Publications

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community.

Summary The cellular and subcellular distributions of trace elements can provide important clues to understanding how the elements are transported and stored in plant cells, but mapping their distributions is a challenging task. The distributions of arsenic, iron, zinc, manganese and copper, as well as physiologically related macro‐elements, were mapped in the node, internode and leaf sheath of rice ( Oryza sativa ) using synchrotron X‐ray fluorescence (S‐XRF) and high‐resolution secondary ion mass spectrometry (NanoSIMS). Although copper and silicon generally showed cell wall localization, arsenic, iron and zinc were strongly localized in the vacuoles of specific cell types. Arsenic was highly localized in the companion cell vacuoles of the phloem in all vascular bundles, showing a strong co‐localization with sulfur, consistent with As(III)–thiol complexation. Within the node, zinc was localized in the vacuoles of the parenchyma cell bridge bordering the enlarged and diffuse vascular bundles, whereas iron and manganese were localized in the fundamental parenchyma cells, with iron being strongly co‐localized with phosphorus in the vacuoles. The highly heterogeneous and contrasting distribution patterns of these elements imply different transport activities and/or storage capacities among different cell types. Sequestration of arsenic in companion cell vacuoles may explain the limited phloem mobility of arsenite.

Excessive accumulation of cadmium (Cd) in rice grains threatens food safety and human health. Growing low Cd accumulating rice cultivars is an effective approach to produce low-Cd rice. However, field screening of low-Cd rice cultivars is laborious, time-consuming, and subjected to the influence of environment × genotype interactions. In the present study, we investigated whether machine learning-based methods incorporating genotype and soil Cd concentration can identify high and low-Cd accumulating rice cultivars. One hundred and sixty-seven locally adapted high-yielding rice cultivars were grown in three fields with different soil Cd levels and genotyped using four molecular markers related to grain Cd accumulation. We identified sixteen cultivars as stable low-Cd accumulators with grain Cd concentrations below the 0.2 mg kg−1 food safety limit in all three paddy fields. In addition, we developed eight machine learning-based models to predict low- and high-Cd accumulating rice cultivars with genotypes and soil Cd levels as input data. The optimized model classifies low- or high-Cd cultivars (i.e., the grain Cd concentration below or above 0.2 mg kg−1) with an overall accuracy of 76%. These results indicate that machine learning-based classification models constructed with molecular markers and soil Cd levels can quickly and accurately identify the high- and low-Cd accumulating rice cultivars.

Microorganisms play a key role in arsenic (As) biogeochemistry, transforming As species between inorganic and organic forms and different oxidation states. Microbial As methylation is enhanced in anoxic paddy soil, producing primarily dimethylarsenic (DMAs), which can cause rice straighthead disease and large yield losses. DMAs can also be demethylated in paddy soil, but the microorganisms driving this process remain unclear. In this study, we showed that the enrichment culture of methylotrophic methanogens from paddy soil demethylated pentavalent DMAs(V) efficiently. DMAs(V) was reduced to DMAs(III) before demethylation. 16S rRNA gene diversity and metagenomic analysis showed that Methanomassiliicoccus dominated in the enrichment culture, with Methanosarcina and Methanoculleus also being present. We isolated Methanomassiliicoccus luminyensis CZDD1 and Methanosarcina mazei CZ1 from the enrichment culture; the former could partially demethylate trivalent DMAs(III) but not DMAs(V) and the latter could demethylate neither. Addition of strain CZDD1 to the enrichment culture greatly accelerated DMAs(V) demethylation. Demethylation of DMAs(V) in the enrichment culture was suppressed by ampicillin, suggesting the involvement of bacteria. We isolated three anaerobic bacterial strains including Clostridium from the enrichment culture, which could produce hydrogen and reduce DMAs(V) to DMAs(III). Furthermore, augmentation of the Methanomassiliicoccus-Clostridium coculture to a paddy soil decreased DMAs accumulation by rice and alleviated straighthead disease. The results reveal a synergistic relationship whereby anaerobic bacteria reduce DMAs(V) to DMAs(III) for demethylation by Methanomassiliicoccus and also produce hydrogen to promote the growth of Methanomassiliicoccus; enhancing their populations in paddy soil can help alleviate rice straighthead disease.

Rice consumption is the primary route of cadmium (Cd) exposure to the populations with rice as the staple food. To accurately assess the potential health risks of Cd exposure via rice consumption, determination of Cd relative bioavailability (RBA) in rice is necessary. However, large variations exist in Cd-RBA, hindering the application of source-specific Cd-RBA values to different rice samples. In this study, we collected 14 rice samples from Cd contaminated areas and determined both rice compositions and Cd-RBA using in vivo mouse bioassay. Total Cd concentration varied from 0.19 to 2.54 mg/kg in the 14 rice samples, while Cd-RBA in rice ranged from 42.10% to 76.29%. Cadmium-RBA in rice correlated positively with calcium (Ca) (R = 0.76) and amylose content (R = 0.75) but negatively with the concentrations of sulfur (R = -0.85), phosphorus (R = -0.73), phytic acid (R = -0.68), and crude protein (R = -0.53). Cd-RBA in rice can be predicted by Ca and phytic acid concentrations in a regression model (R2 = 0.80). Based on the total and bioavailable Cd concentrations in rice, weekly dietary Cd intake for adults was estimated to be 4.84-64.88 and 2.04-42.29 μg/kg bw/week, respectively. This work demonstrates the possibility of Cd-RBA prediction based on rice compositions and provides valuable suggestions for health risk assessment with consideration of Cd-RBA.

Summary Arsenic (As) contamination in a paddy environment can cause phytotoxicity and elevated As accumulation in rice ( Oryza sativa ). The mechanism of As detoxification in rice is still poorly understood. We isolated an arsenate (As(V))‐sensitive mutant of rice. Genomic resequencing and complementation identified OsCLT1 , encoding a CRT‐like transporter, as the causal gene for the mutant phenotype. OsCLT1 is localized to the envelope membrane of plastids. The glutathione and γ‐glutamylcysteine contents in roots of Osclt1 and RNA interference lines were decreased markedly compared with the wild‐type (WT). The concentrations of phytochelatin PC 2 in Osclt1 roots were only 32% and 12% of that in WT after As(V) and As(III) treatments, respectively. OsCLT1 mutation resulted in lower As accumulation in roots but higher As accumulation in shoots when exposed to As(V). Under As(III) treatment, Osclt1 accumulated a lower As concentration in roots but similar As concentration in shoots to WT. Further analysis showed that the reduction of As(V) to As(III) was decreased in Osclt1 . Osclt1 was also hypersensitive to cadmium (Cd). These results indicate that OsCLT1 plays an important role in glutathione homeostasis, probably by mediating the export of γ‐glutamylcysteine and glutathione from plastids to the cytoplasm, which in turn affects As and Cd detoxification in rice.

Arsenic (As) constitutes a substantial threat to global ecosystems and public health. An accurate quantification of inorganic arsenite (As(III)) in rice grains is crucial for ensuring food safety and human well-being. Herein, we constructed an electrochemiluminescence (ECL) biosensor utilizing aggregation-induced emission (AIE) active Pdots for the sensitive detection of As(III) in rice. We synthesized tetraphenylethylene-based AIE-active Pdots, exhibiting stable and highly efficient ECL emission in their aggregated states. Owing to the overlap of spectra, we employed an electrochemiluminescence resonance energy transfer (ECL-RET) system, with the Pdots as the donor and black hole quencher (BHQ) as the acceptor. Upon the introduction of As(III), the conformational changes of As(III)-specific aptamer could trigger the detachment of BHQ-labeled DNA aptamer from the electrode surface, leading to the recovery of the ECL signal. The target-induced "signal-on" bioassay enabled the sensitive and specific detection of As(III) with a linear range of 10 pM to 500 nM, with an ultralow limit of detection (LOD) of 5.8 pM/0.4 ppt. These values significantly surpass those of existing sensors designed for As(III) quantification in rice. Furthermore, by employing amylase hydrolysis for efficient extraction, we successfully applied our sensor to measure As(III) in actual rice samples sourced from diverse regions of China. The results obtained using our sensor were in close agreement with those derived from the reference method of HPLC-ICP-MS. This study not only presents a sensitive and reliable method for detecting arsenite but also underscores its potential applications in enhancing food safety, agriculture practices, and environmental monitoring.

Lead (Pb) is a toxic heavy metal and its long-term accumulation in human bodies can lead to serious diseases. Investigation on Pb exposure provides an effective intervention opportunity to reduce the blood lead levels (BLLs) of the populations. Although the phase-out of the gasoline has been conducted in many developing countries (e.g., China), the BLLs of these populations are still higher than the alert BLL (5.0 μg/dL) set by World Health Organization (WHO) and Centers for Disease Control and Prevention of USA (CDC). Here, we reviewed the BLLs of the populations in different countries and summarized the sources and intake pathways of blood Pb which were associated with dietary Pb intake and non-dietary Pb intake. Extensive progress has been made in the studies of soil biogeochemistry and the plant biological processes, including the effects of soil pH, redox potential, Fe/Mn oxides, and organic matter on the availability of soil Pb, as well as the mechanisms regulating the Pb absorption by plant root and transport from root to shoot. The oral-nasal respiration and skin infiltration pathways have been specifically identified as the main causes of the increased BLLs of the populations exposed to different Pb sources. In the developing countries, complex dietary and non-dietary Pb intakes increase the BLLs, making intervention strategies to reduce BLLs difficult. This review provides a systematic understanding in the processes and mechanisms of Pb intake from environment to human blood and helps to guide safe strategies to reduce the BLLs and enhance human health.

Rice (Oryza sativa) takes up arsenite mainly through the silicic acid transport pathway. Understanding the uptake and sequestration of arsenic (As) into the rice plant is important for developing strategies to reduce As concentration in rice grain. In this study, the cellular and subcellular distributions of As and silicon (Si) in rice roots were investigated using high-pressure freezing, high-resolution secondary ion mass spectrometry, and transmission electron microscopy. Rice plants, both the lsi2 mutant lacking the Si/arsenite efflux transporter Lsi2 and its wild-type cultivar, with or without an iron plaque, were treated with arsenate or arsenite. The formation of iron plaque on the root surface resulted in strong accumulation of As and phosphorous on the epidermis. The lsi2 mutant showed stronger As accumulation in the endodermal vacuoles, where the Lsi2 transporter is located in the plasma membranes, than the wild-type line. As also accumulated in the vacuoles of some xylem parenchyma cells and in some pericycle cells, particularly in the wild-type mature root zone. Vacuolar accumulation of As is associated with sulfur, suggesting that As may be stored as arsenite-phytochelatin complexes. Si was localized in the cell walls of the endodermal cells with little apparent effect of the Lsi2 mutation on its distribution. This study reveals the vacuolar sequestration of As in rice roots and contrasting patterns of As and Si subcellular localization, despite both being transported across the plasma membranes by the same transporters.

Pentavalent methylated arsenic (As) species such as monomethylarsonic acid [MMA(V)] and dimethylarsinic acid [DMA(V)] are used as herbicides or pesticides, and can also be synthesized by soil microorganisms or algae through As methylation. The mechanism of MMA(V) and DMA(V) uptake remains unknown. Recent studies have shown that arsenite is taken up by rice (Oryza sativa) roots through two silicon transporters, Lsi1 (the aquaporin NIP2;1) and Lsi2 (an efflux carrier). Here we investigated whether these two transporters also mediate the uptake of MMA(V) and DMA(V). MMA(V) was partly reduced to trivalent MMA(III) in rice roots, but only MMA(V) was translocated to shoots. DMA(V) was stable in plants. The rice lsi1 mutant lost about 80% and 50% of the uptake capacity for MMA(V) and DMA(V), respectively, compared with the wild-type rice, whereas Lsi2 mutation had little effect. The short-term uptake kinetics of MMA(V) can be described by a Michaelis-Menten plus linear model, with the wild type having 3.5-fold higher V max than the lsi1 mutant. The uptake kinetics of DMA(V) were linear with the slope being 2.8-fold higher in the wild type than the lsi1 mutant. Heterologous expression of Lsi1 in Xenopus laevis oocytes significantly increased the uptake of MMA(V) but not DMA(V), possibly because of a very limited uptake of the latter. Uptake of MMA(V) and DMA(V) by wild-type rice was increased as the pH of the medium decreased, consistent with an increasing proportion of the undissociated species. The results demonstrate that Lsi1 mediates the uptake of undissociated methylated As in rice roots.