Publications

Root gravitropism relies on gravity perception by the root cap and requires tightly regulated phytohormone signaling. Here, we isolate a rice mutant that displays root coiling in hydroponics but normal gravitropic growth in soil. We identify COILING ROOT IN WATER 1 (CRW1) encoding an ETHYLENE-INSENSITIVE3 (EIN3)-BINDING F-BOX PROTEIN (OsEBF1) as the causative gene for the mutant phenotype. We show that the OsCRW1-EIN3 LIKE 1 and 2 (OsEIL1/2)-ETHYLENE RESPONSE FACTOR 82 (OsERF82) module controls the production of reactive oxygen species in the root tip, subsequently impacting root cap stability, polar localization of PIN-FORMED 2 (OsPIN2), symmetric distribution of auxin, and ultimately gravitropic growth of roots. The OsEIL1/2-OsERF82 ethylene signaling module is effectively impeded by applying gentle mechanical resistance to root tips, including growing in water-saturated paddy soil. We further show that mechanosensing-induced calcium signaling is required and sufficient for antagonizing the ethylene signaling pathway. This study has revealed previously unanticipated interplay among ethylene, auxin, and mechanosensing in the control of plant gravitropism.

Iron (Fe) plays an important role within environmental systems. Synchrotron-based X-ray approaches, including X-ray absorption spectroscopy (XAS), provide powerful tools for in situ analyses of Fe speciation, but beam damage during analysis may alter Fe speciation during its measurement. XAS was used to examine whether experimental conditions affect the analysis of Fe speciation in plant tissues. Even when analyzed in a cryostat at 12 K, it was found that Fe III can rapidly (within 0.5–1 min) photoreduce to Fe II , although the magnitude of photoreduction varied depending upon the hydration of the sample, the coordination chemistry of the Fe, as well as other properties. For example, photoreduction of Fe III was considerably higher for aqueous standard compounds than for hydrated plant-root tissues. The use of freeze-dried samples in the cryostat (12 K) markedly reduced the magnitude of this Fe III photoreduction, and there was no evidence that the freeze-drying process itself resulted in experimental artefacts under the current experimental conditions, such as through the oxidation of Fe II , although some comparatively small differences were observed when comparing spectra of hydrated and freeze-dried Fe II compounds. The results of this study have demonstrated that Fe III photoreduction can occur during X-ray analysis, and provides suitable conditions to preserve Fe speciation to minimize the extent of beam damage when analyzing environmental samples. All studies utilizing XAS are encouraged to include a preliminary experiment to determine if beam damage is occurring, and, where appropriate, to take the necessary steps (such as freeze drying) to overcome these issues.

Background and aims Iron (Fe) deficiency in plants is a common problem affecting agricultural production. Cadmium (Cd) is a toxic metal that can be taken up and transported within plants by transporters for divalent metals including Fe(II). The present study aims to investigate the functions of OsNRAMP2 (Natural Resistance-Associated Macrophage Protein 2) in the remobilization and distribution of Fe and Cd in rice. Methods The expression pattern of OsNRAMP2 was determined by quantitative real-time PCR and pOsNRAMP2:GUS assay. Knockout mutants of OsNRAMP2 were generated by using CRISPR/Cas9 gene editing. Localization of Fe in the vacuolar globoids of germinating seeds was imaged by high-resolution transmission electron microscopy coupled with energy-dispersive X-ray spectroscopy. Distributions of Fe and Cd between different plant tissues were investigated in hydroponic and soil pot experiments. Results OsNRAMP2 was mainly expressed in the embryo of germinating seeds, roots, leaf sheaths and leaf blades. OsNRAMP2 was localized at the tonoplast. Knockout of OsNRAMP2 delayed seed germination and produced chlorotic seedling leaves. Remobilization of Fe stored in the protein storage vacuoles in the scutellum of germinating seeds was restricted in osnramp2 mutants compared with wild type. Expression of genes related to Fe uptake was enhanced in the seedlings of osnramp2 mutants. Knockout of OsNRAMP2 significantly decreased the distribution of Cd, but not Fe, from leaves and straws to rice grains. Conclusions OsNRAMP2 plays an important role in remobilizing vacuolar Fe during seed germination and affects translocation of Cd from vegetative tissues to rice grains.

Plants have evolved sophisticated mechanisms for adaptation to fluctuating availability of nutrients in soil. Such mechanisms are of importance for plants to maintain homeostasis of nutrient elements for their development and growth. The molecular mechanisms controlling the homeostasis of nutrient elements at the genetic level have been gradually revealed, including the identification of regulatory factors and transporters responding to nutrient stresses. Recent studies have suggested that such responses are controlled not only by genetic regulation but also by epigenetic regulation. In this review, we present recent studies on the involvement of DNA methylation, histone modifications, and non-coding RNA-mediated gene silencing in the regulation of sulfur homeostasis and the response to sulfur deficiency. We also discuss the potential effect of sulfur-containing metabolites such as S-adenosylmethionine on the maintenance of DNA and histone methylation.

The retention and speciation of selenium in flour and bread was determined following experimental applications of selenium fertilisers to a high-yielding UK wheat crop. Flour and bread were produced using standard commercial practices. Total selenium was measured using inductively coupled plasma-mass spectrometry (ICP-MS) and the profile of selenium species in the flour and bread were determined using high performance liquid chromatography (HPLC) ICP-MS. The selenium concentration of flour ranged from 30ng/g in white flour and 35ng/g in wholemeal flour from untreated plots up to >1800ng/g in white and >2200ng/g in wholemeal flour processed from grain treated with selenium (as selenate) at the highest application rate of 100g/ha. The relationship between the amount of selenium applied to the crop and the amount of selenium in flour and bread was approximately linear, indicating minimal loss of Se during grain processing and bread production. On average, application of selenium at 10g/ha increased total selenium in white and wholemeal bread by 155 and 185ng/g, respectively, equivalent to 6.4 and 7.1μg selenium per average slice of white and wholemeal bread, respectively. Selenomethionine accounted for 65–87% of total extractable selenium species in Se-enriched flour and bread; selenocysteine, Se-methylselenocysteine selenite and selenate were also detected. Controlled agronomic biofortification of wheat crops for flour and bread production could provide an appropriate strategy to increase the intake of bioavailable selenium.

Animal production contributes substantially to the dissemination of antibiotic resistance genes (ARGs) in the environment. Thermophilic composting is cost-effective for reducing hazards in animal wastes. However, ARGs can still persist in composts and the mechanism remains largely unclear. In the present study, metagenomics and real-time quantitative PCR were employed to assess the dynamics of ARGs, especially those of high risk to human health, their host species and pathogenicity of the bacterial community during thermophilic composting of chicken manure. The results showed that thermophilic composting was effective at reducing the majority of the spreading risk of antibiotic resistance by 1) eliminating more than half of allARGs that accounted for 80% of the total abundance, 2) reducing the number and abundance of high-risk ARGs significantly, and 3) removing the ARG hosts and the pathogenicity of the bacterial community substantially. The attenuation of ARGs was primarily driven by the bacterial community succession. However, the abundance of some ARGs, especially those associated with plasmids, rebounded during the cooling phase, likely caused by horizontal gene transfer. Our research reveals that minimising the horizontal transfer of plasmid-associated ARGs during the cooling phase of thermophilic composting is crucial for a more effective reduction of the hazards associated with the spread of antibiotic resistance.

Arsenic (As) is one of the most widespread environmental contaminants. The aim of our study was to test a novel bioremediation system based on the symbiosi

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 (r 2 = 0.83) and also with the relative abundance of genus Clostridium_sensu_stricto_10 (r 2 = 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.

Chromate (Cr[VI]) is a highly phytotoxic contaminant that is ubiquitous in soils. However, how Cr(VI) is taken up by plant roots remains largely unknown. Here, we show that the high-affinity sulfate transporter Sultr1;2 is responsible for Cr(VI) uptake by the roots of Arabidopsis thaliana. Sultr1;2 showed a much higher transport activity for Cr(VI) than Sultr1;1 when expressed in yeast cells. Knockdown of Sultr1;2 expression in Arabidopsis markedly reduced the Cr(VI) uptake rate, whereas knockout of Sultr1;1 had no or little effect. A double-knockout mutant (DKO) of the two genes lost the ability of Cr(VI) uptake almost completely. The Sultr1;2 knockdown mutant or DKO plants displayed higher resistance to Cr(VI) under normal sulfate conditions as a consequence of the lower tissue Cr accumulation. Overexpression of Sultr1;2 substantially increased Cr(VI) uptake with shoot Cr concentration being 1.6–2.0 times higher than that in the wild-type. These results indicate that Sultr1;2 is a major transporter responsible for Cr(VI) uptake in Arabidopsis, while Sultr1;1 plays a negligible role. Taken together, our study has identified a major transporter for Cr(VI) uptake in plants, providing potential strategies for engineering plants with low Cr accumulation and consequently enhanced Cr(VI) resistance and also plants with enhanced accumulation of Cr for the purpose of phytoremediation.

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