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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Host-specific and tissue-dependent orchestration of microbiome community structure in traditional rice paddy ecosystems

Abstract Background and aim Rice and duckweed are two monocotyledonous plants that naturally coexist in paddy fields. While the presence of duckweed in paddy fields significantly improves rice productivity, the interplay between soil microbes and the two plant hosts in this agroecosystem remains unexplored. Methods We compared the bacterial community structure between duckweed, rice and soil from multiple rice paddies. We also isolated bacteria from these communities and characterized their modes of bacterial colonization and plant growth-promotion using model plants. Results Our data indicate that host-specific and tissue-dependent factors reproducibly orchestrate the bacterial community structure associated with their plant hosts. This is corroborated by results from culture-dependent approaches in which the dominant genus Pantoea isolated from rice aerial tissues can strongly attach and colonize gnotobiotic duckweed in spite of the low representation of this bacterial genus in the natural duckweed microbiome. Our study identified a core of 254 bacterial taxa that are consistently found in all rice and duckweed tissue samples from rice paddy fields. Furthermore, characterizing auxin-producing bacteria isolates from both plant species identified potential plant growth-promoting bacteria that may improve growth for both duckweed and rice in paddy fields. Conclusions Results from this work provide evidence for the importance of the host tissue and species context in determining plant colonization by microbes in the paddy field system. The resources generated in this study could facilitate the agronomic deployment of microbes for more sustainable rice production.

Agriculture↗
DOE OSTI2021

Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance

Improvements in yield and quality of rice are crucial for global food security. However, global rice production is substantially hindered by various biotic and abiotic stresses. Making further improvements in rice yield is a major challenge to the rice research community, which can be accomplished through developing abiotic stress-resilient rice varieties and engineering durable agrochemical-independent pathogen resistance in high-yielding elite rice varieties. This, in turn, needs increased understanding of the mechanisms by which stresses affect rice growth and development. Alternative splicing (AS), a post-transcriptional gene regulatory mechanism, allows rapid changes in the transcriptome and can generate novel regulatory mechanisms to confer plasticity to plant growth and development. Mounting evidence indicates that AS has a prominent role in regulating rice growth and development under stress conditions. Several regulatory and structural genes and splicing factors of rice undergo different types of stress-induced AS events, and the functional significance of some of them in stress tolerance has been defined. Both rice and its pathogens use this complex regulatory mechanism to devise strategies against each other. This review covers the current understanding and evidence for the involvement of AS in biotic and abiotic stress-responsive genes, and its relevance to rice growth and development. Furthermore, we discuss implications of AS for the virulence of different rice pathogens and highlight the areas of further research and potential future avenues to develop climate-smart and disease-resistant rice varieties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Fingerprint of rice paddies in spatial–temporal dynamics of atmospheric methane concentration in monsoon Asia

Agriculture (e.g., rice paddies) has been considered one of the main emission sources responsible for the sudden rise of atmospheric methane concentration (XCH 4 ) since 2007, but remains debated. Here we use satellite-based rice paddy and XCH 4 data to investigate the spatial-temporal relationships between rice paddy area, rice plant growth, and XCH 4 in monsoon Asia, which accounts for ~87% of the global rice area. We find strong spatial consistencies between rice paddy area and XCH 4 and seasonal consistencies between rice plant growth and XCH 4 . Our results also show a decreasing trend in rice paddy area in monsoon Asia since 2007, which suggests that the change in rice paddy area could not be one of the major drivers for the renewed XCH 4 growth, thus other sources and sinks should be further investigated. Our findings highlight the importance of satellite-based paddy rice datasets in understanding the spatial-temporal dynamics of XCH 4 in monsoon Asia.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Metabolomics analysis reveals differences in evolution between maize and rice

SUMMARY Metabolites are the intermediate and final products of metabolism, which play essential roles in plant growth, evolution and adaptation to changing climates. However, it is unclear how evolution contributes to metabolic variation in plants. Here, we investigated the metabolomics data from leaf and seed tissues in maize and rice. Using principal components analysis based on leaf metabolites but not seed metabolites, metabolomics data could be clearly separated for rice Indica and Japonica accessions, while two maize subgroups, temperate and tropical, showed more visible admixture. Rice and maize seed exhibited significant interspecific differences in metabolic variation, while within rice, leaf and seed displayed similar metabolic variations. Among 10 metabolic categories, flavonoids had higher variation in maize than rice, indicating flavonoids are a key constituent of interspecific metabolic divergence. Interestingly, metabolic regulation was also found to be reshaped dramatically from positive to negative correlations, indicative of the differential evolutionary processes in maize and rice. Moreover, perhaps due to this divergence significantly more metabolic interactions were identified in rice than maize. Furthermore, in rice, the leaf was found to harbor much more intense metabolic interactions than the seed. Our result suggests that metabolomes are valuable for tracking evolutionary history, thereby complementing and extending genomic insights concerning which features are responsible for interspecific differentiation in maize and rice.

Deng, Min↗
DOE OSTI2024

Biochemical Characterization of Rice Xylan Biosynthetic Enzymes in Determining Xylan Chain Elongation and Substitutions

Abstract Grass xylan consists of a linear chain of β-1,4-linked xylosyl residues that often form domains substituted only with either arabinofuranose (Araf) or glucuronic acid (GlcA)/methylglucuronic acid (MeGlcA) residues, and it lacks the unique reducing end tetrasaccharide sequence found in dicot xylan. The mechanism of how grass xylan backbone elongation is initiated and how its distinctive substitution pattern is determined remains elusive. Here, we performed biochemical characterization of rice xylan biosynthetic enzymes, including xylan synthases, glucuronyltransferases and methyltransferases. Activity assays of rice xylan synthases demonstrated that they required short xylooligomers as acceptors for their activities. While rice xylan glucuronyltransferases effectively glucuronidated unsubstituted xylohexaose acceptors, they transferred little GlcA residues onto (Araf)-substituted xylohexaoses and rice xylan 3-O-arabinosyltransferase could not arabinosylate GlcA-substituted xylohexaoses, indicating that their intrinsic biochemical properties may contribute to the distinctive substitution patterns of rice xylan. In addition, we found that rice xylan methyltransferase exhibited a low substrate binding affinity, which may explain the partial GlcA methylation in rice xylan. Furthermore, immunolocalization of xylan in xylem cells of both rice and Arabidopsis showed that it was deposited together with cellulose in secondary walls without forming xylan-rich nanodomains. Together, our findings provide new insights into the biochemical mechanisms underlying xylan backbone elongation and substitutions in grass species.

Cell Biology↗
DOE OSTI2022

Important Roles of Thiols in Methylmercury Uptake and Translocation by Rice Plants

We report the bioaccumulation of the neurotoxin methylmercury (MeHg) in rice is a significant concern due to its potential risk to humans. Thiols have been known to affect MeHg bioavailability in microorganisms, but how thiols influence MeHg accumulation in rice plants remains unknown. Here, we investigated effects of common low-molecular-weight thiols, including cysteine (Cys), glutathione (GSH), and penicillamine (PEN), on MeHg uptake and translocation by rice plants. Results show that rice roots can rapidly take up MeHg, and this process is influenced by the types and concentrations of thiols in the system. The presence of Cys facilitated MeHg uptake by roots and translocation to shoots, while GSH could only promote MeHg uptake, but not translocation, by roots. Conversely, PEN significantly inhibited MeHg uptake and translocation to shoots. Using labeled 13 Cys assays, we also found that MeHg uptake was coupled with Cys accumulation in rice roots. Moreover, analyses of comparative transcriptomics revealed that key genes associated with metallothionein and SULTR transporter families may be involved in MeHg uptake. These findings provide new insights into the uptake and translocation of MeHg in rice plants and suggest potential roles of thiol attributes in affecting MeHg bioavailability and bioaccumulation in rice.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Belowground plant allocation regulates rice methane emissions from degraded peat soils

Carbon-rich peat soils have been drained and used extensively for agriculture throughout human history, leading to significant losses of their soil carbon. One solution for rewetting degraded peat is wet crop cultivation. Crops such as rice, which can grow in water-saturated conditions, could enable agricultural production to be maintained whilst reducing CO 2 and N 2 O emissions from peat. However, wet rice cultivation can release considerable methane (CH 4 ). Water table and soil management strategies may enhance rice yield and minimize CH 4 emissions, but they also influence plant biomass allocation strategies. It remains unclear how water and soil management influences rice allocation strategies and how changing plant allocation and associated traits, particularly belowground, influence CH 4 -related processes. We examined belowground biomass (BGB), aboveground biomass (AGB), belowground:aboveground ratio (BGB:ABG), and a range of root traits (root length, root diameter, root volume, root area, and specific root length) under different soil and water treatments; and evaluated plant trait linkages to CH 4 . Rice (Oryza sativa L.) was grown for six months in field mesocosms under high (saturated) or low water table treatments, and in either degraded peat soil or degraded peat covered with mineral soil. We found that BGB and BGB:AGB were lowest in water saturated conditions where mineral soil had been added to the peat, and highest in low-water table peat soils. Furthermore, CH 4 and BGB were positively related, with BGB explaining 60% of the variation in CH 4 but only under low water table conditions. Our results suggest that a mix of low water table and mineral soil addition could minimize belowground plant allocation in rice, which could further lower CH 4 likely because root-derived carbon is a key substrate for methanogenesis. Minimizing root allocation, in conjunction with water and soil management, could be explored as a strategy for lowering CH 4 emissions from wet rice cultivation in degraded peatlands.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

On the roots of wetland plants such as rice, Fe(II) oxidation forms Fe(III) oxyhydroxide-rich plaques that modulate plant nutrient and metal uptake. The microbial roles in catalyzing this oxidation have been debated and it is unclear if these iron-oxidizers mediate other important biogeochemical and plant interactions. To investigate this, we studied the microbial communities, metagenomes, and geochemistry of iron plaque on field-grown rice, plus the surrounding rhizosphere and bulk soil. Plaque iron content (per mass root) increased over the growing season, showing continuous deposition. Analysis of 16S rRNA genes showed abundant Fe(II)-oxidizing and Fe(III)-reducing bacteria (FeOB and FeRB) in plaque, rhizosphere, and bulk soil. FeOB were enriched in relative abundance in plaque, suggesting FeOB affinity for the root surface. Gallionellaceae FeOB Sideroxydans were enriched during vegetative and early reproductive rice growth stages, while a Gallionella was enriched during reproduction through grain maturity, suggesting distinct FeOB niches over the rice life cycle. FeRB Anaeromyxobacter and Geobacter increased in plaque later, during reproduction and grain ripening, corresponding to increased plaque iron. Metagenome-assembled genomes revealed that Gallionellaceae may grow mixotrophically using both Fe(II) and organics. The Sideroxydans are facultative, able to use non-Fe substrates, which may allow colonization of rice roots early in the season. FeOB genomes suggest adaptations for interacting with plants, including colonization, plant immunity defense, utilization of plant organics, and nitrogen fixation. Taken together, our results strongly suggest that rhizoplane and rhizosphere FeOB can specifically associate with rice roots, catalyzing iron plaque formation, with the potential to contribute to plant growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Novel Mutant Alleles Reveal a Role of the Extra-Large G Protein in Rice Grain Filling, Panicle Architecture, Plant Growth, and Disease Resistance

Plant growth and grain filling are the key agronomical traits for grain weight and yield of rice. The continuous improvement in rice yield is required for a future sustainable global economy and food security. The heterotrimeric G protein complex containing a canonical α subunit (RGA1) couples extracellular signals perceived by receptors to modulate cell function including plant development and grain weight. We hypothesized that, besides RGA1, three atypical, extra-large GTP-binding protein (XLG) subunits also regulate panicle architecture, plant growth, development, grain weight, and disease resistance. Here, we identified a role of XLGs in agronomic traits and stress tolerance by genetically ablating all three rice XLGs individually and in combination using the CRISPR/Cas9 genome editing in rice. For this study, eight (three single, two double, and three triple) null mutants were selected. Three XLG proteins combinatorically regulate seed filling, because loss confers a decrease in grain weight from 14% with loss of one XLG and loss of three to 32% decrease in grain weight. Null mutations in XLG2 and XLG4 increase grain size. The mutants showed significantly reduced panicle length and number per plant including lesser number of grains per panicle compared to the controls. Loss-of-function of all individual XLGs contributed to 9% more aerial biomass compared to wild type (WT). The double mutant showed improved salinity tolerance. Moreover, loss of the XLG gene family confers hypersensitivity to pathogens. Our findings suggest that the non-canonical XLGs play important roles in regulating rice plant growth, grain filling, panicle phenotype, stress tolerance, and disease resistance. Genetic manipulation of XLG s has the potential to improve agronomic properties in rice.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Partial substitution of rice husks for manure in greenhouse vegetable fields: Insight from soil carbon stock and aggregate stability

Abstract Soil aggregate stability and C stock are key factors in greenhouse vegetable production, which are influenced by the application of different organic materials. However, the responses of soil aggregate stability and C stock to organic amendment in greenhouse vegetable fields are not well understood. A 5‐year study was carried out in greenhouse vegetable fields to investigate the effect of partial substitution of rice husks for manure on soil aggregate stability, C compositions, and their relationships. Four treatments included: (a) no organic fertilization (control), (b) 30 t ha −1 chicken manure (CM), (c) 30 t ha −1 rice husks (RH), and (d) 10 t ha −1 chicken manure plus 20 t ha −1 rice husks (MR). Rice husks addition significantly increased the proportion of >2 mm aggregates and mean weight diameter (MWD), while manure addition showed no difference with control. Polysaccharide and humin (HM) were increased with rice husks addition (RH and MR) compared with that in CM treatment. Polysaccharide and HM caused 86.03% variation of soil aggregate, in which polysaccharide and HM contributed 76.3 and 9.7%, respectively. The soil C stock in CM, RH, and MR treatments was increased by 146, 175, and 164% compared with control, respectively. Aliphatic‐C and amorphous Fe‐oxides (Fe‐ox) content were as higher in MR added soil than those in RH treatment. Partial substitution of rice husk for manure improved soil aggregation stability and thus enhanced C stock by suppling more polysaccharide, HM and liberated soil minerals, which was conducive to the sustainable development in greenhouse vegetable production.

Fei, Chao↗
DOE OSTI2021

A combined management scheme to simultaneously mitigate As and Cd concentrations in rice cultivated in contaminated paddy soil

Paddy soils in southern China are heavily co-polluted by arsenic (As) and cadmium (Cd). The accumulation of these contaminants in rice grains may pose a high health risk. We evaluated the impact of adjusted water management practice (i.e., conventional irrigation and aerobic treatment after heading stage) and the application of two immobilization agents (i.e., CaO and Fe2O3) on the accumulation of As and Cd in rice grains of three rice varieties (i.e., Jinyou-463, Jinyou-268, and Mabayouzhan). The different schemes were tested via conducting a field experiment in paddy soil in Shaoguan, Guangdong Province, China. The results showed that the combined scheme (selecting Jinyou-268, aerobic water management after the heading stage, and 0.09% CaO and 0.5% Fe2O3 amendments) exhibited the best performance in the reduction of As and Cd accumulation in rice grains. This combined scheme decreased the grain As concentration by 26.19% and maintained the Cd at a low level (0.056 mg/kg) as compared to the use of local conventional irrigation patterns. Moreover, health risk assessment demonstrated that by applying the optimal scheme, neither As nor Cd content in rice had carcinogenic risk. However, the grain As remains at a high non-carcinogenic risk. We suggest that future field study design should fully incorporate the uncertainty of the natural environment to make the research conclusions more feasible for popularization and utilization. This study demonstrated an approach of utilizing the synergy effects of various measures for safe rice production in fields subjected to As and Cd contaminations.

Yang, Xiao↗
DOE OSTI2023

Assessing the methane mitigation potential of innovative management in US rice production

Abstract Rice is an important global crop while also contributing significant anthropogenic methane (CH 4 ) emissions. To support the future of rice production, more information is needed on the impacts of sustainability-driven management used to grow rice with lower associated methane emissions. Recent support for the impacts of different growing practices in the US has prompted the application of a regional methodology (Tier 2) to estimate methane emissions in different rice growing regions. The methodology estimates rice methane emissions from the US Mid-South (MdS) and California (Cal) using region-specific scaling factors applied to a region-specific baseline flux. In our study, we leverage land cover data and soil clay content to estimate methane emissions using this approach, while also examining how changes in common production practices can affect overall emissions in the US. Our results indicated US rice cultivation produced between 0.32 and 0.45 Tg CH 4 annually, which were approximately 7% and 42% lower on average compared to Food and Agriculture Organization of the UN (FAO) and US Environmental Protection Agency (EPA) inventories, respectively. Our estimates were 63% greater on average compared to similar methods that lack regional context. Introducing aeration events into irrigation resulted in the greatest methane reductions across both regions. When accounting for differences between baseline and reduction scenarios, the US MdS typically had higher mitigation potential compared to Cal. The differences in cumulative mitigation potential across the 2008–2020 period were likely driven by lower production area clay content for the US MdS compared to Cal. The added spatial representation in the Tier 2 approach is useful in surveying how impactful methane-reducing practices might be within and across regions.

Environmental Sciences & Ecology↗
DOE OSTI2022

Extreme Low-Temperature Stress Affects Nutritional Quality of Amino Acids in Rice

Global climate change has increased the frequency of extreme climate events, and their effects on the nutritional quality, especially on amino acids in rice, have not been quantified. The data from a 3-year low temperature stress (LTS) experiment including two rice varieties (Huaidao 5 and Nanjing 46), seven minimum/maximum temperature levels (one optimal 21/27°C and six LTS levels from 17/23 to 6/12°C), and three LTS durations (3, 6, and 9 days) after flowering, revealed significant interactive effects of LTS at different stages, durations, and temperature levels on the content and accumulation of amino acids. LTS increased rice total amino acid content, while decreasing its accumulation, with higher sensitivities to LTS at the flowering stage than at the grain filling stage. In most treatments, the lysine (the first limiting amino acid) and phenylalanine content were increased under LTS at early and peak flowering stages but decreased at the grain filling stage in both varieties, and only leucine content was increased at all three stages after flowering, while the content of other essential amino acids differed among the two varieties. With an increase of 1°C·d per day in the accumulated cold degree days, the relative content of the essential amino acids was increased by 0.01–0.41%, depending on the rice variety and growth stage. Our results suggest that LTS can improve nutritional quality of amino acids of rice grains in terms of amino acids content, especially at flowering stage. These results provide critical insights for assessing the potential impact of extreme climates on the nutrient quality of rice under future climate change.

Kang, Min↗
DOE OSTI2025

Status on Genetic Resistance to Rice Blast Disease in the Post-Genomic Era

Rice blast, caused by Magnaporthe oryzae, is a major threat to global rice production, necessitating the development of resistant cultivars through genetic improvement. Breakthroughs in rice genomics, including the complete genome sequencing of japonica and indica subspecies and the availability of various sequence-based molecular markers, have greatly advanced the genetic analysis of blast resistance. To date, approximately 122 blast-resistance genes have been identified, with 39 of these genes cloned and molecularly characterized. The application of these findings in marker-assisted selection (MAS) has significantly improved rice breeding, allowing for the efficient integration of multiple resistance genes into elite cultivars, enhancing both the durability and spectrum of resistance. Pangenomic studies, along with AI-driven tools like AlphaFold2, RoseTTAFold, and AlphaFold3, have further accelerated the identification and functional characterization of resistance genes, expediting the breeding process. Future rice blast disease management will depend on leveraging these advanced genomic and computational technologies. Emphasis should be placed on enhancing computational tools for the large-scale screening of resistance genes and utilizing gene editing technologies such as CRISPR-Cas9 for functional validation and targeted resistance enhancement and deployment. These approaches will be crucial for advancing rice blast resistance, ensuring food security, and promoting agricultural sustainability.

Pedrozo, Rodrigo↗