Publications

Representing the staple crop for half of the world population, rice can accumulate high levels of cadmium (Cd) in its grain, posing concerns on food safety. Different soil amendments have been proposed to decrease Cd accumulation in rice grain by either decreasing soil Cd availability, introducing competitive ions on Cd uptake, or down-regulating the expression of transporters for Cd uptake. However, the effectiveness of soil amendments applied alone or in combinations needs to be tested under field conditions. Here, we present results of field trials with two rice cultivars differing in Cd accumulation grown at three field sites in southern China in two years, to investigate the effects of two Mn-containing soil amendments (MnO2, Mn-loaded biochar (MB)), Si fertilizer (Si), limestone, and K2SO4, as well as interactions among MnO2, Si, and limestone on decreasing Cd accumulation in rice grain. We found that single applications of MnO2 or MB to acidic soils low in Mn decreased grain Cd concentrations by 44–53 % or 78–82 %, respectively, over two years without decrease in performance. These effects were comparable to or greater than those induced by limestone liming alone (45–62 %). Strong interactions between MnO2 and limestone resulting from their influence on soil extractable Cd and Mn led to non-additive effects on lowering grain Cd. MB addition minimized grain Cd concentrations, primarily by increasing extractable and dissolved Mn concentrations, but also by decreasing Cd extractability in soil. In comparison, Si and K2SO4 amendments affected grain Cd levels only weakly. We conclude that the amendments that decrease labile Cd and increase labile Mn in soils are most effective at reducing Cd accumulation in rice grain, thus contributing to food safety.

Mineral binding is a major mechanism for soil carbon (C) stabilization, and mineral availability for C binding critically affects C storage. Yet, the mechanisms regulating mineral availability are poorly understood. Here, we showed that organic amendments in three long-term (23, 154, and 170 yrs, respectively) field experiments significantly increased mineral availability, particularly of short-range-ordered (SRO) phases. Two microcosm studies demonstrated that the presence of roots significantly increased mineral availability and promoted the formation of SRO phases. Mineral transformation experiments and isotopic labeling experiments provided direct evidence that citric acid, a major component of root exudates, promoted the formation of SRO minerals, and that SRO minerals acted as "nuclei" for C retention. Together, these findings indicate that soil organic amendments initialize a positive feedback loop by increasing mineral availability and promoting the formation of SRO minerals for further C binding, thereby possibly serving as a management tool for enhancing carbon storage in soils.

Microbial arsenic (As) methylation is an important process of As biogeochemistry. Only a few As-methylating microorganisms have been isolated from paddy soil, hindering the mechanistic understanding of the process involved. We isolated 54 anaerobic and 32 aerobic bacteria from paddy soil with a high As methylation potential. Among the 86 isolates, 14 anaerobes, including 7 sulfate-reducing bacteria (SRB), but none of the aerobes were able to methylate arsenite [As(III)] or monomethylarsenite [MMA(III)] or both, suggesting that the As-methylating ability is much more prevalent in anaerobes than in aerobes. We performed a detailed investigation on As methylation by a SRB isolate,

Arsenic is a ubiquitous environmental toxin. Some microbes detoxify inorganic arsenic through biomethylation, generating relatively nontoxic pentavalent methylated arsenicals, such as methylarsenate.

Metabolomics aims at determining a sample's metabolites profile and hence provides a straight functional statement of an organism's physiological condition. Here, we investigated comprehensive profiling, natural variation and species-specific accumulation of both primary and secondary metabolites in foxtail millet using LC-MS, and inheritance patterns of metabolome in millet hybrids. The application of a broad target metabolomics method facilitated the simultaneous identification and quantification of more than three hundred metabolites. The metabolic analysis of these compounds, such as flavonoids, phenolamides, hydrocinnamoyl derivatives, vitamins and LPCs, revealed their developmentally controlled accumulation and natural variation in different tissues/varieties. Species-specific accumulation of secondary metabolites was observed based on a comparative metabolic analysis between millet and rice, such as flavonoid O-rutinosides/neohesperidosides and malonylated flavonoid O-glycosides. In analyzing the metabolic variations between hybrid progenies and their parental lines, including a photothermo-sensitive genic male sterility line and five Zhangzagu varieties, metabolic overdominant and dominant patterns of inheritance could be observed. For example, hydrocinnamoyl derivatives and feruloylated flavonoids were identified as over-parent heterosis (overdominant) metabolites in milet hybrids. Our work paves the way for developing predictors of hybrid performance and the future analysis of the biosynthesis and regulation of relevant metabolic pathways in millet.

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

Inorganic arsenic is a carcinogen, and its ingestion through foods such as rice presents a significant risk to human health. Plants chemically reduce arsenate to arsenite. Using genome-wide association (GWA) mapping of loci controlling natural variation in arsenic accumulation in Arabidopsis thaliana allowed us to identify the arsenate reductase required for this reduction, which we named High Arsenic Content 1 (HAC1). Complementation verified the identity of HAC1, and expression in Escherichia coli lacking a functional arsenate reductase confirmed the arsenate reductase activity of HAC1. The HAC1 protein accumulates in the epidermis, the outer cell layer of the root, and also in the pericycle cells surrounding the central vascular tissue. Plants lacking HAC1 lose their ability to efflux arsenite from roots, leading to both increased transport of arsenic into the central vascular tissue and on into the shoot. HAC1 therefore functions to reduce arsenate to arsenite in the outer cell layer of the root, facilitating efflux of arsenic as arsenite back into the soil to limit both its accumulation in the root and transport to the shoot. Arsenate reduction by HAC1 in the pericycle may play a role in limiting arsenic loading into the xylem. Loss of HAC1-encoded arsenic reduction leads to a significant increase in arsenic accumulation in shoots, causing an increased sensitivity to arsenate toxicity. We also confirmed the previous observation that the ACR2 arsenate reductase in A. thaliana plays no detectable role in arsenic metabolism. Furthermore, ACR2 does not interact epistatically with HAC1, since arsenic metabolism in the acr2 hac1 double mutant is disrupted in an identical manner to that described for the hac1 single mutant. Our identification of HAC1 and its associated natural variation provides an important new resource for the development of low arsenic-containing food such as rice.

The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel.