Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice

Mutation of rice SM1 enhances solid leaf midrib formation and increases methane emissions

The leaf midrib system is essential for plant growth and development, facilitating nutrient transport, providing structural support, enabling gas exchange, and enhancing resilience to environmental stresses. However, the molecular mechanism regulating leaf midrib development is still unclear.In this study, we reported a rice solid midrib 1 (sm1) mutant, exhibiting solid leaf aerenchyma and abaxial rolling leaves due to abnormal development of parenchyma and bulliform cells. Map-based cloning revealed that SM1 encodes a litter zipper protein (ZPR). SM1 was mainly expressed in the sheaths and basal midrib and was associated with the nucleus. Further experiments indicated that SM1 can interact with OSHB1, preventing the formation of OSHB:OSHB dimers and subsequently repressing the expression of OSH1 involved in the regulation and maintenance of apical stem meristem formation. The sm1 mutant reduced long-distance oxygen transport ability from shoot to root. The impaired oxygen transport in the sm1 mutant may have contributed to the increase in methanogens and elevated methane emissions. Collectively, our findings revealed that the SM1-OSHB1-OSH1 modules regulate leaf aerenchyma development in rice. These modules not only enhance our understanding of the molecular mechanism of rice leaf aerenchyma development but also offer insights for reducing methane emissions through genetic modification.

Photosynthesis regulates tillering bud elongation and nitrogen-use efficiency via sugar-induced NGR5 in rice

Rice tillering is one of the most important agronomical traits largely determining grain yield. Photosynthesis and nitrogen availability are two important factors affecting rice tiller bud elongation; however, underlying mechanism and their cross-talk is poorly understood. Here, we used map-based cloning, transcriptome profiling, phenotypic analysis, and molecular genetics to understand the roles of the Decreased Tiller Number 1 (DTN1) gene that encodes the fructose-1,6-bisphosphate aldolase and involves in photosynthesis required for light-induced axillary bud elongation in rice. Deficiency of DTN1 results in the reduced photosynthetic rate and decreased contents of sucrose and other sugars in both leaves and axillary buds, and the reduced tiller number in dtn1 mutant could be partially rescued by exogenous sucrose treatment. Furthermore, we found that the expression of nitrogen-mediated tiller growth response 5 (NGR5) was remarkably decreased in shoot base of dtn1-2, which can be activated by sucrose treatment. Overexpression of NGR5 in the dtn1-2 could partially rescue the reduced tiller number, and the tiller number of dtn1-2 was insensitive to nitrogen supply. This work demonstrated that the sugar level regulated by photosynthesis and DTN1 could positively regulate NGR5 expression, which coordinates the cross-talk between carbon and nitrate to control tiller bud outgrowth in rice.

Fumarate reductase drives methane emissions in the genus Oryza through differential regulation of the rhizospheric ecosystem

The emergence of waterlogged Oryza species ∼15Mya (million years ago) supplied an anoxic warm bed for methane-producing microorganisms, and methane emissions have hence accompanied the entire evolutionary history of the genus Oryza. However, to date no study has addressed how methane emission has been altered during Oryza evolution. In this paper we used a diverse collection of wild and cultivated Oryza species to study the relation between Oryza evolution and methane emissions. Phylogenetic analyses and methane detection identified a co-evolutionary pattern between Oryza and methane emissions, mediated by the diversity of the rhizospheric ecosystems arising from different oxygen levels. Fumarate was identified as an oxygen substitute used to retain the electron transport/energy production in the anoxic rice root, and the contribution of fumarate reductase to Oryza evolution and methane emissions has also been assessed. We confirmed the between-species patterns using genetic dissection of the traits in a cross between a low and high methane-emitting species. Our findings provide novel insights on the evolutionary processes of rice paddy methane emissions: the evolution of wild rice produces different Oryza species with divergent rhizospheric ecosystem attributing to the different oxygen levels and fumarate reductase activities, methane emissions are comprehensively assessed by the rhizospheric environment of diversity Oryza species and result in a co-evolution pattern.

Rice rhizobiome engineering for climate change mitigation

The year 2023 was the warmest year since 1850. Greenhouse gases, including CO2 and methane, played a significant role in increasing global warming. Among these gases, methane has a 25-fold greater impact on global warming than CO2. Methane is emitted during rice cultivation by a group of rice rhizosphere microbes, termed methanogens, in low oxygen (hypoxic) conditions. To reduce methane emissions, it is crucial to decrease the methane production capacity of methanogens through water and fertilizer management, breeding of new rice cultivars, regulating root exudation, and manipulating rhizosphere microbiota. In this opinion article we review the recent developments in hypoxia ecology and methane emission mitigation and propose potential solutions based on the manipulation of microbiota and methanogens for the mitigation of methane emissions.

Spatiotemporal dynamic of rice production and its carbon footprint in Hainan, China: Implications for food security and environmental sustainability

Rice (Oryza sativa L.) feeds more than half of the global population and faces the critical issues related to food security and environmental sustainability. This study analyzed double rice production data from 2010 to 2020 to assess its spatiotemporal dynamic in food production and carbon (C) footprint in Hainan province, China. The results revealed a 29.5% reduction in rice planting area, leading to a significantly decreased rice self-sufficiency rate from 38% to 33% from 2010 to 2020. During this period, the carbon footprint per unit area (CFa) for early, late, and double rice showed a fluctuating upward trend ranging from 8.1 to 8.4, 8.9 to 9.2, and 17.0 to 17.4 t CO2-eq ha-1, respectively. The total greenhouse gas (GHG) emissions of rice production decreased to around 2 million t CO2-eq, primarily due to reduced planting area. The C sequestration initially increased before decreasing to 1.2 million t C in 2020 at a temporal scale. Spatially, the northeast and southwest regions exhibited ∼70% of the total GHG emissions and ∼80% of C sequestration. The regional C footprint per unit yield displayed less favorable outcomes, with some areas (e.g., Wenchang and Haikou) experiencing emission hotspots in recent years. Higher yield and smaller CFa for Lingao and Tunchang were observed compared to the average between 2010 and 2020. This study provides insights into the spatiotemporal dynamics of double rice production and GHG emissions in Hainan, offering a scientific reference for regional food security and environmental sustainability.

Ingrained: Rice farming and the risk of zoonotic spillover, examples from Cambodia

Rice cultivation in Southeast Asia is a One Health interface intersecting human, animal, and environmental health. This complexity creates a potential for zoonotic transmission between diverse reservoirs. Bats harbor viruses like Nipah; mosquitoes transmit arboviruses; rodents spread hantaviruses. Domestic animals- including pigs with influenza and dogs with rabies and aquatic animals can also transmit pathogens. Climate change and urbanization may further disrupt rice agro-ecologies. This paper explores animal viral reservoirs, vectors, and historical practices associated with risk in rice farming. Climate and land use changes could enhance spillover. Solutions are proposed, including surveillance of animals, vectors, water, and air to detect threats before major outbreaks, such as improved biosecurity, hygiene, and livestock vaccinations. Ecological viral surveillance and agricultural interventions together can reduce zoonotic transmission from rice farming.

A low-methane rice with high-yield potential realized via optimized carbon partitioning

Global rice cultivation significantly contributes to anthropogenic methane emissions. The methane emissions are caused by methane-producing microorganisms (methanogenic archaea) that are favoured by the anoxic conditions of paddy soils and small carbon molecules released from rice roots. However, different rice cultivars are associated with differences in methane emission rates suggesting that there is a considerable natural variation in this trait. Starting from the hypothesis that sugar allocation within a plant is an important factor influencing both yields and methane emissions, the aim of this study was to produce high-yielding rice lines associated with low methane emissions. In this study, the offspring (here termed progeny lines) of crosses between a newly characterized low-methane rice variety, Heijing 5, and three high-yielding elite varieties, Xiushui, Huayu and Jiahua, were selected for combined low-methane and high-yield properties. Analyses of total organic carbon and carbohydrates showed that the progeny lines stored more carbon in above-ground tissues than the maternal elite varieties. Also, metabolomic analysis of rhizospheric soil surrounding the progeny lines showed reduced levels of glucose and other carbohydrates. The carbon allocation, from roots to shoots, was further supported by a transcriptome analysis using massively parallel sequencing of mRNAs that demonstrated elevated expression of the sugar transporters SUT-C and SWEET in the progeny lines as compared to the parental varieties. Furthermore, measurement of methane emissions from plants, grown in greenhouse as well as outdoor rice paddies, showed a reduction in methane emissions by approximately 70 % in the progeny lines compared to the maternal elite varieties. Taken together, we report here on three independent low-methane-emission rice lines with high yield potential. We also provide a first molecular characterisation of the progeny lines that can serve as a foundation for further studies of candidate genes involved in sugar allocation and reduced methane emissions from rice cultivation.

Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils

Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria-methanotrophs and their respective traits.

TabHLH95-TaNF-YB1 module promotes grain starch synthesis in bread wheat

Starch is the most abundant substance in wheat (Triticum aestivum L.) endosperm and provides the major carbohydrate energy for human daily life. Starch synthesis-related (SSR) genes are believed to be spatiotemporally specific, but their transcriptional regulation remains unclear in wheat. Here, we investigate the role of the basic helix-loop-helix (bHLH) transcription factor TabHLH95 in starch synthesis. TabHLH95 is preferentially expressed in the developing grains in wheat and encodes a nucleus localized protein without autoactivation activity. The Tabhlh95 knockout mutants display smaller grain size and less starch content than wild type, whereas overexpression of TabHLH95 enhances starch accumulation and significantly improves thousand grain weight. Transcriptome analysis reveals that the expression of multiple SSR genes is significantly reduced in the Tabhlh95 mutants. TabHLH95 binds to the promoters of ADP-glucose pyrophosphorylase large subunit 1 (AGPL1-1D/-1B), AGPL2-5D, and isoamylase (ISA1-7D) and enhances their transcription. Intriguingly, TabHLH95 interacts with the nuclear factor Y (NF-Y) family transcription factor TaNF-YB1, thereby synergistically regulating starch synthesis. These results suggest that the TabHLH95-TaNF-YB1 complex positively modulates starch synthesis and grain weight by regulating the expression of a subset of SSR genes, thus providing a good potential approach for genetic improvement of grain productivity in wheat.

Ratoon Rice Cropping Mitigates the Greenhouse Effect by Reducing CH4 Emissions through Reduction of Biomass during the Ratoon Season

The ratoon rice cropping system (RR) is developing rapidly in China due to its comparable annual yield and lower agricultural and labor inputs than the double rice cropping system (DR). Here, to further compare the greenhouse effects of RR and DR, a two-year field experiment was carried out in Hubei Province, central China. The ratoon season showed significantly lower cumulative CH4 emissions than the main season of RR, the early season and late season of DR. RR led to significantly lower annual cumulative CH4 emissions, but no significant difference in cumulative annual N2O emissions compared with DR. In RR, the main and ratoon seasons had significantly higher and lower grain yields than the early and late seasons of DR, respectively, resulting in comparable annual grain yields between the two systems. In addition, the ratoon season had significantly lower global warming potential (GWP) and greenhouse gas intensity-based grain yield (GHGI) than the main and late seasons. The annual GWP and GHGI of RR were significantly lower than those of DR. In general, the differences in annual CH4 emissions, GWP, and GHGI could be primarily attributed to the differences between the ratoon season and the late season. Moreover, GWP and GHGI exhibited significant positive correlations with cumulative emissions of CH4 rather than N2O. The leaf area index (LAI) and biomass accumulation in the ratoon season were significantly lower than those in the main season and late season, and CH4 emissions, GWP, and GHGI showed significant positive correlations with LAI, biomass accumulation and grain yield in the ratoon and late season. Finally, RR had significantly higher net ecosystem economic benefits (NEEB) than DR. Overall, this study indicates that RR is a green cropping system with lower annual CH4 emissions, GWP, and GHGI as well as higher NEEB.

Characterisation of a low methane emission rice cultivar suitable for cultivation in high latitude light and temperature conditions

Rice cultivation on paddy soil is commonly associated with emissions of methane, a greenhouse gas, but rice varieties may differ in their actual level of emissions. This study analysed methane emissions associated with 22 distinct rice genotypes, using gas chromatography, and identified the cultivar Heijing 5 from northern China as a potential low-methane rice variety. To confirm this and to examine whether Heijing 5 can perform similarly at higher latitudes, Heijing 5 was cultivated in field trials in China (lat. 32° N) and Sweden (lat. 59° N) where (i) methane emissions were measured, (ii) methanogen abundance in the rhizosphere was determined using quantitative PCR, and (iii) the concentrations of nutrients in water and of heavy metals in rice grain and paddy soil were analysed. The results demonstrated that the low-methane rice cultivar Heijing 5 can successfully complete an entire growth period at high-latitude locations such as central Sweden. Massively parallel sequencing of mRNAs identified candidate genes involved in day length and cold acclimatisation. Cultivation of Heijing 5 in central Sweden was also associated with relatively low heavy metal accumulation in rice grains and lowered nutrient losses to neighbouring water bodies.

Genetically Modified Rice Is Associated with Hunger, Health, and Climate Resilience

While nearly one in nine people in the world deals with hunger, one in eight has obesity, and all face the threat of climate change. The production of rice, an important cereal crop and staple food for most of the world's population, faces challenges due to climate change, the increasing global population, and the simultaneous prevalence of hunger and obesity worldwide. These issues could be addressed at least in part by genetically modified rice. Genetic engineering has greatly developed over the century. Genetically modified rice has been approved by the ISAAA's GM approval database as safe for human consumption. The aim behind the development of this rice is to improve the crop yield, nutritional value, and food safety of rice grains. This review article provides a summary of the research data on genetically modified rice and its potential role in improving the double burden of malnutrition, primarily through increasing nutritional quality as well as grain size and yield. It also reviews the potential health benefits of certain bioactive components generated in genetically modified rice. Furthermore, this article discusses potential solutions to these challenges, including the use of genetically modified crops and the identification of quantitative trait loci involved in grain weight and nutritional quality. Specifically, a quantitative trait locus called grain weight on chromosome 6 has been identified, which was amplified by the Kasa allele, resulting in a substantial increase in grain weight and brown grain. An overexpressing a specific gene in rice, Oryza sativa plasma membrane H+-ATPase1, was observed to improve the absorption and assimilation of ammonium in the roots, as well as enhance stomatal opening and photosynthesis rate in the leaves under light exposure. Cloning research has also enabled the identification of several underlying quantitative trait loci involved in grain weight and nutritional quality. Finally, this article discusses the increasing threats of climate change such as methane-nitrous oxide emissions and global warming, and how they may be significantly improved by genetically modified rice through modifying a water-management technique. Taken together, this comprehensive review will be of particular importance to the field of bioactive components of cereal grains and food industries trying to produce high-quality functional cereal foods through genetic engineering.

Variations in the archaeal community and associated methanogenesis in peat profiles of three typical peatland types in China

BACKGROUND

Peatlands contain about 500 Pg of carbon worldwide and play a dual role as both a carbon sink and an important methane (CH₄) source, thereby potentially influencing climate change. However, systematic studies on peat properties, microorganisms, methanogenesis, and their interrelations in peatlands remain limited, especially in China. Therefore, the present study aims to investigate the physicochemical properties, archaeal community, and predominant methanogenesis pathways in three typical peatlands in China, namely Hani (H), Taishanmiao (T), and Ruokeba (R) peatlands, and quantitively determine their CH₄ production potentials.

RESULTS

These peatlands exhibited high water content (WC) and total carbon content (TC), as well as low pH values. In addition, R exhibited a lower dissolved organic carbon concentration (DOC), as well as higher total iron content (TFe) and pH values compared to those observed in T. There were also clear differences in the archaeal community between the three peatlands, especially in the deep peat layers. The average relative abundance of the total methanogens ranged from 10 to 12%, of which Methanosarcinales and Methanomicrobiales were the most abundant in peat samples (8%). In contrast, Methanobacteriales were mainly distributed in the upper peat layer (0-40 cm). Besides methanogens, Marine Benthic Group D/Deep-Sea Hydrothermal Vent Euryarchaeotic Group 1 (MBG-D/DHVEG-1), Nitrosotaleales, and several other orders of Bathyarchaeota also exhibited high relative abundances, especially in T. This finding might be due to the unique geological conditions, suggesting high archaeal diversity in peatlands. In addition, the highest and lowest CH₄ production potentials were 2.38 and 0.22 μg g^-1 d^-1 in H and R, respectively. The distributions of the dominant methanogens were consistent with the respective methanogenesis pathways in the three peatlands. The pH, DOC, and WC were strongly correlated with CH₄ production potentials. However, no relationship was found between CH₄ production potential and methanogens, suggesting that CH₄ production in peatlands may not be controlled by the relative abundance of methanogens.

CONCLUSIONS

The results of the present study provide further insights into CH₄ production in peatlands in China, highlighting the importance of the archaeal community and peat physicochemical properties for studies on methanogenesis in distinct types of peatlands.

Improved bioenergy value of residual rice straw by increased lipid levels from upregulation of fatty acid biosynthesis

BACKGROUND

Rice (Oryza sativa) straw is a common waste product that represents a considerable amount of bound energy. This energy can be used for biogas production, but the rate and level of methane produced from rice straw is still low. To investigate the potential for an increased biogas production from rice straw, we have here utilized WRINKLED1 (WRI1), a plant AP2/ERF transcription factor, to increase triacylglycerol (TAG) biosynthesis in rice plants. Two forms of Arabidopsis thaliana WRI1 were evaluated by transient expression and stable transformation of rice plants, and transgenic plants were analyzed both for TAG levels and biogas production from straw.

RESULTS

Both full-length AtWRI1, and a truncated form lacking the initial 141 amino acids (including the N-terminal AP2 domain), increased fatty acid and TAG levels in vegetative and reproductive tissues of Indica rice. The stimulatory effect of the truncated AtWRI1 was significantly lower than that of the full-length protein, suggesting a role for the deleted AP2 domain in WRI1 activity. Full-length AtWRI1 increased TAG levels also in Japonica rice, indicating a conserved effect of WRI1 in rice lipid biosynthesis. The bio-methane production from rice straw was 20% higher in transformants than in the wild type. Moreover, a higher producing rate and final yield of methane was obtained for rice straw compared with rice husks, suggesting positive links between methane production and a high amount of fatty acids.

CONCLUSIONS

Our results suggest that heterologous WRI1 expression in transgenic plants can be used to improve the metabolic potential for bioenergy purposes, in particular methane production.

The role of rice cultivation in changes in atmospheric methane concentration and the Global Methane Pledge

Resumption of the increase in atmospheric methane (CH₄ ) concentrations since 2007 is of global concern and may partly have resulted from emissions from rice cultivation. Estimates of CH₄ emissions from rice fields and abatement potential are essential to assess the contribution of improved rice management in achieving the targets of the Global Methane Pledge agreed upon by over 100 countries at COP26. However, the contribution of CH₄ emissions from rice fields to the resumed CH₄ growth and the global abatement potential remains unclear. In this study, we estimated the global CH₄ emissions from rice fields to be 27 ± 6 Tg CH₄ year^-1 in the recent decade (2008-2017) based on the 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories. The trend of CH₄ emissions from rice cultivation showed an increase followed by no significant change and then, a stabilization over 1990-2020. Consequently, the contribution of CH₄ emissions from rice fields to the renewed increase in atmospheric CH₄ concentrations since 2007 was minor. We summarized the existing low-cost measures and showed that improved water and straw management could reduce one-third of global CH₄ emissions from rice fields. Straw returned as biochar could reduce CH₄ emissions by 12 Tg CH₄ year^-1 , equivalent to 10% of the total reduction of all anthropogenic emissions. We conclude that other sectors than rice cultivation must have contributed to the renewed increase in atmospheric CH₄ concentrations, and that optimizing multiple mitigation measures in rice fields could contribute significantly to the abatement goal outlined in the Global Methane Pledge.

More than the main structural genes: Regulation of resistant starch formation in rice endosperm and its potential application

In the past decade, research on resistant starch has evoked interest due to the prevention and inhibition of chronic human diseases, such as diabetes, cancer, and obesity. Increasing the amylose content (AC) and resistant starch (RS) has been pivotal in improving the nutritional benefit of rice. However, the exact mechanism of RS formation is complex due to interconnected genetic factors regulating amylose-amylopectin variation. In this review, we discussed the regulatory factors influencing the RS formation centered on the transcription, post-transcriptional, and post-translational processes. Furthermore, we described the developments in RS and AC levels in rice compared with other high RS cereals. Briefly, we enumerated potential applications of high RS mutants in health, medical, and other industries. We contest that the information captured herein can be deployed for marker-assisted breeding and precision breeding techniques through genome editing to improve rice varieties with enhanced RS content.

High-yielding nitrate transporter cultivars also mitigate methane and nitrous oxide emissions in paddy

Development of high yield rice varieties is critical to ensuring global food security. However, the emission of greenhouse gases (GHG) such as Methane (CH₄) and Nitrous oxide (N₂O) from paddy fields threatens environmental sustainability. In this study, we selected overexpressed high-affinity nitrate transporters (NRT2.3 along with their partner protein NAR2.1) cultivars, which are effective nitrogen use efficient transgenic lines pOsNAR2.1: OsNAR2.1 (Ox2) and p35S:OsNRT2.3b (O8). We used high (270 kg N/ha) and low (90 kg N/ha) nitrogen (N) fertilizers in paddy fields to evaluate morphophysiological traits, including GHG emission. We found that Ox2 and O8 reduced CH₄ emissions by 40% and 60%, respectively, compared to their wild type (WT). During growth stages, there was no consistent N₂O discharge pattern between WT and transgenics (Ox2, O8) in low and high N application. However, total cumulative N₂O in a cropping season reduced in O8 and increased in Ox2 cultivars, compared to WT. Root aerenchyma formation reduced by 30-60% in transgenic lines. Methanogens like mcrA in low and high N were also reduced by up to 50% from rhizosphere of Ox2 and O8. However, the nitrifying bacterial population such as nosZ reduced in both transgenics significantly, but nirK and nirS did not show a consistent variation. The high yield of transgenic rice with limited aerenchyma mitigates the discharge of CH₄ and N₂O by reducing root exudates that provide substrates for GHG. Our results improve understanding for breeders to serve the purpose of sustainable development.

Effects of the bioelectrochemical technique on methane emission and energy recovery in constructed wetlands (CWs) and related biological mechanisms

In this study, effects of bioelectrochemical technique on methane emission and energy recovery, and related mechanism underlying microbial competition were investigated. The results showed that running MFC was beneficial in reducing CH₄ emissions and promoting COD removal rates, regardless of whether the plant roots were located at the anode or the cathode. CH₄ emission was significantly higher in open-circuit reactors (6.2 mg m^-2 h^-1) than in closed-circuit reactors (3.1 mg m^-2 h^-1). Plant roots at the cathode had the highest electricity generation and the lowest CH4 emissions. The highest power generation (0.49 V, 0.33 w m^-3) and the lowest CH₄ emissions (2.3 mg m^-2 h^-1) were observed in the reactors where Typha orientalis was planted with plant roots at the cathode. The role of plants in strengthening electron acceptor was greater than that of plant rhizodeposits in strengthening electron donors. Real-time quantitative PCR (q-PCR) and correlation analysis indicated that the mcrA genes and CH₄ emissions were positively correlated (r = 0.98, p < 0.01), while no significant relationship between CH₄ emissions and pmoA genes was observed. Illumina sequencing revealed that more abundant exoelectrogens and denitrifying bacteria were observed when plant roots were located in cathodes. Strictly acetotrophic archae (Methanosaetaceae) were likely the main electron donor competitors with exoelectrogens. The results showed that the location of both plant species and plant roots at the electrode played an important role in CH₄ control and electricity generation. Therefore, it is necessary to strengthen plant configuration to reduce CH₄ emissions, to promote sustainable development of wastewater treatment.

Understanding the Potential Gene Regulatory Network of Starch Biosynthesis in Tartary Buckwheat by RNA-Seq

Starch is a major component of crop grains, and its content affects food quality and taste. Tartary buckwheat is a traditional pseudo-cereal used in food as well as medicine. Starch content, granule morphology, and physicochemical properties have been extensively studied in Tartary buckwheat. However, the complex regulatory network related to its starch biosynthesis needs to be elucidated. Here, we performed RNA-seq analyses using seven Tartary buckwheat varieties differing in starch content and combined the RNA-seq data with starch content by weighted correlation network analysis (WGCNA). As a result, 10,873 differentially expressed genes (DEGs) were identified and were functionally clustered to six hierarchical clusters. Fifteen starch biosynthesis genes had higher expression level in seeds. Four trait-specific modules and 3131 hub genes were identified by WGCNA, with the lightcyan and brown modules positively correlated with starch-related traits. Furthermore, two potential gene regulatory networks were proposed, including the co-expression of FtNAC70, FtPUL, and FtGBSS1-3 in the lightcyan module and FtbHLH5, C3H, FtBE2, FtISA3, FtSS3-5, and FtSS1 in the brown. All the above genes were preferentially expressed in seeds, further suggesting their role in seed starch biosynthesis. These results provide crucial guidance for further research on starch biosynthesis and its regulatory network in Tartary buckwheat.

Achieving of high-diet-fiber barley via managing fructan hydrolysis

High fructan content in the grain of cereals is an important trait in agriculture such as environmental resilience and dietary fiber food production. To understand the mechanism in determining final grain fructan content and achieve high fructan cereal, a cross breeding strategy based on fructan synthesis and hydrolysis activities was set up and have achieved barley lines with 11.8% storage fructan in the harvested grain. Our study discovered that high activity of fructan hydrolysis at later grain developmental stage leads to the low fructan content in mature seeds, simultaneously increasing fructan synthesis at early stage and decreasing fructan hydrolysis at later stage through crossing breeding is an efficient way to elevate grain diet-fiber content. A good correlation between fructan and beta glucans was also discovered with obvious interest. Field trials showed that the achieved high fructan barley produced over seven folds higher fructan content than control barley and pull carbon-flux to fructan through decreasing fructan hydrolysis without disruption starch synthesis will probably not bring yield deficiency.

Environmental life cycle assessment of rice production in northern Italy: a case study from Vercelli

Purpose

The study's objective is to assess the environmental performance of rice production in Northern Italy, in particular in Piedmont, the first Italian and European district for the rice-growing area, and thus identify the most critical hotspots and agricultural processes. In particular, as a case study, a farm located in Vercelli (VC) has been chosen. Subsequently, the study results were compared with other different cultivation practices to evaluate the most sustainable choice.

Methods

The application of the LCA has been performed, highlighting the phases of rice production that have the most significant impact. Then, uncertainty and sensitivity analyses have been made to estimate the robustness of the results and assess the influence of changing some input variables on emission reduction. Finally, multivariate statistical, specifically a principal component analysis (PCA), was conducted to aid the interpretation of the output dataset of this case study. LCA, uncertainty analysis, and sensitivity analysis were performed with SimaPro 9.2.0, using ReCiPe 2016 Midpoint (H) methodology, and PCA with R software.

Results and discussions

The hotspot with the highest environmental load is irrigation, which compared to the other phases impacts more in 15 out of 18 categories, including 12 with impacts greater than + 75%. This is because irrigation causes direct impacts, related to the methanogenesis in rice fields, but also indirect impacts related mainly to the production of the energy mix required to move the large masses of irrigation water. Therefore, different water management systems were compared and results show that the irrigation systems based on intermittent paddy submergence (DSI) could result in - 40% lower impacts, resulting to be the preferable technique over the other irrigation systems analyzed, including the traditional one used in this study.

Conclusions

In order to reduce the environmental impacts related to the irrigation process, a water management system characterized by intermittent flooding of the paddy field (DSI) could be used as it reduces the environmental impacts the most (- 40%), while the least suitable system is one characterized by continuous flooding without drought periods, as it causes the highest impacts.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11367-022-02109-x.

Profiling of transcriptional regulators associated with starch biosynthesis in sorghum (Sorghum bicolor L.)

Starch presents as the major component of grain endosperm of sorghum (Sorghum bicolor L.) and other cereals, serving as the main energy supplier for both plants and animals, as well as important industrial raw materials of human beings, and was intensively concerned world widely. However, few documents focused on the pathway and transcriptional regulations of starch biosynthesis in sorghum. Here we presented the RNA-sequencing profiles of 20 sorghum tissues at different developmental stages to dissect key genes associated with sorghum starch biosynthesis and potential transcriptional regulations. A total of 1,708 highly expressed genes were detected, namely, 416 in grains, 736 in inflorescence, 73 in the stalk, 215 in the root, and 268 genes in the leaf. Besides, 27 genes encoded key enzymes associated with starch biosynthesis in sorghum were identified, namely, six for ADP-glucose pyrophosphorylase (AGPase), 10 for starch synthases (SSs), four for both starch-branching enzymes (SBE) and starch-debranching enzymes (DBEs), two for starch phosphorylases (SPs), and one for Brittle-1 (BT1). In addition, 65 transcription factors (TFs) that are highly expressed in endosperm were detected to co-express with 16 out of 27 genes, and 90 cis-elements were possessed by all 27 identified genes. Four NAC TFs were cloned, and the further assay results showed that three of them could in vitro bind to the CACGCAA motif within the promoters of SbBt1 and SbGBSSI, two key genes associated with starch biosynthesis in sorghum, functioning in similar ways that reported in other cereals. These results confirmed that sorghum starch biosynthesis might share the same or similar transcriptional regulations documented in other cereals, and provided informative references for further regulatory mechanism dissection of TFs involved in starch biosynthesis in sorghum.

Prospecting the significance of methane-utilizing bacteria in agriculture

Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.

Effects of different carbon sources on methane production and the methanogenic communities in iron rich flooded paddy soil

Various carbon sources as substrates and electron donors can produce methane via different metabolic pathways. In particular, the methane produced by rice cultivation has a severe impact on climate change. However, how Fe³⁺, the most abundant oxide in paddy soil, mediates the methanogenesis of different carbon sources is unknown. In this study, we investigated the effect of four carbon sources with different chain lengths (acetate, glucose, nonanoate, and starch) on CH₄ production and associated methanogens in iron-rich paddy soil over 90 days of anaerobic incubation. We found that glucose and starch were the more preferential substrates for liberating methane compared to acetate, and the rate was also faster. Nonanoate was unable to support methane production. Methanosarcinales and Methanobacteriales were the most predominant methanogenic archaea as shown by 16S rRNA gene sequencing, though their abundance changed over time. Additionally, a significantly higher content of iron-reducing bacteria was observed in the glucose and starch treatments, and it was significantly positively correlated with the copy number of the methanogenic mcrA gene. Together, we confirmed the methanogenic capacity of different carbon sources and their related microorganisms. We also showed that iron oxides play a central role in regulating methane emissions from paddy soils and need more attention to be paid to them.

Cereal Endosperms: Development and Storage Product Accumulation

The persistent triploid endosperms of cereal crops are the most important source of human food and animal feed. The development of cereal endosperms progresses through coenocytic nuclear division, cellularization, aleurone and starchy endosperm differentiation, and storage product accumulation. In the past few decades, the cell biological processes involved in endosperm formation in most cereals have been described. Molecular genetic studies performed in recent years led to the identification of the genes underlying endosperm differentiation, regulatory network governing storage product accumulation, and epigenetic mechanism underlying imprinted gene expression. In this article, we outline recent progress in this area and propose hypothetical models to illustrate machineries that control aleurone and starchy endosperm differentiation, sugar loading, and storage product accumulations. A future challenge in this area is to decipher the molecular mechanisms underlying coenocytic nuclear division, endosperm cellularization, and programmed cell death.

Unexpected Parabolic Temperature Dependency of CH4 Emissions from Rice Paddies

Global warming is expected to affect methane (CH₄) emissions from rice paddies, one of the largest human-induced sources of this potent greenhouse gas. However, the large variability in warming impacts on CH₄ emissions makes it difficult to extrapolate the experimental results over large regions. Here, we show, through meta-analysis and multi-site warming experiments using the free air temperature increase facility, that warming stimulates CH₄ emissions most strongly at background air temperatures during the flooded stage of ∼26 °C, with smaller responses of CH₄ emissions to warming at lower and higher temperatures. This pattern can be explained by divergent warming responses of plant growth, methanogens, and methanotrophs. The effects of warming on rice biomass decreased with the background air temperature. Warming increased the abundance of methanogens more strongly at the medium air temperature site than the low and high air temperature sites. In contrast, the effects of warming on the abundance of methanotrophs were similar across the three temperature sites. We estimate that 1 °C warming will increase CH₄ emissions from paddies in China by 12.6%─substantially higher than the estimates obtained from leading ecosystem models. Our findings challenge model assumptions and suggest that the estimates of future paddy CH₄ emissions need to consider both plant and microbial responses to warming.

A review of starch biosynthesis in cereal crops and its potential breeding applications in rice (Oryza Sativa L.)

Starch provides primary storage of carbohydrates, accounting for approximately 85% of the dry weight of cereal endosperm. Cereal seeds contribute to maximum annual starch production and provide the primary food for humans and livestock worldwide. However, the growing demand for starch in food and industry and the increasing loss of arable land with urbanization emphasizes the urgency to understand starch biosynthesis and its regulation. Here, we first summarized the regulatory signaling pathways about leaf starch biosynthesis. Subsequently, we paid more attention to how transcriptional factors (TFs) systematically respond to various stimulants via the regulation of the enzymes during starch biosynthesis. Finally, some strategies to improve cereal yield and quality were put forward based on the previous reports. This review would collectively help to design future studies on starch biosynthesis in cereal crops.

Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication

Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.

Biochar promotes soil organic carbon sequestration and reduces net global warming potential in apple orchard: A two-year study in the Loess Plateau of China

The Loess Plateau is China's primary apple-growing area, and the orchard is a significant source of greenhouse gases (GHGs) emissions due to high nitrogen fertilizer input. Thus, a two-year field study was carried out to investigate the effects of apple wood derived biochar on GHGs emissions during apple orchard production, including soil organic carbon sequestration (SOCSR) and net global warming potential (NGWP) assessments. There are four treatments in this study: 20 t ha^-1 biochar in a non-fertilized plot (B); no biochar in a fertilized plot (F); 20 t ha^-1 biochar in a fertilized plot (FB); no biochar in a non-fertilized plot (CK). Results showed that the combined application of biochar and fertilizer stimulated CO₂ emissions by 9.25% and 8.39% than either biochar or fertilizer alone. Meanwhile, biochar in fertilized plot increased annual N₂O emissions by 32.6% as compared to fertilized plot without biochar amendment. Compared with CK, biochar had no significant effect on GHG emissions in unfertilized plot. The N₂O emission factor of FB and F were 0.91% and 0.45% respectively in 2017-2018 and they were both 0.34% in 2018-2019. Moreover, compared with CK, the FB and B treatments increased the SOCSR by 316.52% and 354.78%, while, decreased the NGWP by 368.93% and 480.91%, respectively. Thus, biochar application may help reduce the impact of apple production on climate change by sequestering more soil organic carbon and decreasing the NGWP.

Regulators of Starch Biosynthesis in Cereal Crops

Starch is the main food source for human beings and livestock all over the world, and it is also the raw material for production of industrial alcohol and biofuel. A considerable part of the world’s annual starch production comes from crops and their seeds. With the increasing demand for starch from food and non-food industries and the growing loss of arable land due to urbanization, understanding starch biosynthesis and its regulators is essential to produce the desirable traits as well as more and better polymers via biotechnological approaches in cereal crops. Because of the complexity and flexibility of carbon allocation in the formation of endosperm starch, cereal crops require a broad range of enzymes and one matching network of regulators to control the providential functioning of these starch biosynthetic enzymes. Here, we comprehensively summarize the current knowledge about regulatory factors of starch biosynthesis in cereal crops, with an emphasis on the transcription factors that directly regulate starch biosynthesis. This review will provide new insights for the manipulation of bioengineering and starch biosynthesis to improve starch yields or qualities in our diets and in industry.

Novel technologies for emission reduction complement conservation agriculture to achieve negative emissions from row-crop production

Plants remove carbon dioxide from the atmosphere through photosynthesis. Because agriculture's productivity is based on this process, a combination of technologies to reduce emissions and enhance soil carbon storage can allow this sector to achieve net negative emissions while maintaining high productivity. Unfortunately, current row-crop agricultural practice generates about 5% of greenhouse gas emissions in the United States and European Union. To reduce these emissions, significant effort has been focused on changing farm management practices to maximize soil carbon. In contrast, the potential to reduce emissions has largely been neglected. Through a combination of innovations in digital agriculture, crop and microbial genetics, and electrification, we estimate that a 71% (1,744 kg CO₂e/ha) reduction in greenhouse gas emissions from row crop agriculture is possible within the next 15 y. Importantly, emission reduction can lower the barrier to broad adoption by proceeding through multiple stages with meaningful improvements that gradually facilitate the transition to net negative practices. Emerging voluntary and regulatory ecosystems services markets will incentivize progress along this transition pathway and guide public and private investments toward technology development. In the difficult quest for net negative emissions, all tools, including emission reduction and soil carbon storage, must be developed to allow agriculture to maintain its critical societal function of provisioning society while, at the same time, generating environmental benefits.

Comprehensive analysis of SUSIBA2 rice: The low-methane trait and associated changes in soil carbon and microbial communities

Rice cultivation is the primary source of anthropogenic methane (CH₄), which dramatically impacts global climate change. A growing body of evidence shows that optimizing photosynthate distribution is important for increasing rice yields and mitigating CH₄ emissions. Therefore, the molecular rice breeding with a barley HvSUSIBA2 gene that confers elevated photosynthate flux to grains, is predicted to enhance rice yield and mitigate CH₄ emissions in paddies. Here, in a series of field experiments with differences in growing season and rice variety, we show that SUSIBA2 rice reduced CH₄ emissions from paddies. SUSIBA2 rice grown in the early rice season and late rice season showed similar mitigation effects, with reduction rates of 50.98% for early rice and 50.97% for late rice. The reduction rate of SUSIBA2 rice during the winter rice season was significantly lower (22.26%) than those of other rice seasons. The reduction rates also varied between rice varieties, and SUSIBA2 japonica rice showed a more significant CH₄ mitigation effect than SUSIBA2 indica rice. Further yield-scaled CH₄ emission analyses indicated that the SUSIBA2 effect did not mitigate CH₄ emissions at the expense of yield. Compared with the wild type, SUSIBA2 rice significantly reduced soil organic carbon properties and the abundance of CH₄-related microbes, and altered methanogenic and methanotrophic communities, indicating that SUSIBA2 rice released less carbon to the soil, which reduced CH₄ production. Furthermore, a comparison of microbial communities between SUSIBA2 japonica and indica rice revealed different responses of methanogenic and methanotrophic communities, which may partly explain their differences in growth performance and CH₄ mitigation effect. Thus, our results show that SUSIBA2 rice substantially reduces CH₄ emissions and that SUSIBA2 can potentially mitigate the CH₄ emissions of japonica and indica rice under distinct cultivation conditions.

Regulating CH4, N2O, and NO emissions from an alkaline paddy field under rice-wheat rotation with controlled release N fertilizer

Controlled release fertilizer (CRF) has been shown to increase crop yield and N use efficiency (NUE) compared with traditional chemical fertilizer (TF). However, few studies examined the effects of CRF on CH₄, N₂O, and NO emissions simultaneously in alkaline paddy fields under rice-wheat rotation. In the present study, we conducted a 2-year field experiment to compare the effects of different CRF application strategies on these gas emissions with those of TF and explored the effects of CRF on global warming potential (GWP), crop yields, and greenhouse gas emission intensity (GHGI). Results showed that CRF can reduce 0.98-14.3%, 13.3-21.1%, and 8.22-16.3% of CH₄, N₂O, and NO emissions, respectively, in the studied alkaline paddy field. CRF reduce CH₄ emission probably by regulating soil NH₄⁺ concentration. CRF reduce N₂O and NO emissions probably by regulating inorganic N content in the studied alkaline paddy soil. CRF had the same effect on annual crop yield as TF, especially when CRF was applied twice in each season and had the same N application rate as TF. Annual crop yields and the agronomic efficiency of N (AE_N) increased by 8.24% and 21.6%, respectively. On the average of the two rice-wheat rotation cycles, GHGI significantly decreased by up to 14.1% after the application of CRF as relative to that after the application of TF (P < 0.05). These results suggest that CRF is an environment-friendly N fertilization strategy for mitigating GWP and ensuring high crop yield in an alkaline paddy field under rice-wheat rotation.

Adaptation of Rice to the Nordic Climate Yields Potential for Rice Cultivation at Most Northerly Site and the Organic Production of Low-Arsenic and High-Protein Rice

There is an urgent demand for low-arsenic rice in the global market, particularly for consumption by small children. Soils in Uppsala, Sweden, contain low concentrations of arsenic (As). We hypothesize that if certain japonica paddy rice varieties can adapt to the cold climate and long day length in Uppsala and produce normal grains, such a variety could be used for organic production of low-arsenic rice for safe rice consumption. A japonica paddy rice variety, "Heijing 5," can be cultivated in Uppsala, Sweden, after several years' adaptation, provided that the rice plants are kept under a simple plastic cover when the temperature is below 10°C. Uppsala-adapted "Heijing 5" has a low concentration of 0.1 mg per kg and high protein content of 12.6% per dry weight in brown rice grain, meaning that it thus complies with all dietary requirements determined by the EU and other countries for small children. The high protein content is particularly good for small children in terms of nutrition. Theoretically, Uppsala-adapted "Heijing 5" can produce a yield of around 5100 kg per ha, and it has a potential for organic production. In addition, we speculate that cultivation of paddy rice can remove nitrogen and phosphorus from Swedish river water and reduce nutrient loads to the Baltic Sea and associated algae blooms.

Lower-than-expected CH4 emissions from rice paddies with rising CO2 concentrations

Elevated atmospheric CO2 (eCO2 ) generally increases carbon input in rice paddy soils and stimulates the growth of methane-producing microorganisms. Therefore, eCO2 is widely expected to increase methane (CH4 ) emissions from rice agriculture, a major source of anthropogenic CH4 . Agricultural practices strongly affect CH4 emissions from rice paddies as well, but whether these practices modulate effects of eCO2 is unclear. Here we show, by combining a series of experiments and meta-analyses, that whereas eCO2 strongly increased CH4 emissions from paddies without straw incorporation, it tended to reduce CH4 emissions from paddy soils with straw incorporation. Our experiments also identified the microbial processes underlying these results: eCO2 increased methane-consuming microorganisms more strongly in soils with straw incorporation than in soils without straw, with the opposite pattern for methane-producing microorganisms. Accounting for the interaction between CO2 and straw management, we estimate that eCO2 increases global CH4 emissions from rice paddies by 3.7%, an order of magnitude lower than previous estimates. Our results suggest that the effect of eCO2 on CH4 emissions from rice paddies is smaller than previously thought and underline the need for judicious agricultural management to curb future CH4 emissions.

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters

Rice cultivation worldwide accounts for ∼7 to 17% of global methane emissions. Methane cycling in rice paddies is a microbial process not only involving methane producers (methanogens) and methane metabolizers (methanotrophs) but also other microbial taxa that affect upstream processes related to methane metabolism. Rice cultivars vary in their rates of methane emissions, but the influence of rice genotypes on methane cycling microbiota has been poorly characterized. Here, we profiled the rhizosphere, rhizoplane, and endosphere microbiomes of a high-methane-emitting cultivar (Sabine) and a low-methane-emitting cultivar (CLXL745) throughout the growing season to identify variations in the archaeal and bacterial communities relating to methane emissions. The rhizosphere of the high-emitting cultivar was enriched in methanogens compared to that in the low emitter, whereas the relative abundances of methanotrophs between the cultivars were not significantly different. Further analysis of cultivar-sensitive taxa identified families enriched in the high emitter that are associated with methanogenesis-related processes. The high emitter had greater relative abundances of sulfate-reducing and iron-reducing taxa which peak earlier in the season than methanogens and are necessary to lower soil oxidation reduction potential before methanogenesis can occur. The high emitter also had a greater abundance of fermentative taxa which produce methanogenesis precursors (acetate, CO2, and H2). Furthermore, the high emitter was enriched in taxa related to acetogenesis which compete with methanogens for CO2 and H2 These taxa were enriched in a spatio-specific manner and reveal a complex network of microbial interactions on which plant genotype-dependent factors can act to affect methanogenesis and methane emissions.IMPORTANCE Rice cultivation is a major source of anthropogenic emissions of methane, a greenhouse gas with a potentially severe impact on climate change. Emission variation between rice cultivars suggests the feasibility of breeding low-emission rice, but there is a limited understanding of how genotypes affect the microbiota involved in methane cycling. Here, we show that the root microbiome of the high-emitting cultivar is enriched both in methanogens and in taxa associated with fermentation, iron, and sulfate reduction and acetogenesis, processes that support methanogenesis. Understanding how cultivars affect microbes with methanogenesis-related functions is vital for understanding the genetic basis for methane emission in rice and can aid in the development of breeding programs that reduce the environmental impact of rice cultivation.

Expression of galactinol synthase from Ammopiptanthus nanus in tomato improves tolerance to cold stress

Soluble carbohydrates not only directly affect plant growth and development but also act as signal molecules in processes that enhance tolerance to cold stress. Raffinose family oligosaccharides (RFOs) are an example and play an important role in abiotic stress tolerance. This study aimed to determine whether galactinol, a key limiting factor in RFO biosynthesis, functions as a signal molecule in triggering cold tolerance. Exposure to low temperatures induces the expression of galactinol synthase (AnGolS1) in Ammopiptanthus nanus, a desert plant that survives temperatures between -30 °C to 47 °C. AnGolS1 has a greater catalytic activity than tomato galactinol synthase (SlGolS2). Moreover, SlGolS2 is expressed only at low levels. Expression of AnGolS1 in tomato enhanced cold tolerance and led to changes in the sugar composition of the seeds and seedlings. AnGolS1 transgenic tomato lines exhibited an enhanced capacity for ethylene (ET) signaling. The application of galactinol abolished the repression of the ET signaling pathway by 1-methylcyclopropene during seed germination. In addition, the expression of ERF transcription factors was increased. Galactinol may therefore act as a signal molecule affecting the ET pathway.

Methyl-coenzyme M reductase-dependent endogenous methane enhances plant tolerance against abiotic stress and alters ABA sensitivity in Arabidopsis thaliana

Our study firstly elaborated the underlying mechanism of endogenous CH₄-induced abiotic tolerance, along with an alteration of ABA sensitivity by mimicking the endogenous CH₄ production in MtMCR transgenic Arabidopsis. Endogenous methane (CH₄) production and/or emission have been ubiquitously observed in stressed plants. However, their physiological roles remain unclear. Here, the methyl-coenzyme M reductase gene from Methanobacterium thermoautotrophicum (MtMCR), encoding the enzyme of methanogenesis, was expressed in Arabidopsis thaliana, to mimic the production of endogenous CH₄. In response to salinity and osmotic stress, MtMCR expression was up-regulated in transgenic plants, resulting in significant increase of endogenous CH₄ levels. Similar results were observed in abscisic acid (ABA) treatment. The functions of endogenous CH₄ were characterized by the changes in plant phenotypes related to stress and ABA sensitivity during the germination and post-germination periods. When challenged with osmotic stress, a reduction in water loss and stomatal closure, were observed. Redox homeostasis was reestablished during osmotic and salinity stress, and ion imbalance was also restored in salinity conditions. The expression of several stress/ABA-responsive genes was up-regulated, and ABA sensitivity, in particularly, was significantly altered in the MtMCR transgenic plants. Together, our genetic study for the first time elaborated the possible mechanism of endogenous CH₄-enhanced salinity and osmotic tolerance, along with an alteration of ABA sensitivity. These findings thus provided novel cues for understanding the possible roles of endogenous CH₄ in plants.

Methanogenesis

Methanogenesis is an anaerobic respiration that generates methane as the final product of metabolism. In aerobic respiration, organic matter such as glucose is oxidized to CO₂, and O₂ is reduced to H₂O. In contrast, during hydrogenotrophic methanogenesis, H₂ is oxidized to H⁺, and CO₂ is reduced to CH₄. Although similar in principle to other types of respiration, methanogenesis has some distinctive features: the energy yield is very low, ≤1 ATP per methane generated, and only methanogens - organisms capable of this specialized metabolism - carry out biological methane production. Methanogens, like the process they catalyze, are similarly distinctive. Methanogens are comprised exclusively of archaea. They are obligate methane producers, that is, they do not grow using fermentation or alternative electron acceptors for respiration. Finally, methanogens are strict anaerobes and do not grow in the presence of O₂. Historically, methanogenesis has been viewed as a highly specialized metabolism restricted to a narrow group of prokaryotes. However, recent developments have revealed enormous diversity within the methanogens and suggest that this metabolism is one of the most ancient on earth.

Characterization of AtWRI1 in fatty acids and starch synthesis in rice

WRINKLED1 (WRI1) belongs to AP2/EREBP transcription factor. Its function in dicots for fatty acids synthesis has been deeply studied, but its role in monocot, especially in rice, is still poorly understood. Here, with the overexpression of AtWRI1 in rice, we found its overexpression increased fatty acids content in vegetative organs and seed coat including aleurone layer (SCAL) but decreased fatty acids content in endosperm. Meanwhile, the overexpression of AtWRI1 increased starch content in endosperm. These results provide a new insight into the function of AtWRI1in monocot and make a previous basement for the study of the connection of fatty acids and starch synthesis in rice.

Genetic Dissection of Root System Architectural Traits in Spring Barley

Breeding new crop cultivars with efficient root systems carries great potential to enhance resource use efficiency and plant adaptation to unstable climates. Here, we evaluated the natural variation of root system architectural traits in a diverse spring barley association panel and conducted genome-wide association mapping to identify genomic regions associated with root traits. For six studied traits, root system depth, root spreading angle, seminal root number, total seminal root length, and average seminal root length 1.9- to 4.2-fold variations were recorded. Using a mixed linear model, 55 QTLs were identified cumulatively explaining between 12.1% of the phenotypic variance for seminal root number to 48.1% of the variance for root system depth. Three major QTLs controlling root system depth, root spreading angle and total seminal root length were found on Chr 2H (56.52 cM), Chr 3H (67.92 cM), and Chr 2H (76.20 cM) and explained 12.4%, 18.4%, and 22.2% of the phenotypic variation, respectively. Meta-analysis and allele combination analysis indicated that root system depth and root spreading angle are valuable candidate traits for improving grain yield by pyramiding of favorable alleles.

Three-Source Partitioning of Methane Emissions from Paddy Soil: Linkage to Methanogenic Community Structure

Identification of the carbon (C) sources of methane (CH₄) and methanogenic community structures after organic fertilization may provide a better understanding of the mechanism that regulate CH₄ emissions from paddy soils. Based on our previous field study, a pot experiment with isotopic ¹³C labelling was designed in this study. The objective was to investigate the main C sources for CH₄ emissions and the key environmental factor with the application of organic fertilizer in paddies. Results indicated that 28.6%, 64.5%, 0.4%, and 6.5% of ¹³C was respectively distributed in CO₂, the plants, soil, and CH₄ at the rice tillering stage. In total, organically fertilized paddy soil emitted 3.51 kg·CH₄ ha⁻¹ vs. 2.00 kg·CH₄ ha⁻¹ for the no fertilizer treatment. Maximum CH₄ fluxes from organically fertilized (0.46 mg·m⁻²·h⁻¹) and non-fertilized (0.16 mg·m⁻²·h⁻¹) soils occurred on day 30 (tillering stage). The total percentage of CH₄ emissions derived from rice photosynthesis C was 49%, organic fertilizer C < 0.34%, and native soil C > 51%. Therefore, the increased CH₄ emissions from paddy soil after organic fertilization were mainly derived from native soil and photosynthesis. The 16S rRNA sequencing showed Methanosarcina (64%) was the dominant methanogen in paddy soil. Organic fertilization increased the relative abundance of Methanosarcina, especially in rhizosphere. Additionally, Methanosarcina sp. 795 and Methanosarcina sp. 1H1 co-occurred with Methanobrevibacter sp. AbM23, Methanoculleus sp. 25XMc2, Methanosaeta sp. HA, and Methanobacterium sp. MB1. The increased CH₄ fluxes and labile methanogenic community structure in organically fertilized rice soil were primarily due to the increased soil C, nitrogen, potassium, phosphate, and acetate. These results highlight the contributions of native soil- and photosynthesis-derived C in paddy soil CH₄ emissions, and provide basis for more complex investigations of the pathways involved in ecosystem CH₄ processes.

Transplanting the pathway engineering toolbox to methanogens

Biological methanogenesis evolved early in Earth's history and was likely already a major process by 3.5 Ga. Modern methanogenesis is now a key process in virtually all anaerobic microbial communities, such as marine and lake sediments, wetland and rice soils, and human and cattle digestive tracts. Owing to their long evolution and extensive adaptations to various habitats, methanogens possess enormous metabolic and physiological diversity. Not only does this diversity offers unique opportunities for biotechnology applications, but also reveals their direct impact on the environment, agriculture, and human and animal health. These efforts are facilitated by an advanced genetic toolbox, emerging new molecular tools, and systems-level modelling for methanogens. Further developments and convergence of these technical advancements provide new opportunities for bioengineering methanogens.

Metabotyping as a Stopover in Genome-to-Phenome Mapping

Predicting phenotypic expression from genomic and environmental information is arguably the greatest challenge in today's biology. Being able to survey genomic content, e.g., as single-nucleotide polymorphism data, within a diverse population and predict the phenotypes of external traits, represents the holy grail across genome-informed disciplines, from personal medicine and nutrition to plant breeding. In the present study, we propose a two-step procedure in bridging the genome to phenome gap where external phenotypes are viewed as emergent properties of internal phenotypes, such as molecular profiles, in interaction with the environment. Using biomass accumulation and shoot-root allometry as external traits in diverse genotypes of the model grass Brachypodium distachyon, we established correlative models between genotypes and metabolite profiles (metabotypes) as internal phenotypes, and between metabotypes and external phenotypes under two contrasting watering regimes. Our results demonstrate the potential for employing metabotypes as an integrator in predicting external phenotypes from genomic information.

L-Cysteine desulfhydrase-dependent hydrogen sulfide is required for methane-induced lateral root formation

Methane-triggered lateral root formation is not only a universal event, but also dependent on L-cysteine desulfhydrase-dependent hydrogen sulfide signaling. Whether or how methane (CH₄) triggers lateral root (LR) formation has not been elucidated. In this report, CH₄ induction of lateral rooting and the role of hydrogen sulfide (H₂S) were dissected in tomato and Arabidopsis by using physiological, anatomical, molecular, and genetic approaches. First, we discovered that CH₄ induction of lateral rooting is a universal event. Exogenously applied CH₄ not only triggered tomato lateral rooting, but also increased activities of L-cysteine desulfhydrase (DES; a major synthetic enzyme of H₂S) and induced endogenous H₂S production, and contrasting responses were observed in the presence of hypotaurine (HT; a scavenger of H₂S) or DL-propargylglycine (PAG; an inhibitor of DES) alone. CH₄-triggered lateral rooting were sensitive to the inhibition of endogenous H₂S with HT or PAG. The changes in the transcripts of representative cell cycle regulatory genes, miRNA and its target genes were matched with above phenotypes. In the presence of CH₄, Arabidopsis mutant Atdes1 exhibited defects in lateral rooting, compared with the wild-type. Molecular evidence showed that the transcriptional profiles of representative target genes modulated by CH₄ in wild-type plants were impaired in Atdes1 mutant. Overall, our data demonstrate the main branch of the DES-dependent H₂S signaling cascade in CH₄-triggered LR formation.

Limited potential of harvest index improvement to reduce methane emissions from rice paddies

Rice is a staple food for nearly half of the world's population, but rice paddies constitute a major source of anthropogenic CH₄ emissions. Root exudates from growing rice plants are an important substrate for methane-producing microorganisms. Therefore, breeding efforts optimizing rice plant photosynthate allocation to grains, i.e., increasing harvest index (HI), are widely expected to reduce CH₄ emissions with higher yield. Here we show, by combining a series of experiments, meta-analyses and an expert survey, that the potential of CH₄ mitigation from rice paddies through HI improvement is in fact small. Whereas HI improvement reduced CH₄ emissions under continuously flooded (CF) irrigation, it did not affect CH₄ emissions in systems with intermittent irrigation (II). We estimate that future plant breeding efforts aimed at HI improvement to the theoretical maximum value will reduce CH₄ emissions in CF systems by 4.4%. However, CF systems currently make up only a small fraction of the total rice growing area (i.e., 27% of the Chinese rice paddy area). Thus, to achieve substantial CH₄ mitigation from rice agriculture, alternative plant breeding strategies may be needed, along with alternative management.

Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers

Coastal wetlands are widely recognized as atmospheric methane sources. However, recent field studies suggest that some coastal wetlands could also act as methane sinks, but the mechanism is not yet clear. Here, we investigated methane oxidation with different electron acceptors (i.e., oxygen, nitrate/nitrite, sulfate, Fe(III) and Mn(IV)) in four coastal wetlands in China using a combination of molecular biology methods and isotopic tracing technologies. The geochemical profiles and in situ Gibbs free energies suggest that there was significant nitrite-dependent anaerobic oxidation of methane (nitrite-AOM) in the sub-surface sediments; this was subsequently experimentally verified by both the microbial abundance and activity. Remarkably, the methanotrophic communities seemed to exist in the sediments as layered structures, and the surface aerobic methane-oxidizing bacteria were able to take up atmospheric methane at a rate of 0.10-0.18 nmol CH₄ day^-1 cm^-2, while most, if not all, sedimentary methane was being completely consumed by anaerobic methanotrophs (23-58% by methane oxidizers in phylum NC10). These results suggest that coastal methane sinks might be governed by diverse microbial communities where NC10 methane oxidizers contributed significantly. This finding helps to better understand and predict the coastal methane cycle and reduce uncertainties in the estimations of the global methane flux.