To quickly obtain rice plant phenotypic traits, this study put forward the computational process of six rice phenotype features (e.g., crown diameter, perimeter of stem, plant height, surface area, volume, and projected leaf area) using terrestrial laser scanning (TLS) data, and proposed the extraction method for the tiller number of rice plants. Specifically, for the first time, we designed and developed an automated phenotype extraction tool for rice plants with a three-layer architecture based on the PyQt5 framework and Open3D library. The results show that the linear coefficients of determination (R2) between the measured values and the extracted values marked a better reliability among the selected four verification features. The root mean square error (RMSE) of crown diameter, perimeter of stem, and plant height is stable at the centimeter level, and that of the tiller number is as low as 1.63. The relative root mean squared error (RRMSE) of crown diameter, plant height, and tiller number stays within 10%, and that of perimeter of stem is 18.29%. In addition, the user-friendly automatic extraction tool can efficiently extract the phenotypic features of rice plant, and provide a convenient tool for quickly gaining phenotypic trait features of rice plant point clouds. However, the comparison and verification of phenotype feature extraction results supported by more rice plant sample data, as well as the improvement of accuracy algorithms, remain as the focus of our future research. The study can offer a reference for crop phenotype extraction using 3D point clouds.

Phenylpropanoid biosynthesis plays crucial roles in the adaptation to cadmium (Cd) stress. Nevertheless, few reports have dabbled in physiological mechanisms of such super pathway regulating Cd accumulation in plants. Herein, by integrating transcriptomic, histological and molecular biology approaches, the present study dedicated to clarify molecular mechanism on how rice adapt to Cd stress via phenylpropanoid biosynthesis. Our analysis identified that the enhancement of phenylpropanoid biosynthesis was as a key response to Cd stress. Intriguingly, POD occupied a significant part in this process, with the number of POD related genes accounted for 26/29 of all upregulated genes in phenylpropanoid biosynthesis. We further used SHAM (salicylhydroxamic acid, the POD inhibitor) to validate that POD exhibited a negative correlation with the Cd accumulation in rice tissues, and proposed two intrinsic molecular mechanisms on POD in contributing to Cd detoxification. One strategy was that POD promoted the formation of lignin and CSs both in endodermis and exodermis for intercepting Cd influx. In detail, inhibited POD induced by external addition of SHAM decreased the content of lignin by 50.98-66.65 % and delayed percentage of the DTIP-CS to root length by 39.17-104.51 %. The other strategy was expression of transporter genes involved in Cd uptake, including OsIRT1, OsIRT2, OsZIP1 and OsZIP, negatively regulated by POD. In a word, our findings firstly draws a direct link between POD activity and the Cd accumulation, which is imperative for the breeding of rice with low-Cd-accumulating capacity in the future.

Iron (Fe) isotopes were utilized to provide insights into the temporal changes underlying Fe uptake and translocation during rice growth (tillering, jointing, flowering, and maturity stages) in soil-rice systems under typical flooding-drainage alternation. Fe isotopic composition (δ56Fe values) of the soil solution generally decreased at vegetative stages in flooding regimes but increased during grain-filling. Fe plaques were the prevalent source of Fe uptake, as indicated by the concurrent increase in the δ56Fe values of Fe plaques and rice plants during rice growth. The increasing fractionation magnitude from stem/nodes I to flag leaves can be attributed to the preferred phloem transport of light isotopes toward grains, particularly during grain-filling. This study demonstrates that rice plants take up heavy Fe isotopes from Fe plaque and soil solution via strategy II during flooding and the subsequent drainage period, respectively, thereby providing valuable insights into improving the nutritional quality during rice production.

Quantum dots (QDs) are widely applied and inevitably released into the environment. The biotransformation of Se in typical CdSe/ZnS QDs coated with glutathione (CdSe/ZnS-GSH) to volatile alkyl selenides and the fate of alkyl selenides in the hydroponically grown rice system were investigated herein. After a 10-day exposure to CdSe/ZnS-GSH (100 nmol L-1), seven alkyl selenides, dimethyl selenide (DMSe), dimethyl diselenide (DMDSe), methyl selenol (MSeH), ethylmethyl selenide (EMSe), ethylmethyl diselenide (EMDSe), dimethyl selenenyl sulfide (DMSeS), and ethylmethyl selenenyl sulfide (EMSeS), were detected in the exposure system using the suspect screening strategy. CdSe/ZnS-GSH was first biotransformed to DMSe and DMDSe by plant and microorganisms. The generated DMSe was volatilized to the gas phase, adsorbed and absorbed by leaves and stems, downward transported, and released into the hydroponic solution, whereas DMDSe tended to be adsorbed/absorbed by roots and upward transported to stems. The airborne DMSe and DMDSe also partitioned from the gas phase to the hydroponic solution. DMSe and DMDSe in the exposure system were further transformed to DMSeS, EMSeS, EMSe, EMDSe, and MSeH. This study gives a comprehensive understanding on the behaviors of Se in CdSe/ZnS-GSH in a rice plant system and provides new insights into the environmental fate of CdSe/ZnS QDs.

Microplastics (MPs) and nanoplastics (NPs) are global pollutants with emerging concerns. Methods to predict and screen their toxicity are crucial. Elemental dyshomeostasis can be used to assess toxicity of environmental pollutants. Non-targeted metallomics, combining synchrotron radiation X-ray fluorescence (SRXRF) and machine learning, has successfully differentiated cancer patients from healthy individuals. The whole idea of this work is to screen the phytotoxicity of nano polyethylene terephthalate (nPET) and micro polyethylene terephthalate (mPET) through non-targeted metallomics with SRXRF and deep learning algorithms. Firstly, Seed germination, seedling growth, photosynthetic changes, and antioxidant activity were used to evaluate the toxicity of mPET and nPET. It was showed that nPET, at 10 mg/L, was more toxic to rice seedlings, inhibiting growth and impairing chlorophyll content, MDA content, and SOD activity compared to mPET. Then, rice seedling leaves exposed to nPET or mPET was examined with SRXRF, and the SRXRF data was differentiated with deep learning algorithms. It was showed that the one-dimensional convolutional neural network (1D-CNN) model achieved 98.99% accuracy without data preprocessing in screening mPET and nPET exposure. In all, non-targeted metallomics with SRXRF and 1D-CNN can effectively screen the exposure and phytotoxicity of nPET/mPET and potentially other emerging pollutants. Further research is needed to assess the phytotoxicity of different types of MPs/NPs using non-targeted metallomics.

Eighteen pesticide-degrading endophytic bacteria were isolated from the roots, stems, and leaves of healthy rice plants and identified through 16S rRNA gene sequencing. Furthermore, biochemical properties, including enzyme production, dye degradation, anti-bacterial activities, plant-growth-promoting traits, including N-fixation, P-solubilization, auxin production, and ACC-deaminase activities of these naturally occurring endophytic bacteria along with their four consortia, were characterized. Enterobacter cloacae HSTU-ABk39 and Enterobacter sp. HSTU-ABk36 displayed inhibition zones of 41.5 ± 1.5 mm, and 29 ± 09 mm against multidrug-resistant human pathogenic bacteria Staphylococcus aureus and Staphylococcus epidermidis, respectively. FT-IR analysis revealed that all eighteen isolates were able to degrade chlorpyrifos pesticide. Our study confirms that pesticide-degrading endophytic bacteria from rice plants play a key role in enhancing plant growth. Notably, rice plants grown in pots containing reduced urea (30%) mixed with either endophytic bacterial consortium-1, consortium-2, consortium-3, or consortia-4 demonstrated an increase of 17.3%, 38.6%, 18.2%, and 39.1% yields, respectively, compared to the control plants grown in pots containing 100% fertilizer. GC-MS/MS analysis confirmed that consortia treatment caused the degradation of chlorpyrifos into different non-toxic metabolites, including 2-Hydroxy-3,5,6 trichloropyridine, Diethyl methane phosphonate, Phorate sulfoxide, and Carbonochloridic. Thus, these isolates could be deployed as bio-stimulants to improve crop production by creating a sustainable biological system.

Finding a method, which may indicate the contribution of soil parameters including organic matter, pH and clay to pretilachlor leaching (persistence) in the soil, with the use of a suitable indicator, which indicates pretilachlor presence in the soil is of significance. Accordingly, using undisturbed soil columns, four paddy fields (A, B, C, D) in the suburbs of Babol city (Mazandaran province, northern Iran) were sampled before the preparation and irrigation of the fields in April 2021. Soil samples were transferred into PVC pipes (divided into 2 cm layers) measuring 12 (height) × 10 cm (diameter), and were injected with pretilachlor at the recommended (1.75 L/ha) and high doses (3.5 L/ha). The surface layers of all fields had a higher concentration of pretilachlor and organic matter with the highest contribution to pretilachlor persistence followed by clay and pH. In the 0-4 cm depth, herbicide concertation was the lowest in field A (139 mg/kg) and the highest in field C (161 mg/kg). The corresponding values for organic matter were equal to 1.88 and 5.68%, respectively. The bioassay of rice (the indicator plant), with a significant correlation with chemical analysis results, indicated field A and field C had the pretilachlor infiltration of 6 and 4 cm, respectively. Accordingly, rice is a suitable plant indicator for measuring the presence of pretilachlor as examining its shoot length is a good criterion for bioassay. Additionally, changes in the amount of organic matter in different soil layers can be used to predict the leaching level of pretilachlor.

Ferromanganese oxide biochar composite (FMBC) is an efficient remediation material for cadmium -contaminated soils. However, the effect of FMBC under varied water managements on the remediation of Cd-polluted soil is unclear. In this study, we conducted both incubation and field experiments to investigate the combined effects of corn-stover-derived biochar modified with ferromanganese on the immobilization and uptake of Cd by rice under continuous aerobic (A), aerobic-flooded (AF), and flooded-aerobic (FA) water management regimes. The results showed that loading iron-manganese significantly increased the maximum sorption capacity (Qm) of Cd on FMBC (50.46 mg g-1) due to increased surface area, as compared to the pristine biochar (BC, 31.36 mg g-1). The results revealed that soil Eh and pH were significantly affected by FMBC and it\'s synergistic application with different water regimes, thus causing significant differences in the concentrations of DTPA-extractable Cd under different treatments. The lowest DTPA-extractable Cd content (0.28-0.46 mg-1) was observed in the treatment with FMBC (2.5 %) combined FA water amendment, which reduced the content of available Cd in soil by 2.63-28.4 %. Moreover, the treatments with FMBC-FA resulted the proportion of residual Cd increased by 22.2 % compared to the control. Variations in the content and fraction of Cd had a significant influence on its accumulation in the rice grains. The FMBC-FA treatments reduced the Cd concentration in roots, shoots and grains by 37.97 %, 33.98 %, and 53.66 %, respectively, when compared with the control. Predominantly because of the reduction in Cd biological toxicity and the improved soil nutrient content, the combined application increased the biomass and yield of rice to some extent. Taken together, the combination of the Fe-Mn modified biochar and flooded-aerobic water management may potentially be applied in Cd-polluted soil to mitigate the impacts of Cd on rice production.

The aim of this study was to develop an efficient bioinoculant for amelioration of adverse effects from chilling stress (10°C), which are frequently occurred during rice seedling stage. Seed germination bioassay under chilling condition with rice (Oryza sativa L.) cv. Tainan 11 was performed to screen for plant growth-promoting (PGP) bacteria among 41 chilling-tolerant rice endophytes. And several agronomic traits were used to evaluate the effects of bacterial inoculation on rice seedling, which were experienced for 7-d chilling stress in walk-in growth chamber. The field trials were further used to verify the performance of potential PGP endophytes on rice growth. A total of three endophytes with multiple PGP traits were obtained. It was demonstrated that Pseudomonas sp. CC-LS37 inoculation led to 18% increase of maximal efficiency of Photosystem II (PSII) after 7-d chilling stress and 7% increase of chlorophyll a content, and 64% decline of malondialdehyde content in shoot after 10-d recovery at normal temperature in walk-in growth chamber. In field trial, biopriming of seeds with strain CC-LS37 caused rice plants to increase shoot chlorophyll soil plant analysis development values (by 2.9% and 2.5%, respectively) and tiller number (both by 61%) under natural climate and chilling stress during the end of tillering stage, afterward 30% more grain yield was achieved. In conclusion, strain CC-LS37 exerted its function in increase of tiller number of chilling stress-treated rice seedlings via improvement of photosynthetic characteristics, which in turn increases the rice grain yield. This study also proposed multiple indices used in the screening of potential endophytes for conferring chilling tolerance of rice plants.

The Reference Transcriptomic Dataset (RTD) is an accurate and comprehensive collection of transcripts originating from a given organism. It holds the key to precise transcript quantification and downstream analysis of differential expressions and regulations. Currently, transcriptome annotations for most crop plants are far from complete. For example, Oryza sativa indica (O. sativa indica) is reported to have 40,759 transcripts in the Ensembl database without alternative transcript isoforms and alternative splicing (AS) events. To generate a high-quality RTD, we conducted RNA sequencing of rice leaf samples collected at various time points during Rhizoctonia solani infection. The obtained reads were analyzed by adopting the recently developed computational analysis pipeline to assemble the RTD with increased transcript and AS diversity for O. sativa indica (IndicaRTD). After stringent quality filtering, the newly constructed transcriptome annotation was comprised of 122,968 non-redundant transcripts from 53,695 genes. This study identified many novel transcripts compared to Ensembl deposited data that are important for regulating molecular and physiological processes in the plant system. Currently, the assembled IndicaRTD must allow fast quantification of transcript and gene expression with high precision.