Processes that determine the interplay of root exudation, methane emission and yield in rice agriculture

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.

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.

Effect of nitrogen application on greenhouse gas emissions and nitrogen uptake by plants in integrated rice-crayfish farming

Integrated rice-crayfish farming is an ecological rice farming mode. However, limited research has examined the comprehensive impacts of greenhouse gas (GHG) emissions, nitrogen (N) uptake, and N utilization in rice under this farming modality. Herein, a dual-factor experiment was performed from 2021 to 2022 to assess the comprehensive impacts of N application and rice farming mode on greenhouse gas (GHG) emissions, N uptake, N utilization, and rice yield in paddy fields. Under N application, the rice-crayfish co-culture exhibits a 2.3 % decrease in global warming potential (GWP) and a 17.3 % increase in greenhouse gas intensity relative to the rice monoculture. Moreover, the N uptake of rice within the rice-crayfish co-culture is 5.2 %-10.4 % higher than that in the rice monoculture. However, owing to low rice yield under the rice-crayfish co-culture, its N partial factor productivity decreases by 5.6 %-22.6 %, while N agronomic efficiency is reduced by 18.3 %-46.9 % compared with the rice monoculture. In addition, N application significantly inhibits CH4 emissions from paddy fields in the rice-crayfish co-culture mode. Compared with no N application, the CH4 emissions and GWP of N-applied treatment are decreased by 12.1 %-31.0 % and 6.0 %-15.8 %, respectively. Hence, N regulation might reduce GHG emissions in rice-aquatic animal co-culturing agriculture. Collectively, the results of this study suggest that switching from a rice monoculture to rice-crayfish co-culture can mitigate GHG emissions and promote rice N uptake; however, continuously improving the productivity of co-culturing agriculture is key to achieving high N utilization efficiency and low environmental impact.

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.

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.

Effect of long term fertilization management strategies on methane emissions and rice yield

Optimum fertilization is an efficient method to maintain rice yield and reduce N-losses. It is essential though to evaluate methane emissions from paddy fields, to further understand its impact on greenhouse gas budget. Therefore, a field experiment was conducted to investigate the effect of long-term optimum fertilization on CH₄ emissions and rice yield. We collected data in the 7th and 8th year from a field experiment initiated in 2010. Four optimum fertilization strategies, reduced N-fertilizer and zero-P treatment (RNP, 200 kg N/ha), sulfur-coated urea combined with uncoated urea treatment (SCU, 200 kg N/ha), organic fertilizer combined chemical fertilizer treatment (OCN, 200 kg N/ha), organic fertilizer treatment (OF, 200 kg N/ha); and two controls, the farmers' N management (FN, 270 kg N/ha) and zero-N treatment (N0), were employed. The results showed the rice yields achieved for the optimum fertilization treatments (RNP, SCU, OCN, and OF) were similar with those for the FN. No significant differences in CH₄ emissions among all treatments. Cumulative seasonal CH₄ emissions were negatively correlated with grain yield (P < 0.05). In the RNP and SCU treatments, soil available K, mcrA gene and available P were the key variables affecting CH₄ emissions; soil available K, available P and SOC contents were the key emissions factors for OCN and OF treatments. The SCU achieved the highest rice yield and lowest CH₄ emission intensity among optimum fertilization treatments. These results suggest that long-term application of sulfur-coated urea combined with uncoated urea can maintain rice yield and reduce methane emissions from rice paddies.

Soil carbon dioxide venting through rice roots

The growth of rice in submerged soils depends on its ability to form continuous gas channels-aerenchyma-through which oxygen (O2 ) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO2 ) in the opposite direction. Large, potentially toxic concentrations of dissolved CO2 develop in submerged rice soils. We show using X-ray computed tomography and image-based mathematical modelling that CO2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO2 and associated bicarbonate (HCO3- ) in root cells would have been well above levels known to be toxic to roots. Removal of CO2 and hence carbonic acid (H2 CO3 ) from the soil was sufficient to increase the pH in the rhizosphere close to the roots by 0.7 units, which is sufficient to solubilize or immobilize various nutrients and toxicants. A sensitivity analysis of the model showed that such changes are expected for a wide range of plant and soil conditions.

Effect of coupled reduced irrigation and nitrogen fertilizer on soil mite community composition in a wheat field

Groundwater and nitrogen fertilizer overuse severely threatens crop productions; thus, current ecological agriculture requires low irrigation and nitrogen fertilizer inputs. The effects of combined reduced irrigation and nitrogen fertilizer addition on soil organism (e.g., mite) community and biodiversity remain poorly understood. We analyzed soil mite community composition, wheat grain yield, and soil characteristics in a 10-year manipulation experiment with two levels of irrigation (reduced and conventional irrigation) and five nitrogen fertilizer levels (0, 70, 140, 210, and 280 kg N/ha). Reduced irrigation (20% reduction, from 280 to 220 mm) and nitrogen fertilizer (25% reduction, from 280 to 210 kg N/ha) addition did not significantly influence soil mite community and wheat yield. The relative abundances of fungivores and predators showed negative quadratic relationships with wheat yield, while that of plant parasites showed a positive relationship. The relationships between soil mite trophic groups and wheat yield revealed that we can evaluate the impacts of reduced irrigation and nitrogen fertilizer addition from the perspective of soil fauna. Soil mite community composition was altered by soil abiotic factors prior to reduced irrigation and nitrogen fertilizer addition. Overall, moderate reductions of irrigation and nitrogen fertilizer may not threaten to soil mite community and diversity or decrease crop production; in contrast, such reductions will benefit mite community development and the sustainable agriculture.