Rice Tissues Research Articles

Infestation by the Piercing-Sucking Herbivore Nilaparvata lugens Systemically Triggers JA- and SA-Dependent Defense Responses in Rice.

It has been well documented that an infestation of the piercing-sucking herbivore, brown planthopper (BPH), Nilaparvata lugens, activates strong local defenses in rice. However, whether a BPH infestation elicits systemic responses in rice remains largely unknown. In this study, we investigated BPH-induced systemic defenses by detecting the change in expression levels of 12 JA- and/or SA-signaling-responsive marker genes in different rice tissues upon a BPH attack. We found that an infestation of gravid BPH females on rice leaf sheaths significantly increased the local transcript level of all 12 marker genes tested except OsVSP, whose expression was induced only weakly at a later stage of the BPH infestation. Moreover, an infestation of gravid BPH females also systemically up-regulated the transcription levels of three JA-signaling-responsive genes (OsJAZ8, OsJAMyb, and OsPR3), one SA-signaling-responsive gene (OsWRKY62), and two JA- and SA- signaling-responsive genes (OsPR1a and OsPR10a). Our results demonstrate that an infestation of gravid BPH females systemically activates JA- and SA-dependent defenses in rice, which may in turn influence the composition and structure of the community in the rice ecosystem.

Evaluating the Differential Response of Transcription Factors in Diploid versus Autotetraploid Rice Leaves Subjected to Diverse Saline-Alkali Stresses.

Saline-alkali stress is a significant abiotic stress factor that impacts plant growth, development, and crop yield. Consistent with the notion that genome-wide replication events can enhance plant stress resistance, autotetraploid rice exhibited a higher level of tolerance to saline-alkali stress than its donor counterparts, which is reflected by differential gene expression between autotetraploid and diploid rice in response to salt, alkali, and saline-alkali stress. In this study, we investigated the expression of the transcription factors (TFs) in the leaf tissues of autotetraploid and diploid rice under different types of saline-alkali stress. Transcriptome analysis identified a total of 1040 genes from 55 TF families that were altered in response to these stresses, with a significantly higher number in autotetraploid rice compared to diploid rice. Contrarily, under these stresses, the number of expressed TF genes in autotetraploid rice was greater than that in diploid rice for all three types of stress. In addition to the different numbers, the differentially expressed TF genes were found to be from significantly distinct TF families between autotetraploid and diploid rice genotypes. The GO enrichment analysis unraveled that all the DEGs were distributed with differentially biological functions in rice, in particular those that were enriched in the pathways of phytohormones and salt resistance, signal transduction, and physiological and biochemical metabolism in autotetraploid rice compared to its diploid counterpart. This may provide useful guidance for studying the biological roles of polyploidization in plant resilience in response to saline-alkali stress.

Analysis and subcellular distribution of organophosphate esters (OPEs) in rice tissues.

Recent studies have identified the ability of plants to uptake and translocate organophosphate esters (OPEs) within cells. In response to the increasing interest in OPEs and their occurrence in paddy fields and rice, the current study aimed to present an effective and sensitive GC-MS based methodology for quantitative determination of 11 OPEs with octanol-water coefficients ranging from 1.6 to 10. Rice was sonicated with hexane and dichloromethane, and fractionated on two columns: one consisting of neutral alumina, andneutral silica, and the other consisting of graphitized carbon black. Method precision was validated using spiked rice (n = 30) and procedural blanks (n = 9). The mean recovery of matrix spikes for all target OPEs were within 78-110% with relative standard deviation lower than 25%, with a few exceptions. This method was applied to process the wild rice (O. sativa) in which tri-n-propyl phosphate was the dominant targeted OPE. The recoveries of surrogate standards were 81 ± 17% for d12- tris(2-chloroethyl) phosphate and 95 ± 8.8% for 13C12- triphenyl phosphate. The developed method was further used to examine the recoveries of target OPEs in the subcellular structure of rice tissues, including cell wall, cell organelles, cell water-soluble fractions, and cell residue. Recoveries of most target OPEs were in the range of 50-150%; however, ion enhancement was observed for four OPEs in root and shoot tissues. Hydrophobic OPEs accumulated in the cell wall, cell residue, and cell organelles while chlorinated OPEs mainly distributed in the cell water-soluble fraction. These results provide new insight for the ecological risk assessment of OPEs in an important food staple.

Establishment and application of the Recombinase-Aided Amplification-Lateral Flow Dipstick detection method for Pantoea ananatis on rice.

Pantoea ananatis is a major pathogen that causes the new bacterial blight in rice, and its symptoms very similar to rice bacterial blight. Therefore, there is a dire need for an accurate and rapid method for detecting P. ananatis. In this study, an early and rapid visual detection method for P. ananatis was established. Using GyrB gene as the target sequence, an innovative recombinase-aided amplification detection system integrated with a lateral flow dipstick (RAA-LFD) was constructed. The optimized RAA-LFD detection method can be initiated at body temperature and does not rely on precise instruments. It does not require DNA extraction and can be used directly with plant tissue fluids. The results can be visualized after 10 minutes of amplification. The specificity and sensitivity tests showed that the RAA-LFD method could detect P. ananatis, whereas other common plant pathogens were not detected, and its detection sensitivity for P. ananatis DNA reached 100 copies/µL. The detection of diseased tissues indicated that this method could accurately detect P. ananatis in artificially inoculated rice tissues in the early stages of infection before symptoms. The RAA-LFD detection system established in this study is simple and fast, with visual results, excellent specificity, and high sensitivity. It is semi-quantitative and should be used for the early detection and rapid field diagnosis of new leaf blight, which provides technical support for the early warning and real-time detection of field samples.

Transfer and transformation characteristics of Zn and Cd in soil-rotation plant (Brassica napus L and Oryza sativa L) system and its influencing factors

Rice–rape rotation is a widely practiced cropping system in China. However, changes in soil properties and management could change the bioavailability of Cd, In order to explore the occurrence state, transportation and transformation characteristics of heavy metals Cd and Zn in rice-rape rotation system in Guizhou karst area with high background value of Cd. In the karst rice–rape rotation area, the physical and chemical properties of soil, chemical specifications and activities of Cd and Zn at different soil depths and during various crop growth stages, and the bioaccumulation of Cd and Zn in different tissues of rice and rape were studied by field experiment and laboratory analysis. The bioaccumulation of Cd and Zn and the effects of physical and chemical soil properties on the activities and bioavailabilities of Cd and Zn during rice–rape rotation were explored. The findings revealed that soil particle size, composition, pH, redox potential, soil organic matter, and Cd and Zn contents varied dramatically, especially in deep soils. The physical and chemical properties of the deep and surface soils were significantly related to the bioaccumulation of Cd and Zn. Cd and Zn are activated during crop rotation. Cd was easier to be enriched in rice, while Zn was easier to be enriched in rape. The correlation between Cd and Zn contents in Brassica campestris L and their enrichment abilities were not significant, but that in Oryza sativa L were significant. During rice-rape rotation, the chemical speciations and activities of Cd and Zn changed with the changes of soil properties and waterlogging environment. This study had important basic guiding significance for the evaluation, prevention and control of heavy metal pollution, and improving soil quality in different rotation systems in karst areas, and was conducive to promoting the safe production of rape and rice.

Initiation of scutellum-derived callus is regulated by an embryo-like developmental pathway in rice

In rice (Oryza sativa) tissue culture, callus can be induced from the scutellum in embryo or from the vasculature of non-embryonic organs such as leaves, nodes, or roots. Here we show that the auxin signaling pathway triggers cell division in the epidermis of the scutellum to form an embryo-like structure, which leads to callus formation. Our transcriptome data show that embryo-, stem cell-, and auxin-related genes are upregulated during scutellum-derived callus initiation. Among those genes, the embryo-specific gene OsLEC1 is activated by auxin and involved in scutellum-derived callus initiation. However, OsLEC1 is not required for vasculature-derived callus initiation from roots. In addition, OsIAA11 and OsCRL1, which are involved in root development, are required for vasculature-derived callus formation but not for scutellum-derived callus formation. Overall, our data indicate that scutellum-derived callus initiation is regulated by an embryo-like development program, and this is different from vasculature-derived callus initiation which borrows a root development program.

OsNPF3.1, a nitrate, abscisic acid and gibberellin transporter gene, is essential for rice tillering and nitrogen utilization efficiency

Low-affinity nitrate transporter genes have been identified in subfamilies 4–8 of the rice nitrate transporter 1 (NRT1)/peptide transporter family (NPF), but the OsNPF3 subfamily responsible for nitrate and phytohormone transport and rice growth and development remains unknown. In this study, we described OsNPF3.1 as an essential nitrate and phytohormone transporter gene for rice tillering and nitrogen utilization efficiency (NUtE). OsNPF3.1 possesses four major haplotypes of its promoter sequence in 517 cultivars, and its expression is positively associated with tiller number. Its expression was higher in the basal part, culm, and leaf blade than in other parts of the plant, and was strongly induced by nitrate, abscisic acid (ABA) and gibberellin 3 (GA3) in the root and shoot of rice. Electrophysiological experiments demonstrated that OsNPF3.1 is a pH-dependent low-affinity nitrate transporter, with rice protoplast uptake assays showing it to be an ABA and GA3 transporter. OsNPF3.1 overexpression significantly promoted ABA accumulation in the roots and GA accumulation in the basal part of the plant which inhibited axillary bud outgrowth and rice tillering, especially at high nitrate concentrations. The NUtE of OsNPF3.1-overexpressing plants was enhanced under low and medium nitrate concentrations, whereas the NUtE of OsNPF3.1 clustered regularly interspaced short palindromic repeats (CRISPR) plants was increased under high nitrate concentrations. The results indicate that OsNPF3.1 transports nitrate and phytohormones in different rice tissues under different nitrate concentrations. The altered OsNPF3.1 expression improves NUtE in the OsNPF3.1-overexpressing and CRISPR lines at low and high nitrate concentrations, respectively.

Microbial cell wall sorption and Fe-Mn binding in rhizosphere contribute to the obstruction of cadmium from soil to rice.

Screening high-tolerant microorganisms to cadmium (Cd) and revealing their bio-obstruction mechanism could be significant for Cd regulation from farmland to the food chain. We examined the tolerance and bio-removal efficiency of Cd ions of two bacterial strains, Pseudomonas putida 23483 and Bacillus sp. GY16, and measured the accumulation of Cd ions in rice tissues and its different chemical forms in soil. The results showed that the two strains had high tolerance to Cd, but the removal efficiency was decreased successively with increasing Cd concentrations (0.05 to 5 mg kg-1). Cell-sorption accounted for the major proportion of Cd removal compared with excreta binding in both strains, which was conformed to the pseudo-second-order kinetics. At the subcellular level, Cd was mostly taken up by the cell mantle and cell wall, and only a small amount entered into the cytomembrane and cytoplasmic with time progressed (0 to 24 h) in each concentration. The cell mantle and cell wall sorption decreased with increasing Cd concentration, especially in the cytomembrane and cytoplasmic. The scanning electron microscope (SEM) and energy dispersive X-ray (EDS) analysis verified that Cd ions were attached to the cell surface, and the functional groups of C-H, C-N, C=O, N-H, and O-H in the cell surface may participate in cell-sorption process tested by the FTIR analysis. Furthermore, inoculation of the two strains significantly decreased Cd accumulation in rice straw and grain but increased in the root, increased Cd enrichment ratio in root from soil, decreased Cd translocation ratio from root to straw and grain, and increased the Cd concentrations of Fe-Mn binding form and residual form in rhizosphere soil. This study highlights that the two strains mainly removed Cd ions in solution through biosorption and passivated soil Cd as Fe-Mn combined form ascribe to its characteristics of manganese-oxidizing, eventually achieving bio-obstruction of Cd from soil to rice grain.

Algal polysaccharides-Selenium nanoparticles regulate the uptake and distribution of selenium in rice plants.

Selenium (Se) is an essential trace element required for proper human and animal health. In this paper, we investigated the uptake and distribution characteristics of a new Se fertilizer, which comprises algal polysaccharides-selenium nanoparticles (APS-SeNPs), in rice plants in both hydroponic and pot experiments. The results from the hydroponic experiments revealed that the rice root uptake of APS-SeNPs fitted the Michaelis-Menten equation, with a V max of 13.54μgg-1 root dry weight (DW) per hour, which was 7.69 and 2.23 times those of selenite and selenate treatments, respectively. The root uptake of APS-SeNPs was inhibited by AgNO3 (64.81%-79.09%) and carbonyl cyanide 3-chlorophenylhydrazone (CCCP; 19.83%-29.03%), indicating that the uptake of APS-SeNPs by rice roots is mainly via aquaporins and is also affected by metabolic activity. Moreover, sulfur deficiency caused rice roots to absorb more APS-SeNPs, but treatment with APS-SeNPs increased the expression of the sulfate transporter OsSULTR1;2 in the roots, suggesting that OsSULTR1;2 is probably involved in the uptake of APS-SeNPs. The application of APS-SeNPs significantly increased the Se content in rice plants and the apparent Se uptake efficiency compared with selenate and selenite treatments. Most of the Se in the roots of rice plants was distributed in the cell wall, while it was primarily located in the cytosol in the shoots when treated with APS-SeNPs. The results from the pot experiments indicated that the application of Se enhanced the Se content of each rice tissue. It is worth noting that the Se content in brown rice under APS-SeNP treatment was higher than that under selenite or selenate treatment and was mainly concentrated in the embryo end, with the Se in organic form. Our findings provide important insights into the uptake mechanism and the distribution of APS-SeNPs in rice plants.

A natural variation in the promoter of GRA117 affects carbon assimilation in rice.

GRA117 is crucial in the process of carbon assimilation in rice as it regulates the development of chloroplasts, which in turn facilitates the Calvin-Benson cycle. Carbon assimilation is a critical process for plant growth, and despite numerous relevant studies, there are still unknown constraints. In this study, we isolated a rice mutant, gra117, which exhibited seedling albinism, delayed chloroplast development, decreased chlorophyll content, reduced yield, and seedling stress susceptibility, as compared to WT. Our further investigations revealed that gra117 had a significantly lower net photosynthetic carbon assimilation rate, as well as reduced levels of Rubisco enzyme activity, RUBP, PGA, carbohydrate, protein content, and dry matter accumulation. These findings provide evidence for decreased carbon assimilation in gra117. By mapping cloning, we discovered a 665bp insertion in the GRA117 promoter region that decreases GRA117 transcriptional activity and causes the gra117 phenotype. GRA117 encodes PfkB-type fructokinase-like 2, which is subcellularly localized in chloroplasts and is widely expressed in various rice tissues, particularly at high levels in leaf tissues. GRA117 transcription is regulated by the core region 1029bp before the start codon. Our quantitative RT-PCR and Western blot assays showed that GRA117 promotes the expression and translation of photosynthetic genes. RNA-Seq analysis revealed that GRA117 plays a significant role in photosynthetic carbon fixation, carbon metabolism, and chloroplast ribosome-related pathways. Our study supports that GRA117 promotes the Calvin-Benson cycle by regulating chloroplast development, ultimately leading to enhanced carbon assimilation in rice.

Jasmonate signaling controls negative and positive effectors of salt stress tolerance in rice.

Plant responses to salt exposure involve large reconfiguration of hormonal pathways that orchestrate physiological changes towards tolerance. Jasmonate (JA) hormones are essential to withstand biotic and abiotic assaults, but their roles in salt tolerance remain unclear. Here we describe the dynamics of JA metabolism and signaling in root and leaf of rice, a plant species that is highly exposed and sensitive to salt. Roots activate the JA pathway in an early pulse, while 2 nd leaf displays a biphasic JA response with peaks at 1 hour and 3 days post-exposure. Based on higher salt tolerance of a rice JA-deficient mutant (aoc), we examined through kinetic transcriptome and physiological analysis the salt-triggered processes that are under JA control. Profound genotype-differential features emerged that could underlie observed phenotypes. ABA content and ABA-dependent water deprivation responses were impaired in aoc shoots. Moreover, aoc accumulated more Na + in roots, and less in leaf, with reduced ion translocation correlating with root derepression of the HAK4 Na + transporter. Distinct reactive oxygen species scavengers were also stronger in aoc leaf, along with reduced senescence and chlorophyll catabolism markers. Collectively, the data identify contrasted contributions of JA signaling to different sectors of the salt stress response in rice.

Effects of rapeseed residue organic fertilizer on cadmium toxicity in soil and its uptake and transfer by rice plants (Oryza sativa L.)

AbstractCadmium (Cd) contamination of rice fields is a global agro‐environmental issue. Rapeseed (canola) residue organic fertilizer (RROF) as a potential strategy to minimize Cd accumulation in rice planted in acidic soil. The results showed that application of 7.5–30.0 g kg−1 RROF increased the soil pH value by 0.01–0.55 units, increased soil organic matter (OM) by 7.8–25.0%, increased soil microbial biomass carbon (MBC) and nitrogen (MBN) by 0.0–89.7% and 0.0–47.5%, respectively, and increased soil dehydrogenase (DH), acid phosphatase (ACP), and urease (UA) activities by 14.3–344.0%, 0.0–127.1%, and 3.5–14.3%, respectively. The application of RROF treatments reduced the soil acid‐extractable Cd (ACI–Cd) content by 8.1–36.4% and increased the reducible Cd (RED–Cd) and oxidizable Cd (OXI–Cd) by 1.3–36.4% and 16.2–47.9%, respectively. The path analysis demonstrated that soil OM, ACP activity, Mn, and Ca ions had a significant negative indirect effect on the decrease in soil ACI‐Cd (rOM = −0.628, rACP = −0.582, rMn = −0.627, rCa = −0.341), while Zn ions showed a strong direct effect (bZn = 0.567) and indirect positive effect (rZn = 0.580). In rice plants, the contents of Cd, Fe, K, Mg, P, and Zn in rice tissues increased, and the Cd content in rice grains decreased by 3.1–31.3% under RROF application. The results of the correlation analysis found that K and Zn in rice husks and Mg in grains were significantly and negatively correlated with the husk–grain translocation factor of Cd (r = −0.88** for Zn, r = −0.81** for K, and r = −0.59* for Mg). In addition, a significant negative correlation of root–straw translocation factors of Cd with Ca and Fe ions in the roots was observed (r = −0.63* and r = −0.60* for Ca at the filling and maturity stages of rice, r = −0.61* for Fe at the tillering stage of rice). RDA showed that the distribution fraction of soil Cd controlled the accumulation of Cd in various parts of rice, with soil ACI–Cd content explaining 22.4% of the total eigen values at a significant level, followed by 14.1% for OXI–Cd. This means that ACI–Cd was the primary factor that controlled Cd accumulation in rice grain, followed by OXI–Cd.

UHPLC-Q-Orbitrap HRMS-Based Metabolomic Reveal Biological Pathways Involved in Rice (Oryza sativa L.) under Fe Toxicity Stress

The iron (Fe) toxicity stress is still a serious problem in rice cultivation, especially on land with high Fe content. The Fe toxicity stress affects various complex physiological aspects of plants. The metabolomic analysis using LC-MS is expected to provide information about rice's metabolism regulation under Fe toxicity stress. The objective of this study was to show the biological pathway signature in rice after exposure to Fe toxicity stress using UHPLC-Q-Orbitrap HRMS-based metabolomic analysis. The two rice varieties, i.e., IR64 (Fe-sensitive) and Pokkali (Fe-tolerant) were analyzed their metabolites using UHPLC-Q-Orbitrap HRMS. The metabolite profiles of both varieties were analyzed using MetaboAnalyst 5.0 software. The results showed that Fe toxicity stress affected the metabolite profile in both root and shoot tissues of two rice varieties. A number of 102 metabolites were detected in root and shoot tissues of rice. The comprehensive univariate and multivariate analyses showed that 1-aminocyclopropane-1-carboxylate (ACC) in shoot tissues and galactose in root tissues was suggested as metabolite markers for Fe tolerance character of rice var. Pokkali. The genes encoded the enzymes involved in biosynthetic pathway of both metabolite markers could be a target to be explored for Fe toxicity tolerance in rice.

Changes in the Availability and Distribution of Microelement Copper in Cadmium Contaminated Soil and its Accumulation in Rice (Oryza sativa L.) After Biochar Application.

This experiment explored the side effect of biochar application on the availability and distribution of the soil microelement copper (Cu) in cadmium (Cd) contaminated soil and its uptake in rice tissues. Biochar was added at 0, 10, 20, 30, and 40 t ha-1 on topsoil. Results observed that both the concentration of available Cu in the topsoil and subsoil layer decreased by 16.3%-28.9% and 7.5%-59.3%, respectively, after biochar application. The Cu concentration in the < 0.053mm and 1-2mm soil aggregates increased as biochar application rate increased. Increasing application rate of biochar reduced the proportion of exchangeable Cu, carbonate bound Cu, and Fe/Mn oxide Cu fraction in the soil profile. However, the fraction of organic bound and residual Cu increased by 5.0%-178.4% and 7.0%-15.6%, respectively. Biochar could immobilize microelement Cu in the soil profile and limit Cu uptake by rice.

Effects of Platinum Nanoparticles on Rice Seedlings (Oryza sativa L.): Size-dependent Accumulation, Transformation, and Ionomic Influence.

Platinum nanoparticles (PtNPs) are increasing in the environment largely due to their wide use and application in automobile and medical industries. The mechanism of uptake behavior of different-sized PtNPs and their association with PtNPs-induced phytotoxicity to plants remains unclear. The present study investigated PtNP uptake mechanisms and phytotoxicity simultaneously to further understand the accumulation and transformation dynamics. The uptake mechanisms were investigated by comparing the uptake and toxicological effects of three different-sized PtNPs (25, 50, and 70 nm) on rice seedlings across an experimental concentration gradient (0.25, 0.5, and 1 mg/L) during germination. The quantitative and qualitative results indicated that 70 nm-sized PtNPs were more efficiently transferred in rice roots. The increase in the PtNP concentration restricted the particle uptake. Particle aggregation was common in plant cells and tended to dissolve on root surfaces. Notably, the dissolution of small particles was simultaneous with the growth of larger particles after PtNPs entered the rice tissues. Ionomic results revealed that PtNP accumulation induced element homeostasis in the shoot ionome. We observed a significant positive correlation between the PtNP concentration and Fe and B accumulation in rice shoots. Compared to particle size, the exposure concentration of PtNPs had a stronger effect on the shoot ionomic response. Our study provides better understanding of the correlation of ionomic change and NP quantitative accumulation induced by PtNPs in rice seedlings.

A rice–chicory rotation pattern ensures safe grain production and phytoremediation of cadmium-contaminated paddy fields: A four-year field experiment in southern China

Cadmium (Cd) contamination in paddy systems is a serious problem, and a strategy must be devised that ensures safe grain production and rapid remediation of soil Cd contamination. To investigate the remediation potential of crop rotation and its effect on Cd accumulation in rice, a four-year (seven-season) rice–chicory rotation field trial was conducted on a moderately acidic Cd-contaminated paddy soil. Rice was planted in summers, followed by straw removal, and chicory, a Cd-enrichment plant, was planted during winter fallows. Rotation effects were compared with those with rice only (control). Rice yields between the rotation and control were not significantly different, whereas Cd concentrations in rice tissues decreased in the rotation. Cd concentration in brown rice of the low-Cd variety decreased to less than 0.2 mg/kg (national food safety standard) from the third season onward, whereas in the high-Cd variety, it decreased from 0.43 mg/kg in the first season to 0.24 mg/kg in the fourth season. The highest Cd concentration in chicory aboveground parts was 24.47 mg/kg, with an enrichment factor of 27.81. Chicory had high regenerative capacity and was repeatedly harvested for biomass in multiple mowings, with average aboveground biomass over 2000 kg/ha in a single mowing. Theoretical phytoextraction efficiency (TPE) of one rice season with straw removal was 0.84%–2.44%, whereas the highest TPE of one chicory season reached 8.07%. The seven seasons of rice–chicory rotation extracted up to 407 g/ha Cd from soil with a TPE exceeding 20%. Therefore, rice–chicory rotation and straw removal can effectively reduce Cd accumulation in subsequent rice crops, without interrupting production and simultaneously rapidly remediating Cd-contaminated soil. Thus, the production potential of light to moderately Cd-contaminated paddy fields can be realized with crop rotation.

Efficacy of different amendments and residual effects on nickel toxicity and nutritional quality in wheat/rice continuous system and health risk assessment in Ultisol

ABSTRACT Rice straw (RS), biochar (BC) and lime (LM) have proved to be effective immobilizing agents in acidic contaminated soil. Up-to-date scientific data is lacking regarding residual effects of these amendments in acidic soils and wheat/rice cropping system. The objective was to analyze the efficacy of amendments to improve grain yields, nutritional quality, and reduce Ni bioavailability of wheat/rice rotation system. A pot experiment was conducted to examine the efficacy of RS, BC 10 and 20 g kg−1 and LM 10 g kg−1 application rates on plant growth, nutritional quality and Ni contents in wheat and rice tissues and grain. Amendments enhanced Ni immobilization, declined their uptake by plants and accumulation in the grains of both crops. Rice straw biochar reduced several factors like health risk assessment, Ni uptake and bioconcentration factor. BC 20 g kg−1 increased shoot, root and grain yields, while enhanced essential nutrients in the wheat/rice cropping system compared to untreated soil. Soil amendments significantly decreased toxicity characteristics leaching procedure (TCLP) extractable Ni by 42.25% and 42.62% and simple bioaccessibility extraction test (SBET) by 42.1% and 45.25% in post- wheat/rice crops. This process enhanced the safety of wheat/rice rotation cropping system to be consumed and mitigated security risks.

Plant Growth Promoting Rhizobacteria (PGPR) and Arbuscular Mycorrhizal Fungi Combined Application Reveals Enhanced Soil Fertility and Rice Production

Rice (Oryza sativa L.) is an important crop that is grown worldwide to supply the world’s expanding food demand. In the current study, the effects of plant growth-promoting rhizobacteria (PGPR) and Arbuscular mycorrhizal fungi (AMF) on soil fertility and rice growth were explored. Rice plants were inoculated to evaluate how AMF fungi and PGPR affect various aspects of soil and plants, implicating abiotic stress tolerances. The experiment was carried out in a completely randomized design with three replicates under the controlled conditions. Results depicted that the plants that were inoculated with a mixture of AMF and PGPR had better yields and nutritional concentrations, while both AMF and PGPR lowered soil pH and organic matter differently. Similarly, AMF and PGPR treatments significantly increased the amount of N, P, K, and B in the post-harvest soil. The PGPR-inoculated plants had a 10–40% higher buildup of N in their tissues. Similarly, when they were compared with non-infected plants, AMF-inoculated treatments demonstrated a greater N accumulation in the rice tissue. The maximum P content in plant tissues was 0.149% in PGPR5-infected plants, either alone or in combination with AMF. In T12, AMF + PGPR5 inoculated rice plants, the maximum K uptake was 1.98%, which was 54% higher than the control treatment. The sole application of AMF raised K buildup in rice tissues by 38% compared with the control treatment. The improved productivity of plants with AMF and PGPR (especially with PGPR5) was attributed to the increased availability of nutrients in the soil. As a result, rice plant growth, yield, and essential element uptakes were boosted significantly. The present study’s results suggested using the combined application of AMF + PGPR5 for improving the rice yield and for sustaining the soil health.

Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice

Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies. However, the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA, which is an important element for the post-transcriptional regulation of gene expression. To comprehensively profile the N6-methyladenosine (m6A) and N5-methylcytosine (m5C) modifications on RNA, direct RNA sequencing (DRS) using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice. Approximately 94 million reads were generated, with an average length ranging from 619 nt to 1013 nt, and a total of 45,707 transcripts across 34,763 genes were detected. Expression profiles of transcripts at the isoform level were quantified among tissues. Transcriptome-wide mapping of m6A and m5C demonstrated that both modifications exhibited tissue-specific characteristics. The transcripts with m6A modifications tended to be modified by m5C, and the transcripts with modifications presented higher expression levels along with shorter poly(A) tails than transcripts without modifications, suggesting the complexity of gene expression regulation. Gene Ontology analysis demonstrated that m6A- and m5C-modified transcripts were involved in central metabolic pathways related to the life cycle, with modifications on the target genes selected in a tissue-specific manner. Furthermore, most modified sites were located within quantitative trait loci that control important agronomic traits, highlighting the value of cloning functional loci. The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome, improving our understanding of the rice genome.

Translocation and metabolism of tricresyl phosphate in rice and microbiome system: Isomer-specific processes and overlooked metabolites

Tricresyl phosphate (TCP) is extensively used organophosphorus flame retardants and plasticizers that posed risks to organisms and human beings. In this study, the translocation and biotransformation behavior of isomers tri-p-cresyl phosphate (TpCP), tri-m-cresyl phosphate (TmCP), and tri-o-cresyl phosphate (ToCP) in rice and rhizosphere microbiome was explored by hydroponic exposure. TpCP and TmCP were found more liable to be translocated acropetally, compared with ToCP, although they have same molecular weight and similar Kow. Rhizosphere microbiome named microbial consortium GY could reduce the uptake of TpCP, TmCP, and ToCP in rice tissues, and promote rice growth. New metabolites were successfully identified in rice and microbiome, including hydrolysis, hydroxylated, methylated, demethylated, methoxylated, and glucuronide- products. The methylation, demethylation, methoxylation, and glycosylation pathways of TCP isomers were observed for the first time in organisms. What is more important is that the demethylation of TCPs could be an important and overlooked source of triphenyl phosphate (TPHP), which broke the traditional understanding of the only manmade source of toxic TPHP in the environment. Active members of the microbial consortium GY during degradation were revealed and metagenomic analysis indicated that most of active populations contained TCP-degrading genes. It is noteworthy that the strains and function genes in microbial consortium GY that responsible for TCP isomers’ transformation were different. These results can improve our understanding of the translocation and transformation of organic pollutant isomers in plants and rhizosphere microbiome.