Implication for Cr risks management in paddy fields

Chromium (Cr) accumulating in soil caused serious pollution to cultivated land. At present, nano zero-valent iron (nZVI) is considered to be a promising remediation material for Cr-contaminated soil. However, the nZVI impact on the behavior of Cr in the soil-rice system under high natural geological background value remains unknown. We studied the effects of nZVI on the migration and transformation of Cr in paddy soil-rice by pot experiment. Three different doses of nZVI (0, 0.001 % and 0.1 % (w/w)) treatments and one dose of 0.1 % (w/w) nZVI treatment without plant rice were set up. Under continuous flooding conditions, nZVI significantly increased rice biomass compared with the control. At the same time, nZVI significantly promoted the reduction of Fe in the soil, increased the concentration of oxalate Fe and bioavailable Cr, then facilitated the absorption of Cr in rice roots and the transportation to the aboveground part. In addition, the enrichment of Fe(III)-reducing bacteria and sulfate-reducing bacteria in soil provided electron donors for Cr oxidation, which helps to form bioavailable Cr that is easily absorbed by plants. The results of this study can provide scientific basis and technical support for the remediation of Cr -polluted paddy soil with high geological background.

Organic fertilization integrated with water management to remediate As and Cd contamination in a paddy soil

Soil heavy metal pollution is the main risk for sustainable agriculture, especially the combination of As and Cd pollution in paddy fields which may lead to the superimposed accumulation in rice. There is an urgent need for environmental-friendly and cost-effective strategies to remediate the contamination of As and Cd in soils. In this work, a pot culture experiment was conducted in a As and Cd polluted paddy soil to explore the effects of organic fertilization (OF) and two water managements (continuous flooding, CF; intermittent irrigation, II) on the fractionation of As and Cd in soil, and the uptake of As and Cd by rice. The results showed that OF integrated with intermittent irrigation performed best in reducing the contents of As and Cd in rice grains by 58.9 % and 69.3 %, respectively, under compound pollution. The significant conversion of available As and Cd to stable species (specifically adsorbed and Fe-Mn/Al oxide bound) under OF + II were supported by the changes in an array of soil attributes such as pH, Eh, soluble Fe and dissolved organic carbon (DOC). Intermittent irrigation was more conducive to the accumulation of As outside the roots, and Fe-plaque prevented As uptake by roots and the translocation to shoots. While more accumulation of Fe-plaque along with Cd on root surface induced by continuous flooding is helpful for depressed assimilation of Cd by rice. Considering the combined contamination of As and Cd polluted in paddy soils, a management approach was proposed based on intermittent irrigation and application of organic fertilizer at the rate of 0.1 % (∼ 2.3 t/ha) in two phases (two weeks before planting or drainage). Organic fertilization will hold great promise in restoring polluted soils and maintaining soil health via suppressing the lability of heavy metals and providing nutrients.

Microbial genome (Illumina MiSeq) sequencing of drinking water treatment residuals to evaluate compatibility with environmental applications

The clarification of drinking water leads to the production of large quantities of water treatment residuals (WTRs). DNA was extracted from six WTR samples collected from water treatment plants within the UK to compare their bacterial communities and examine whether factors such as coagulant usage (aluminium versus iron salt), the type of water source (reservoir or river), or leachable chemical composition influence these communities. Bacterial 16S variable region 4 (V4) was amplified and sequenced using Illumina MiSeq sequencing. The most abundant phyla in WTR samples were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes, collectively representing 92.77-97.8% of the total bacterial sequences. Statistical analysis of microbial profiles indicated that water source played a significant role in microbial community structure, diversity, and richness, however coagulant type did not. PERMANOVA analysis showed that no single chemical variable (pH, organic matter, or extractable element concentration) influenced microbial composition significantly; however, canonical correspondence analysis of WTR microbiomes yielded a model using all these variables that could be used to explain variations in microbial community structures of WTRs (p < 0.05). No common, potentially toxic cyanobacteria, or related pathogens of concern were found. Analysis with PICRUSt showed that WTRs all had similar predicted microbial functional profiles. Overall, the results indicate that WTRs analysed in this study are unlikely to pose any threat to soil microbial community structure when applied to land as a soil conditioner or enhancer and may help to enhance the soil microbial community.

Regulatory Mechanisms Underlying Arsenic Uptake, Transport, and Detoxification in Rice

Arsenic (As) is a metalloid environmental pollutant ubiquitous in nature that causes chronic and irreversible poisoning to humans through its bioaccumulation in the trophic chain. Rice, the staple food crop for 350 million people worldwide, accumulates As more easily compared to other cereal crops due to its growth characteristics. Therefore, an in-depth understanding of the molecular regulatory mechanisms underlying As uptake, transport, and detoxification in rice is of great significance to solving the issue of As bioaccumulation in rice, improving its quality and safety and protecting human health. This review summarizes recent studies on the molecular mechanisms of As toxicity, uptake, transport, redistribution, regulation, and detoxification in rice. It aims to provide novel insights and approaches for preventing and controlling As bioaccumulation in rice plants, especially reducing As accumulation in rice grains.

Remediating flooding paddy soils with schwertmannite greatly reduced arsenic accumulation in rice (Oryza sativa L.) but did not decrease the utilization efficiency of P fertilizer

Planting rice (Oryza sativa L.) in As-contaminated paddy soils can lead to accumulation of arsenic (As) in rice grains, while the application of phosphorus (P) fertilizers during rice growth may aggravate the accumulation effect. However, remediating flooding As-contaminated paddy soils with conventional Fe(III) oxides/hydroxides can hardly achieve the goals of effectively reducing grain As and maintaining the utilization efficiency of phosphate (Pi) fertilizers simultaneously. In the present study, schwertmannite was proposed to remediate flooding As-contaminated paddy soil because of its strong sorption capacity for soil As, and its effect on the utilization efficiency of Pi fertilizer was investigated. Results of a pot experiment showed that Pi fertilization along with schwertmannite amendment was effective to reduce the mobility of As in the contaminated paddy soil and meanwhile increase soil P availability. The schwertmannite amendment along with Pi fertilization reduced the content of P in Fe plaque on rice roots, compared with the corresponding amount of Pi fertilizer alone, which can be attributed to the change in mineral composition of Fe plaque mainly induced by schwertmannite amendment. Such reduction in P retention on Fe plaque was beneficial for improving the utilization efficiency of Pi fertilizer. In particular, amending flooding As-contaminated paddy soil with schwertmannite and Pi fertilizer together has reduced the content of As in rice grains from 1.06 to 1.47 mg/kg to only 0.38-0.63 mg/kg and significantly increased the shoot biomass of rice plants. Therefore, using schwertmannite to remediate flooding As-contaminated paddy soils can achieve the dual goals of effectively reducing grain As and maintaining the utilization efficiency of P fertilizers.

Decreasing arsenic in rice: Interactions of soil sulfate amendment and water management

Accumulation of inorganic arsenic (iAs) and dimethylarsenate (DMA) in rice threatens human health and rice yield, respectively. We studied the yet unclear interactions of soil sulfate amendment and water management for decreasing As accumulation in rice grain in a pot experiment. We show that soil sulfate amendment (+200 mg S/kg soil) decreased grain iAs by 44% without clearly increasing grain DMA under intermittent flooding from booting stage to maturation. Under continuous flooding during this period, sulfate amendment decreased grain iAs only by 25% but increased grain DMA by 68%. The mechanisms of sulfate amendment effects on grain iAs were not explained by porewater composition or in-planta As sequestration but were allocated to the rhizosphere. Grain iAs closely correlated with As in the root iron-plaque (r = 0.92) which was effectively decreased by sulfate amendment and may have acted as an iAs source for rice uptake. Although both sulfate amendment and intermittent flooding substantially increased porewater DMA concentrations, it was the continuous flooding, irrespective of sulfate amendment, that resulted in rice straighthead disease with 47-55% less yield and 258-320% more DMA in grains than intermittent flooding. This study suggests that combining soil sulfate amendment and intermittent flooding can help to secure the quantity and quality of rice produced in As-affected areas. Our results also imply the key role of rhizosphere processes in controlling both iAs and DMA accumulation in rice which should be elucidated in the future.

Active microbial arsenic methylation in saline-alkaline paddy soil

Seawater rice has been cultivated to ensure food security. The salt-tolerant rice strains are resistant to saline and alkali but may be vulnerable to elevated arsenic (As) near coastal regions. Herein, the saline-alkaline paddy soil was incubated with natural irrigation river for three months to explore the mobility and transformation of As. The incubation results showed that 65 ± 1.2 % solid-bound As(V) was reduced to As(III) within two weeks with the release of As(III) to porewater. The dissolved As(III) was methylated after two weeks, resulting in dimethyl arsenate (DMA) as the dominant As species (87 %-100 %). The elevated As methylation was attributed to the most abundant arsenite methyltransferase gene (arsM) (4.1-10.4 × 10⁷/g dry soil), over three orders of magnitude higher than As redox-related genes. The analysis of arsM operational taxonomic units (OTUs) suggested the highest sequence similarity to Proteobacteria (25.7-39.5 %), Actinobacteria (24.9-30.5 %), Gemmatimonadetes (7.5-11.9 %), Basidiomycota (5.1-12.5 %), and Chloroflexi (4.1-8.7 %). Specifically, Chloroflexi and Actinobacteria are salt-tolerant bacteria, probably responsible for As methylation. The As in grain was within a safe regulatory level, and the dominance of methylated As in porewater did not enhance its accumulation in rice grains.

Multiple-functionalized biochar affects rice yield and quality via regulating arsenic and lead redistribution and bacterial community structure in soils under different hydrological conditions

Rice grown in soils contaminated with arsenic (As) and lead (Pb) can cause lower rice yield and quality due to the toxic stress. Herein, we examined the role of functionalized biochars (raw phosphorus (P)-rich (PBC) and iron (Fe)-modified P-rich (FePBC)) coupled with different irrigation regimes (continuously flooded (CF) and intermittently flooded (IF)) in affecting rice yield and accumulation of As and Pb in rice grain. Results showed that FePBC increased the rice yield under both CF (47.4%) and IF (19.6%) conditions, compared to the controls. Grain As concentration was higher under CF (1.94-2.42 mg kg^-1) than IF conditions (1.56-2.31 mg kg^-1), whereas the concentration of grain Pb was higher under IF (0.10-0.76 mg kg^-1) than CF (0.12-0.48 mg kg^-1) conditions. Application of PBC reduced grain Pb by 60.1% under CF conditions, while FePBC reduced grain As by 12.2% under IF conditions, and increased grain Pb by 2.9 and 6.6 times under CF and IF conditions, respectively, compared to the controls. Therefore, application of the multiple-functionalized biochar can be a promising strategy for increasing rice yield and reducing the accumulation of As in rice grain, particularly under IF conditions, whereas it is inapplicable for remediation of paddy soils contaminated with Pb.

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

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

Multiple geochemical and microbial processes regulated by redox and organic matter control the vertical heterogeneity of As and Cd in paddy soil

The heterogeneity of arsenic (As) and cadmium (Cd) in paddy soils seriously hinders the assessment of contamination status and prediction of rice uptake. Their vertical patterns across different environmental conditions and the underlying mechanisms remain largely unexplored. In this study, maximum vertical differences of bioavailable As and Cd within 0-30 cm depth in paddy soils were 4.1-fold and four orders of magnitude, respectively. The vertical patterns of As and Cd followed the vertical redox gradient in long-term reduced paddies, but were shaped by the vertical pH gradient derived from acidic wastewater irrigation in partly oxidized soils. Iron(III)- and sulfate-reducing bacteria played key roles in the formation of vertical pH gradient and the immobilization of As and Cd by iron (hydr)oxides and sulfides under varied redox conditions. Soil redox and organic matter determined the transition between these two mechanisms via regulating microbial iron(III) and sulfate reduction processes. The work proposes that soil vertical As and Cd patterns directly affect the accumulation of As and Cd in different rice cultivars with different vertical root patterns. This is the first study elucidating the controlling mechanisms governing the vertical As and Cd patterns in paddy fields, providing important references to identify, manage and remediate contaminated paddy fields.

A manganese-oxidizing bacterium-Enterobacter hormaechei strain DS02Eh01: Capabilities of Mn(II) immobilization, plant growth promotion and biofilm formation

While biogenic Mn oxides (BioMnO_x) generated by Mn(II)-oxidizing bacteria (MOB) have attracted increasing attention, a MOB strain isolated from Mn-polluted sediments was identified and assigned as Enterobacter hormaechei DS02Eh01. Its Mn(II) immobilization activity, plant growth-promoting traits, and biofilm formation capability were investigated. The results showed that strain DS02Eh01 was found to be able to tolerate Mn(II) up to 122 mM. The strain immobilized Mn(II) in aquatic media mainly through extracellular adsorption, bio-oxidation and pH-induced precipitation as well as manganese oxidation. DS02Eh01-derived BioMnO_x are negatively charged and have a larger specific surface area (86.70 m²/g) compared to the previously reported BioMnO_x. The strain can immobilize Mn(II) at extreme levels, for instance, when it was exposed to 20 mM Mn(II), about 59% of Mn(II) were found immobilized and 17% of Mn(II) were converted to MnO_x. The SEM and TEM observation revealed that the DS02Eh01-derived BioMnO_x were aggregates doped with granules and microbial pellets. The precipitated Mn(II) and the Mn(III)/Mn(IV) oxides co-existed in BioMnO_x, in which Mn(II) and Mn(IV) were found dominant with Mn(II) accounting for 49.6% and Mn(IV) accounting for 41.3%. DS02Eh01 possesses plant growth-promoting traits and biofilm formation capacity even under Mn(II) exposure. Mn(II) exposure at 5 mM was found to stimulate strain DS02Eh01 to form biofilms, from which, the extracted EPS was mainly composed of aromatic proteins. This study reveals that E. hormaechei strain DS02Eh01 possesses the potential in environmental ecoremediation via coupling processes of macrophytes extraction, biochemical immobilization and biosorption.

Microbial mediated reaction of dimethylarsinic acid in wetland water and sediments

The biogeochemical reactions of dimethylarsinic acid (DMAs(V)) were investigated using simulated wetland systems in a laboratory. DMAs(V) was injected into the wetland water, and the As concentrations in the water, plants, and sediments were monitored. Aqueous and solid-phase As speciation was evaluated, and the results revealed that the DMAs(V) was completely transported to the sediments and plants. X-ray absorption spectroscopic measurement of the As in the sediment revealed that approximately 85-95% of As existed as inorganic As species, demonstrating the important role of microorganisms in the biogeochemical reaction of DMAs(V). The influences of microbes were further investigated in smaller batches under aerobic and anaerobic conditions. The microbial batch results showed that DMAs(V) demethylation reduced the total aqueous As concentration, demonstrating that As(V) has higher affinity to wetland sediment than DMAs(V). The redox conditions were also revealed as an important controlling factor of the As reaction and, under anaerobic conditions, we observed the presence of the most toxic form of inorganic As(III) in the aqueous phase. Although this study reports one example from a specific wetland, the important roles of the redox conditions and microbial influences were identified from the comprehensive analysis of As speciation and mass balance.

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

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

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Soil microbiomes harbour unparalleled functional and phylogenetic diversity. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. As methylation was proposed to be catalysed by sulfate-reducing bacteria. However, to date, there are no available anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harbouring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.

Effects and Mechanisms of Copper Oxide Nanoparticles with Regard to Arsenic Availability in Soil-Rice Systems: Adsorption Behavior and Microbial Response

Copper oxide nanoparticles (CuO NPs) are widely used as fungicides in agriculture. Arsenic (As) is a ubiquitous contaminant in paddy soil. The present study was focused on the adsorption behavior of CuO NPs with regard to As as well as the characteristics of the microbial community changes in As-contaminated soil-rice systems in response to CuO NPs. The study found that CuO NPs could be a temporary sink of As in soil; a high dose of CuO NPs promoted the release of As from crystalline iron oxide, which increased the As content in the liquid phase. The study also found that the As bioavailability changed significantly when the dose of CuO NPs was higher than 50 mg kg^-1 in the soil-rice system. The addition of 100 mg kg^-1 CuO NPs increased the microbial diversity and the abundance of genes involved in As cycling, decreased the abundance of Fe(III)-reducing bacteria and sulfate-reducing genes, and decreased As accumulation in grains. Treatment with 500 mg kg^-1 CuO NPs increased the abundance of Fe(III)-reducing bacteria and sulfate-reducing genes, decreased Fe plaques, and increased As accumulation in rice. The adverse effects of CuO NPs on crops and associated risks need to be considered carefully.

Soil ridge cultivation maintains grain As and Cd at low levels and inhibits As methylation by changing arsM-harboring bacterial communities in paddy soils

The simultaneous mitigation of toxic arsenic (As) and cadmium (Cd) in rice grain remains a global challenge. The over-accumulation of husk dimethylarsinic acid (DMAs) induces the rice straight-head disease, which threatens rice production worldwide. In this study, we investigated various soil ridge height treatments with Eh ranging from - 225-87 mV and pH ranging from 6.3 to 4.1. Soil ridge cultivation can maintain grain As and Cd at low levels for slightly co-contaminated paddy soils, especially when the ridge height is 11 cm (Eh of 43 mV and pH of 4.6), where grain inorganic As decreased-at maximum-by 48% and DMAs by 55%. Grain Cd (0.14 mg kg^-1) increased but was still below the limit (0.2 mg kg^-1) in China, and the cost of ridging is acceptable. There were definite correlations among porewater As, Cd, Fe, S, and Mn contents across various Eh and pH values. Soil ridge cultivation significantly (P < 0.05) diminished the copy number of As-reducing (harboring arsC and arrA), As-methylating (harboring arsM), and sulfate-reducing (harboring dsrA) bacteria. Moreover, soil ridge cultivation shifted the arsM-harboring microbiota. In response to ridge height increase, the abundance of the bacterial biomarker phylum Euryachaeota declined and the families Halorubrum and Planctomyces were gradually replaced by Sandaracinus in paddy soil.

Iron and sulfur reduction caused by different growth seasons inhibits cadmium transfer in the soil-rice system

Effects of iron and sulfur redox states in the soil caused by different growth seasons on Cd uptake by rice remain unclear. In this study, three early rice cultivars and three late rice cultivars were cultivated in a double-cropping system in Cd-contaminated paddy fields. The total Cd accumulation of early rice cultivars was 20.5-51.1 µg plant^-1, and the Cd concentration in grains was 0.19-0.73 mg kg^-1, significantly lower than those of late rice cultivars by 8-15 times and 3-9 times, respectively. The filling and mature stages were identified as the most crucial stages of Cd uptake by both early and late rice cultivars. The growth season of early rice cultivars was characterized by more abundant rainfall and lower soil Eh than that for late rice cultivars. Therefore, the abundances of Fe-reducing bacteria (FeRB, 36.9-39%) and S-reducing bacteria (SRB, 1.77-2.79%) were higher during the filling and mature stages of early rice. They primarily belonged to the Clostridium, Geobacter, and Desulfuromonadales genera. Stimulation of FeRB and SRB activity promoted Fe(III) and S reduction and increased the content of Fe²⁺ and S^2- in rhizosphere soil. This promoted the binding of Cd to amorphous Fe oxides and sulfides or Fe sulfides, thereby decreasing the available Cd content. Moreover, the Cd in the iron plaque (IP) and Cd transfer from IP to roots were lower in early rice. These findings suggest that maintaining high moisture content in the soil during the filling and mature stages, especially for late rice cultivars, could efficiently reduce Cd uptake by rice planted in contaminated soil.

Inhibition of methanogenesis leads to accumulation of methylated arsenic species and enhances arsenic volatilization from rice paddy soil

Flooded soils are important environments for the biomethylation and subsequent volatilization of arsenic (As), a contaminant of global concern. Conversion of inorganic to methylated oxyarsenic species is thought to be the rate-limiting step in the production and emission of volatile (methyl)arsines. While methanogens and sulfate-reducing bacteria (SRB) have been identified as important regulators of methylated oxyarsenic concentrations in anaerobic soils, the effects of these microbial groups on biovolatilization remain unclear. Here, microcosm and batch incubation experiments with an Arkansas, USA, rice paddy soil were performed in conjunction with metabolic inhibition to test the effects of methanogenic activity on As speciation and biovolatilization. Inhibition of methanogenesis with 2-bromoethanesulfonate (BES) led to the accumulation of methylated oxyarsenic species, primarily dimethylarsinic acid (DMAs(V)), and a four-fold increase in As biovolatilization compared to a control soil. Our results support a conceptual model that methanogenic activity suppresses biovolatilization by enhancing As demethylation rates. This work refines understanding of biogeochemical processes regulating As biovolatilization in anaerobic soil environments, and extends recent insights into links between methanogenesis and As metabolism to soils from the mid-South United States rice production region.

Distribution, bioavailability, and human health risk assessment of arsenic in groundwater-soil-rice system in the Jianghan Plain, Central China

Many studies have reported high arsenic concentrations in the groundwater and soil of the Jianghan Plain (JHP), an important rice production base in China. However, no comprehensive study on the occurrence and risk of As in groundwater-soil-rice systems in this region has been conducted. In this study, As concentrations in groundwater, soil, rice straw, and rice grain samples were analyzed. Arsenic concentrations were found to range from BDL to 42.88 μg/L (median 0.34 μg/L) in phreatic water, BDL to 41.77 μg/L (median 8.64 μg/L) in soil pore water, 10.20 to 21.90 mg/kg (mean 16.52 mg/kg) in soil, 0.204 to 2.860 mg/kg (mean 0.847 mg/kg) in rice straw, and 0.131 to 0.951 mg/kg (mean 0.449 mg/kg) in rice grain. Arsenic uptake by rice from soils was evaluated according to bioavailable As defined by chemical extraction and diffusive gradients in thin films. The results indicated that owing to the low content of highly mobile As fractions, the less mobile As fraction (mainly bound with amorphous Fe/Al (hydr)oxides) also contributed to bioavailable As, suggesting that amorphous Fe/Al bound As should be considered in analyzing bioavailable As. In terms of the geoaccumulation index and the Chinese paddy soil standard (GB15618-2018) limit (25 mg/kg), As pollution in water and soils in the study area is at a low level and can be considered relatively safe. However, the target hazard quotients and cancer risk assessment indicated that As pollution is at a dangerous level with potential human health risk. According to the bioconcentration factor, the bioavailability of soil is higher in JHP compared with other rice-growing areas owing to the unique hydrogeological conditions and irrigation using groundwater with high As content. Rice planting areas in JHP should be set as far away from large rivers as possible, and groundwater with high As concentrations must be pre-treated prior to irrigation.

Using an improved Si-rich husk ash to decrease inorganic arsenic in rice grain

Paddy rice is efficient at arsenite accumulation by sharing the uptake and transport pathway for silicic acid. To limit As entry into rice by increasing soil Si availability, rice husk with concentrated Si deposition was subject to an ethanol-aided open combustion in this work to promote Si release from organic matrix. Compared to original husk, the content of amorphous silica was almost tripled in the resultant ash (Si-ash) with an apparent elimination of hydrocarbon groups. Following its incorporation into soil, 3.4-fold higher Si dissolution was maintained in rice rhizosphere compared to control, which was accompanied by 15.9-40.5% decrease in porewater As from tillering to harvest. Correspondingly, As sequestration in soil solid phase and root plaque increased by 8.0% and 26.9% with Si-ash, which could result from promoted FeAs co-precipitation by the liming effect of Si-ash and was linked to a notable decline in As transport through node I. Consequently, inorganic As (iAs) in white rice decreased from 0.36 mg kg^-1 in control to 0.17 mg kg^-1 with Si-ash, which is 15% lower than Chinese food safety standard. Results from this study highlight the advantage of Si-ash in securing rice production by mitigating iAs accumulation in white rice with fortified Si nutrition.

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.

Water management of alternate wetting and drying combined with phosphate application reduced lead and arsenic accumulation in rice

Lead (Pb) and arsenic (As) exist in soil with different ionic forms, and it is difficult to immobilize simultaneously Pb and As in soil. The objective of this study is to determine the effects of water management including flooding (FL), alternate wetting and drying (AWD) and dry farming (DF) combined with addition of phosphate (P) on the accumulation of Pb and As in rice. Our results showed that Pb accumulated in root during vegetative stage, and most of As in root was transported to the above ground parts during the reproductive stage. Pb was evenly distributed in grains, and As was mostly accumulated in bran and aleurone layer. Water management had a reverse effect on the accumulation of Pb and As in rice. However, the effects of P on arid soil environment and Pb, As accumulation in rice were stronger than that in flooded soil. Application of P under AWD treatment could maintain a similar quantity of Fe plaque with flooding, decrease the availability of Pb in rhizosphere soil, reduce Pb and As accumulation in root, and result in the reduction of Pb and As accumulation in grains by 86% and 66% respectively. Besides, our study also found that flooding or AWD during vegetative stage facilitated the formation of iron plaque. In conclusion, AWD combined with P application could maintain a relatively lower concentrations of Pb and As in grains.

Manganese oxides in Phragmites rhizosphere accelerates ammonia oxidation in constructed wetlands

Phragmites reeds are widely used in constructed wetlands (CWs) for treating wastewater. The enrichment of microorganisms and Fe/Mn plaque in Phragmites rhizospheres largely contributes to pollutant removal. However, their interactions and potential synergistic roles in water purification are poorly understood. To address the issue, we first compared the microbial community traits in the Phragmites rhizosphere and adjacent bulk soil in six long-term operated CWs. Results showed that enriched microbes and functional genes in the Phragmites rhizosphere were largely involved in Mn oxidation, resulting in a two to three times enrichment of Mn oxides in the rhizosphere. In turn, the enriched Mn oxides played significant roles in driving microbial community composition and function. To further understand the biological manganese oxidation in the rhizosphere, we identified Mn-oxidizing bacteria using genome-centric analysis and found that 92% of identified Mn-oxidizing bacteria potentially participated in nitrogen cycling. We then conducted relationships between Mn-oxidizing genes and different nitrogen cycling genes and found Mn-oxidizing gene abundance was significantly correlated with ammonia oxidation gene amoA (R = 0.65). Remarkably, complete ammonia oxidation (comammox) Nitrospira, accounting for 39.11% of ammonia oxidizers, also positively correlated with Mn-oxidizing microbes. Based on the above observations, we inferred that the use of Mn oxides as a substrate in CWs may enhance ammonia oxidation. To apply this to actual engineering, we explored treatment performance in a pilot-scale Mn-amending CW. As expected, ammonia removal capacity improved by 23.34%, on average, in the Mn-amending CW. In addition, the abundance of amoA genes increased significantly in the Mn-amending CW, indicating improved biological processes rather than chemical reactions.

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)).

Arsenic behavior across soil-water interfaces in paddy soils: Coupling, decoupling and speciation

The sharp redox gradient at soil-water interfaces (SWI) plays a key role in controlling arsenic (As) translocation and transformation in paddy soils. When Eh drops, As is released to porewater from solid iron (Fe) and manganese (Mn) minerals and reduced to arsenite. However, the coupling or decoupling processes operating within the redox gradient at the SWI in flooded paddy soils remain poorly constrained due to the lack of direct evidence. In this paper, we reported the mm-scale mapping of Fe, As and other associated elements across the redox gradient in the SWI of five different paddy soils. The results showed a strong positive linear relationship between dissolved Fe, Mn, As, and phosphorus (P) in 4 out of the 5 paddy soils, indicating the general coupling of these elements. However, decoupling of Fe, Mn and As was observed in one of the paddy soils. In this soil, distinct releasing profiles of Mn, As and Fe were observed, and the releasing order followed the redox ladder. Further investigation of As species showed the ratio of arsenite to total As dropped from 100% to 75.5% and then kept stable along depth of the soil profile, which indicates a dynamic equilibrium between arsenite oxidization and arsenate reduction. This study provides direct evidence of multi-elements' interaction along redox gradient of SWI in paddy soils.

Simultaneous measurement of aqueous redox-sensitive elements and their species across the soil-water interface

The redox-sensitive elements, such as iron, manganese, sulfur, phosphorus, and arsenic, shift their speciation every millimeter (mm) across the soil-water interface in the flooded soil environments. Monitoring of element speciation at this high-resolution (HR) within the SWI is still difficult. The key challenge lies in obtaining sufficient porewater samples at specific locations along the soil gradient for downstream analysis. Here with an optimized inductively coupled plasma mass spectrometry (ICP-MS) method and a HR porewater sampler, we demonstrate mm-scale element profiles mapping across the SWI in paddy soils. High-concentrations of iron and manganese (> 10 mg/L) were measured by ICP-MS in an extended dynamic range mode to avoid signal overflow. The iron profile along the SWI generated by the ICP-MS method showed no significant difference (p < 0.05) compared to that measured independently using a colorimetric method. Furthermore, four arsenic (arsenite, arsenate, monomethylarsonic and dimethylarsinic acid), two phosphorus (phosphite and phosphate) and two sulfur (sulfide and sulfate) species were separated in 10 min by ion chromatography -ICP-MS with the NH₄HCO₃ mobile phase. We verified the technique using paddy soils collected from the field, and present the mm-scale profiles of iron, manganese, and arsenic, phosphorus, sulfur species (relative standard deviation < 8%). The technique developed in this study will significantly promote the measurement throughput in limited samples (e.g. 100 μL) collected by HR samplers, which would greatly facilitate redox-sensitive elements biogeochemical cycling in saturated soils.

Arsenic transformation behavior mediated by arsenic functional genes in landfills

Landfill arsenic pollution is a complicated problem because of the sophisticated species and transformation of fractions involved. This study investigated arsenic transformation behavior from the viewpoint of arsenic functional genes based on analysis of 29 aged refuse samples collected from 11 sanitary landfills in 10 cities in Zhejiang Province, China. Arsenic species distribution varied significantly with landfill process. Landfill contains rich arsenic resistant microbes. arrA genes were the key factor responsible for arsenic transformation and migration in landfill. Although the abundance of aioA genes was the lowest among the four tested arsenic functional genes, it was the second important genes for arsenic distribution. Microbial metabolic activity was the main cause of arsenic transformation, and arsenate reduction by microbes was a key driver of arsenic mobilization in landfills. Moreover, arsenate was reduced to arsenite and further methylated to monomethylarsine (MMA) and dimethylarsine (DMA), decreasing the total arsenic content during the landfill process, but also inducing a new risk because of the arsenic effluent will be more easily as the state of arsenite, MMA, and DMA in the liquid phase. Overall, this study provides a picture of arsenic species transformation and insight into key roles involved in arsenic pollution during landfill processes.

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.

Variability in Arsenic Methylation Efficiency across Aerobic and Anaerobic Microorganisms

Microbially-mediated methylation of arsenic (As) plays an important role in the As biogeochemical cycle, particularly in rice paddy soils where methylated As, generated microbially, is translocated into rice grains. The presence of the arsenite (As(III)) methyltransferase gene (arsM) in soil microbes has been used as an indication of their capacity for As methylation. Here, we evaluate the ability of seven microorganisms encoding active ArsM enzymes to methylate As. Amongst those, only the aerobic species were efficient methylators. The anaerobic microorganisms presented high resistance to As exposure, presumably through their efficient As(III) efflux, but methylated As poorly. The only exception were methanogens, for which efficient As methylation was seemingly an artifact of membrane disruption. Deletion of an efflux pump gene (acr3) in one of the anaerobes, Clostridium pasteurianum, rendered the strain sensitive to As and capable of more efficiently methylating As. Our results led to the following conclusions: (i) encoding a functional ArsM enzyme does not guarantee that a microorganism will actively drive As methylation in the presence of the metalloid and (ii) there is an inverse relationship between efficient microbial As efflux and its methylation, because the former prevents the intracellular accumulation of As.

The mechanism of polystyrene microplastics to affect arsenic volatilization in arsenic-contaminated paddy soils

Different concentrations and sizes of polystyrene microplastics (PS-MP) were added to low (25.9) and high (56.8) mg kg^-1 As-contaminated soil to investigate the effects of PS-MP on soil As volatilization. Either S₁ (10 μm) or S₂ (0.1-1 μm) PS-MP was added to As-contaminated soil at 0.8%, which increased As volatilization by 13.7% and 7.4% in low As-contaminated soil; and 21.8% and 16.5% in high As-contaminated soil, respectively. The addition of PS-MP reduced the water-soluble (WS) As content, increased the non-specifically-sorbed (NSS), specifically-sorbed (SS) As content, soil catalase (CAT) and urease (UE) activities. The abundance of Proteobacteria and Firmicutes showed opposite trends to As volatilization, while the abundance of Bacteroidetes and arsM gene expression exhibited similar variability to As volatilization over the 7-week experiment. Therefore, we postulate that in As-contaminated soil, As volatilization was enhanced in the presence of PS-MP due to two possible mechanisms: 1) PS-MP affects the abundance of Proteobacteria, Firmicutes, Bacteroidetes, and arsM gene in soil; 2) PS-MP increases As volatilization via reducing soil nutrient and increasing the content of SS As. Our results highlighted the importance of investigating impacts of microplastics on the volatility of specific contaminants to implement effective environmental remediation strategies in polluted farmlands.

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.

Effects of Fe-Mn-Ce oxide-modified biochar on As accumulation, morphology, and quality of rice (Oryza sativa L.)

The fluidity of arsenic (As) in soil used for rice cultivation under flooding conditions is the main reason for its high accumulation in rice, which poses a serious threat to human's health. Biochar can immobilize heavy metal (for example lead) of soil because of the strong binding of heavy metals to the inner biochar particles. We conducted a pot experiment to evaluate the effects of biochar (BC) and Fe-Mn-Ce oxide-modified biochar composites (FMCBCs) on the morphology, As accumulation, and grain quality of rice grown in As-contaminated soils. The biochar and FMCBC treatments significantly increased the dry weight of roots, stems, leaves, and rice grains grown in As-contaminated soil (P < 0.05). The As concentration in different parts of rice was significantly lower with treatment FMCBC_3-2 (BC, Fe, Mn, and Ce weight ratio of 24:2:3:10) than with the BC and control (no BC) treatments. The application of FMCBC_3-2 maximized the yield and quality of rice grains: rice grain yields were 61.45-68.41% higher over control and the proportion of essential amino acids in the rice grains was 31.01-44.62%. The application of FMCBCs also increased the concentration of Fe-Mn plaques, which prevent the uptake of As by rice, thereby mitigating the toxic effects of As-contaminated soil on rice. In summary, Fe-Mn-Ce oxide-modified BC composites fixed As, reducing its fluidity and the As concentration in rice. Our results show that FMCBC₃ could play an important role in reducing As accumulation and increasing the grain yield and quality of rice, thus ensuring food safety in regions contaminated with As.

Biochar impact on chromium accumulation by rice through Fe microbial-induced redox transformation

Iron (Fe) dissimilatory reduction might impact chromium (Cr) mobility in the rice rhizosphere, but it is poorly understood. We assessed rhizosphere microbes' role in Cr immobilization and bioavailability by conducting the pot experiment to test different biochar sources (PMB - pig manure and PSB - pine sawdust) and phosphorus (P) levels impact on Cr mobility. Results showed that PMB application increased root biomass (23-65 %) and decreased root Cr concentration (46-74 %) regardless P treatment. However, P addition reduced root and shoot biomass in control and PMB treatments by 33-43 % and 25-26 %. Therefore, low P input is recommended in Cr-contaminated soil. Moreover, Geobacter was the key microbial groups which may be involved in promoting Cr release by increasing Fe dissolution. Finally, Geobacter and Fe dissimilatory reduction play a central role in Cr translocation and they should be considered in strategies to reduce rice Cr uptake by biochar application.

Simultaneous stimulation of arsenic methylation and inhibition of cadmium bioaccumulation in rice grain using zero valent iron and alternate wetting and drying water management

Studies aiming to limit bioaccumulation of arsenic (As) and cadmium (Cd) in rice grain has attracted global attention. In this study, simultaneous impact of zero valent iron (Fe⁰) and various water management regimes (continuous flooding (CF), alternate wetting and drying (AWD) and low water (LW)) on rice grain yield (GYM) and bioaccumulation of As and Cd in unpolished rice grain (URG) were investigated. Compared to respective control treatments, Fe⁰ significantly reduced GYM under LW by 32% (p < 0.001) and significantly increased GYM under AWD by 24% (p = 0.009; F = 5.9) but had no significant effect on GYM under CF water management regime (p > 0.05). The grain harvest index was significantly higher in Fe⁰ amended rice under AWD (67%; p < 0.001) and CF (35%; p = 0.001) compared to those without Fe⁰ amendment. Fe⁰ significantly reduced tAs in URG under LW by 32% (p < 0.017) and significantly increased tAs in URG under AWD by 37% (p = 0.007) but had no significant effect on tAs in URG under CF (p > 0.05). The Cd concentrations were significantly reduced by 51% (p = 0.002) and 61% (p < 0.003) in URG under LW and AWD respectively compared to the respective control treatments. The Dimethylarsinic acid (DMA) in unpolished rice (URG) under AWD (+Fe⁰) was significantly higher (p < 0.01; F = 11.3) compared to that accumulated in URG under AWD(-Fe°). Despite increasing As accumulation in AWD water management, simultaneous use of AWD water management and Fe° increased grain yield, enhanced accumulation of less toxic methylated As in rice grains and accumulated low Cd concentrations comparable to that attainable with CF water management indicating that simultaneous use AWD and Fe° can be effective in controlling Cd accumulation in paddies highly contaminated with Cd.