Microbial mechanism for rice variety control on methane emission from rice field soil

Rice variety is one of the key factors regulating methane (CH₄) production and emission from the paddy fields. However, the relationships between rice varieties and populations of microorganisms involved in CH₄ dynamics are poorly understood. Here we investigated CH₄ dynamics and the composition and abundance of CH₄‐producing archaea and CH₄‐oxidizing bacteria in a Chinese rice field soil planted with three types of rice. Hybrid rice produced 50–60% more of shoot biomass than Indica and Japonica cultivars. However, the emission rate of CH₄ was similar to Japonica and lower than Indica. Furthermore, the dissolved CH₄ concentration in the rhizosphere of hybrid rice was markedly lower than Indica and Japonica cultivars. The rhizosphere soil of hybrid rice showed a similar CH₄ production potential but a higher CH₄ oxidation potential compared with the conventional varieties. Terminal restriction fragment length polymorphism analysis of the archaeal 16S rRNA genes showed that the hydrogenotrophic methanogens dominated in the rhizosphere whereas acetoclastic methanogens mainly inhabited the bulk soil. The abundance of total archaea as determined by quantitative (real‐time) PCR increased in the later stage of rice growth. However, rice variety did not significantly influence the structure and abundance of methanogenic archaea. The analysis of pmoA gene fragments (encoding the α‐subunit of particulate methane monooxygenase) revealed that rice variety also did not influence the structure of methanotrophic proteobacteria, though variable effects of soil layer and sampling time were observed. However, the total copy number of pmoA genes in the rhizosphere of hybrid rice was approximately one order of magnitude greater than the two conventional cultivars. The results suggest that hybrid rice stimulates the growth of methanotrophs in the rice rhizosphere, and hence enhances CH₄ oxidation which attenuates CH₄ emissions from the paddy soil. Hybrid rice is becoming more and more popular in Asian countries. The present study demonstrated that planting of hybrid rice will not enhance CH₄ emissions albeit a higher grain production than the conventional varieties.     

Characterization of Root Exudates at Different Growth Stages of Ten Rice (Oryza sativa L.) Cultivars

Abstract: Plant root exudates play important roles in the rhizosphere. We tested three media (nutrient solution, deionized water and CaSO₄ solution) for three periods of time (2, 4 and 6 h) for collecting root exudates of soil‐grown rice plants. Nutrient culture solution created complications in the analyses of exudates for total organic C (TOC) by the wet digestion method and of organic acids by HPLC due to the interference by its components. Deionized water excluded such interference in analytical analyses but affected the turgor of root cells; roots of four widely different rice cultivars excreted 20 to 60 % more TOC in deionized water than in 0.01 M CaSO₄. Furthermore, the proportion of carbohydrates in TOC was also enhanced. Calcium sulfate solution maintained the osmotic environment for root cells and did not interfere in analytical procedures. Collection for 2 h avoided under‐estimation of TOC and its components exuded by rice roots, which occurred during prolonged exposure. By placing plants in 0.01 M CaSO₄ for 2 h, root exudates of soil‐grown traditional, tall rice cultivars (Dular, B40 and Intan), high‐yielding dwarf cultivars (IR72, IR52, IR64 and PSBRc 20), new plant type cultivars (IR65598 and IR65600) and a hybrid (Magat) were collected at seedling, panicle initiation, flowering and maturity and characterized for TOC and organic acids. The exudation rates were, in general, lowest at seedling stage, increased until flowering but decreased at maturity. Among organic acids, malic acid showed the highest concentration followed by tartaric, succinic, citric and lactic acids. With advancing plant growth, exudation of organic acids substituted exudation of sugars. Root and shoot biomass were positively correlated with carbon exudation suggesting that it is driven by plant biomass. As root exudates provide substrates for methanogenesis in rice fields, large variations in root exudation by cultivars and at different growth stages could greatly influence CH₄ emissions. Therefore, the use of high‐yielding cultivars with lowest root excretions, for example IR65598 and IR65600, would mediate low exudate‐induced CH₄ production. The screening of exciting rice cultivars and breeding of new cultivars with low exudation rates could offer an important option for mitigation of CH₄ emission from rice agriculture to the atmosphere.     

长江三角洲主要超级稻CH4排放特征及其与植株生长特性的关系

采用盆栽试验研究了长江三角洲14个主要超级稻品种(6个粳型超级稻和8个籼型杂交超级稻)CH₄排放特征及其与植株生长特性之间的关系.结果表明: 粳型和籼型超级稻全生育期CH₄排放均呈双峰模式,排放峰值分别出现在分蘖盛期和孕穗期.粳型超级稻的平均CH₄排放总量比籼型超级稻高37.6%(P<0.01),品种间排放差异主要出现在生长后期.虽然两种类型超级稻的CH₄排放总量均与最大叶面积呈显著正相关,但CH₄排放与其他生长特性的关系因品种类型而异.在株高上,粳型超级稻CH₄排放总量与株高呈显著正相关,而籼型超级稻的相关不显著.在生产力上,籼型超级稻CH₄排放总量与其总生物量、籽粒产量和收获指数呈显著负相关,而粳型超级稻的相关不显著.籼型超级稻CH₄排放量低主要是由于其根系生物量显著高于粳型超级稻.     

长江三角洲主要超级稻CH4排放特征及其与植株生长特性的关系

采用盆栽试验研究了长江三角洲14个主要超级稻品种(6个粳型超级稻和8个籼型杂交超级稻)CH₄排放特征及其与植株生长特性之间的关系.结果表明: 粳型和籼型超级稻全生育期CH₄排放均呈双峰模式,排放峰值分别出现在分蘖盛期和孕穗期.粳型超级稻的平均CH₄排放总量比籼型超级稻高37.6%(P<0.01),品种间排放差异主要出现在生长后期.虽然两种类型超级稻的CH₄排放总量均与最大叶面积呈显著正相关,但CH₄排放与其他生长特性的关系因品种类型而异.在株高上,粳型超级稻CH₄排放总量与株高呈显著正相关,而籼型超级稻的相关不显著.在生产力上,籼型超级稻CH₄排放总量与其总生物量、籽粒产量和收获指数呈显著负相关,而粳型超级稻的相关不显著.籼型超级稻CH₄排放量低主要是由于其根系生物量显著高于粳型超级稻.     

Higher yields and lower methane emissions with new rice cultivars

Breeding high‐yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane (CH₄) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high‐yielding rice cultivars actually reduce CH₄ emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH₄ emissions in a soil with a high carbon (C) content. Compared to a low‐yielding cultivar, a high‐yielding cultivar significantly increased root porosity and the abundance of methane‐consuming microorganisms, suggesting that the larger and more porous root systems of high‐yielding cultivars facilitated CH₄ oxidation by promoting O₂ transport to soils. Our results were further supported by a meta‐analysis, showing that high‐yielding rice cultivars strongly decrease CH₄ emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH₄ emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high‐yielding cultivars can substantially mitigate paddy CH₄ emission in China and other rice growing regions.     

Effects of elevated ozone concentration on CH4 and N2O emission from paddy soil under fully open‐air field conditions

We investigated the effects of elevated ozone concentration (E‐O₃) on CH₄ and N₂O emission from paddies with two rice cultivars: an inbred Indica cultivar Yangdao 6 (YD6) and a hybrid one II‐you 084 (IIY084), under fully open‐air field conditions in China. A mean 26.7% enhancement of ozone concentration above the ambient level (A‐O₃) significantly reduced CH₄ emission at tillering and flowering stages leading to a reduction of seasonal integral CH₄ emission by 29.6% on average across the two cultivars. The reduced CH₄ emission is associated with O₃‐induced reduction in the whole‐plant biomass (?13.2%), root biomass (?34.7%), and maximum tiller number (?10.3%), all of which curbed the carbon supply for belowground CH₄ production and its release from submerged soil to atmosphere. Although no significant difference was detected between the cultivars in the CH₄ emission response to E‐O₃, a larger decrease in CH₄ emission with IIY084 (?33.2%) than that with YD6 (?7.0%) was observed at tillering stage, which may be due to the larger reduction in tiller number in IIY084 by E‐O₃. Additionally, E‐O₃ reduced seasonal mean NO_x flux by 5.7% and 11.8% with IIY084 and YD6, respectively, but the effects were not significant statistically. We found that the relative response of CH₄ emission to E‐O₃ was not significantly different from those reported in open‐top chamber experiments. This study has thus confirmed that increasing ozone concentration would mitigate the global warming potential of CH₄ and suggested consideration of the feedback mechanism between ozone and its precursor emission into the projection of future ozone effects on terrestrial ecosystem.     

Methane flux in relation to growth and phenology of a high yielding rice variety as affected by fertilization

Influence of urea application on growth parameters (shoot height, and weight, root volume, weight and porosity; number of tillers; grain yield) and their relationship with methane (CH₄) flux was investigated in Oryza sativa (var. Pant Dhan-4) under flooded soil condition. The study design consisted of (a) fertilized vegetated, (b) control vegetated, (c) fertilized bare, and (d) control bare plots. Crop growth and CH₄ flux measurements were conducted from 9 to 115 days of rice transplanting at regular intervals of 10 days. Results showed that there were significant differences due to days (dates of measurement) and fertilization in all growth parameters except shoot height. Day × fertilization interaction was significant for all growth parameters. CH₄ fluxes ranged from 0.4 to 20.2, 0.1 to 11.9, 0.09 to 2.2 and 0.004 to 1.5 mg m^-2 h^-1 under treatments (a), (b), (c) and (d), respectively. Maximum CH₄ flux was recorded at the flowering stage. All the growth parameters, including number of tillers, showed strong positive relationship with total methane flux. Root porosity was also strongly correlated with total CH₄ emission. It was concluded that CH₄ emission was substantially influenced by crop phenology and growth, and fertilization. The study emphasizes the substrate production and conduit effects of rice plants on CH₄ flux.     

Inhibitory Effects of Oxygen on the Germination of Oryza sativa L. Seeds

Some workers have reported that the breaking of seed dormancyin rice (O. sativa L.) is usually enhanced by higher oxygentension, whereas others have shown that rice seed dormancy canbe broken by incubation under anaerobic conditions. This articleaims to clarify this paradox. The results show that high oxygentensions inhibit seed germination for a certain period afterharvest in Japonica rice, whereas Indica rice cultivars arenot inhibited by oxygen at any stage. Oxygen inhibition, seed germination, aquatic plants, Japonica rice, Indica rice     

Effects of free-air CO2 enrichment (FACE) on CH4 emission from a rice paddy field

Methane (CH₄) is a particularly potent greenhouse gas with a radiative forcing 23 times that of CO₂ on a per mass basis. Flooded rice paddies are a major source of CH₄ emissions to the Earth's atmosphere. A free‐air CO₂ enrichment (FACE) experiment was conducted to evaluate changes in crop productivity and the crop ecosystem under enriched CO₂ conditions during three rice growth seasons from 1998 to 2000 in a rice paddy at Shizukuishi, Iwate, Japan. To understand the influence of elevated atmospheric CO₂ concentrations on CH₄ emission, we measured methane flux from FACE rice fields and rice fields with ambient levels of CO₂ during the 1999 and 2000 growing seasons. Methane production and oxidation potentials of soil samples collected when the rice was at the tillering and flowering stages in 2000 were measured in the laboratory by the anaerobic incubation and alternative propylene substrates methods, respectively. The average tiller number and root dry biomass were clearly larger in the plots with elevated CO₂ during all rice growth stages. No difference in methane oxidation potential between FACE and ambient treatments was found, but the methane production potential of soils during the flowering stage was significantly greater under FACE than under ambient conditions. When free‐air CO₂ was enriched to 550 ppmv, the CH₄ emissions from the rice paddy field increased significantly, by 38% in 1999 and 51% in 2000. The increased CH₄ emissions were attributed to accelerated CH₄ production potential as a result of more root exudates and root autolysis products and to increased plant‐mediated CH₄ emissions because of the larger rice tiller numbers under FACE conditions.     

Methane and nitrous oxide emissions from rice paddy fields as affected by nitrogen fertilisers and water management

Methane and N₂O emissions affected by nitrogen fertilisers were measured simultaneously in rice paddy fields under intermittent irrigation in 1994. Ammonium sulphate and urea were applied at rates of 0 (control), 100 and 300 kg N ha^-1. The results showed that CH₄ emission, on the average, decreased by 42 and 60% in the ammonium sulphate treatments and 7 and 14% in the urea treatments at rates of 100 and 300 kg N ha^-1, respectively, compared to the control. N₂O emission increased significantly with the increase in the nitrogen application rate. N₂O emission was higher from ammonium sulphate treatments than from the urea treatments at the same application rate. A trade-off effect between CH₄ and N₂O emission was clearly observed. The N₂O flux was very small when the rice paddy plots were flooded, but peaked at the beginning of the disappearance of floodwater. In contrast, the CH₄ flux peaked during flooding and was significantly depressed by mid-season aeration (MSA). The results suggest that it is important to evaluate the integrative effects of water management and fertiliser application for mitigating greenhouse gas emissions in order to attenuate the greenhouse effect contributed by rice paddy fields.     

Gene expression of the biosynthetic enzymes and biosynthesis of starch during Rice Grain development

Amylose and amylopectin are determinants of the physicochemical properties for starch and grain quality in rice. Their biosynthesis is catalyzed by the interplay of ADP-glucose pyrophosphorylase (AGPase), granule-bound starch synthase (GBSS), soluble starch synthase (SSS), a starch branching enzyme (SBE), and a starch debranching enzyme (SDE). In this study, the genes for these enzymes were highly expressed 7 to 28 days after flowering during grain development, and their expression closely matched increases in both starch content and grain weight Among all the tested cultivars, amylose contents in the rice grains remained essentially constant throughout their development The AGPase gene was highly expressed in the high-yield cultivars of both glutinous and non-glutinous rice. The SSS gene was actively expressed when mature GBSS mRNA decreased. Genes responsible for amylopectin biosynthesis were simultaneously expressed in the late stage of grain development. We have now demonstrated that the expression patterns of starch biosynthetic genes differ between glutinous and non-glutinous rice, and between Tongil (a Japonica/ Indica hybrid) and Japonica types.     

Diffusion-controlled transport of methane from soil to atmosphere as mediated by rice plants

Methane emission from rice grown in flooded soil was measured in pot experiments using headspaces with different gas composition. The emission rates varied with the atmospheric composition. Based on the kinetic theory of gases the binary diffusion coefficients for methane in various gases were calculated. The ratios of the measured emissions under a certain atmosphere relative to that in air were similar to the ratios of the binary diffusion coefficients showing that plant-mediated CH₄ transport is driven by diffusion. Small deviations from the theoretical ratios of emissions support the hypothesis that mass flow of gas to the submerged parts of the rice plant may depress the upward diffusive CH₄ flux. The results in combination with data from the literature suggest that the rate limiting step in plant-mediated methane transport is diffusion of CH₄ across the root/shoot junction.     

施硅对增温稻田CH4和N2O排放的影响

夜间增温幅度大于白天是气候变暖的显著特征。夜间增温影响水稻生产及CH4和N2O排放。硅是作物有益元素,施硅可提高产量,减少稻田CH4排放。增温或施硅单因子对稻田CH4和N2O排放影响已有报道,但二者耦合如何影响水稻生产及稻田CH4和N2O排放,尚不清楚。通过田间模拟试验,研究了夜间增温下施硅对水稻生长、产量及温室气体持续增温/冷却潜势和排放强度的影响。采用铝箔反光膜夜间(19:00-6:00)覆盖水稻冠层进行模拟夜间增温试验。增温设2水平,即常温对照(CK)和夜间增温(NW);施硅量设2水平,即Si0(不施硅)和Si1(钢渣硅肥,200 kgSiO2/ha)。结果表明,施硅可缓解夜间增温对水稻根系活力的抑制作用,降低夜间增温对水稻地上部、地下部干重和产量的抑制作用。夜间增温显著提高CH4累计排放量,而施硅显著降低CH4累计排放量。夜间增温下施硅处理稻田CH4累计排放量在分蘖期、拔节期、抽穗-扬花期和灌浆成熟期比未施硅处理分别低48.12%、49.16%、61.59%和39.13%。夜间增温或施硅均促进稻田N2O排放,夜间增温下施硅在上述生育期以及全生育期的累计排放量依次比对照高78.17%、51.45%、52.01%、26.14%和40.70%。研究认为,施硅可缓解夜间增温对稻田综合增温潜势和排放强度的促进作用。     

Impact of root exudates of different cultivars and plant development stages of rice (Oryza sativa L.) on methane production in a paddy soil

The impact of root exudates, collected from five rice cultivars, on methane (CH₄) production was studied in a paddy soil under anaerobic conditions. Root exudates of the cultivars Dular, IR72 and IR65598 collected at four growth stages and of B40 and IR65600 collected at two growth stages showed that (a) CH₄ production was commenced rapidly within 2 h upon exudate addition and reached a maximum within a day of addition, and (b) 7-d incubation periods were sufficient to study exudate-induced CH₄ production potentials. Among different cultivars, high C releases from roots, increased the methanogenic source strength of the soil, which finally controlled CH₄ production. The relationship of the amount of CH₄ produced was stronger for the amount of total organic C (r = 0.920) than for the amount of organic acids (r = 0.868) added through exudates. Apparently, CH₄ production and CH₄ emission are more closely related to the release pattern of root exudate-C than to its individual components. The proportion of exudate-C converted to CH₄ ranged between 61 and 83% and remained unaffected by cultivars and growth stages suggesting that the majority of exudate-C served as a methanogenic substrate in the anoxic rice soils. These observations indicate that the use of high-yielding cultivars with lowest excretion (for example IR65598, IR65600) would result in lowest exudate-induced CH₄ production. Therefore, cultivar choice could greatly influence regional and global CH₄ emissions and screening/selection of exiting rice cultivars, and/or breeding new cultivars with low exudation rates could offer an important methane mitigation option as long as yields are not compromised.     

Methane emissions from rice microcosms: The balance of production, accumulation and oxidation

In rice microcosms (Oryza sativa, var. Roma, type japonica),CH₄ emission, CH₄ production, CH₄oxidation and CH₄ accumulation were measured over an entirevegetation period. Diffusive CH₄ emission was measured inclosed chambers, CH₄ production was measured in soil samples,CH₄ oxidation was determined from the difference between oxicand anoxic emissions, and CH₄ accumulation was measured byanalysis of porewater and gas bubbles. The sum of diffusiveCH₄ emission, CH₄ oxidation, andCH₄ accumulation was only 60% of the cumulativeCH₄ production. The two values diverged during the first 50days (vegetative phase) and then again during the last 50 days (latereproductive phase and senescence) of the 150 day vegetation period. Duringthe period of day 50–100 (early reproductive phase/flowering), theprocesses were balanced. Most likely, gas bubbles and diffusion limitationare responsible for the divergence in the early and late phases. The effectof rice on CH₄ production rates and CH₄concentrations was studied by measuring these processes also in unplantedmicrocosms. Presence of rice plants lowered the CH₄concentrations, but had no net effect on the CH₄ productionrates.     

UV-B增强下施硅对稻田CH4和N2O排放及其增温潜势的影响

大气平流层臭氧损耗导致的地表紫外辐射增强作为全球变化重要问题之一,受到广泛关注。硅是水稻生长有益元素,但施硅是否影响稻田CH_4和 N_2O排放,迄今相关报道尚不多见。通过大田试验,研究UV-B增强下施硅对水稻生长、稻田甲烷(CH_4)和氧化亚氮( N_2O)排放及其增温潜势的影响。UV-B辐照设2水平,即对照(A,自然光)和增强20%(E);施硅量设2水平,即对照(Si0,0 kg SiO_2/hm2)和施硅(Si1,200 kg SiO_2/hm2)。结果表明,UV-B增强降低了成熟期水稻地上部和地下部生物量,而施硅能缓解UV-B增强对水稻生长的抑制作用,使水稻地上部和地下部生物量增加。UV-B增强可显著提高稻田CH_4和 N_2O排放通量和累积排放量,增加稻田CH_4和 N_2O排放的综合增温潜势。施硅能明显降低稻田CH_4排放,促进 N_2O排放,降低稻田CH_4和 N_2O排放的综合增温潜势。研究表明,施硅显著降低稻田CH_4和 N_2O的全球增温潜势,缓解UV-B增强对稻田CH_4和 N_2O的全球增温潜势的促进作用。     

The extent of parental genotypic divergence determines maximal heterosis by increasing fertility in inter-subspecific hybrids of rice (Oryza sativa L.)

The magnitude of heterosis in F₁ hybrids is related not only to the performance of parents per se but also to the genetic diversity between two parents. The extent of genotypic divergence between hybrid rice parents was investigated at the molecular level, using two subsets of rice materials: a subset of doubled haploid (DH) lines derived from an Indica × Japonica cross (Gui630/02428) and another subset of Indica or Japonica lines representative of a broad spectrum of the Asian cultivated rice gene pool, including landraces, primitive cultivars, historically important cultivars, modern elite cultivars, super rice and parents of superior hybrids. 57 entries deliberately selected from the 81-DH lines (in total) were testcrossed to two widely used rice lines in China, photoperiod-sensitive genic male sterile (PGMS) N422s and thermo-sensitive genic male sterile (TGMS) Peiai64s. Results of the two sets of test-cross F₁ populations showed congruently that parental genotypic divergence has a relatively low impact on heterosis for the two yield components, i.e., panicle number and 1000-grain weight, but it has a great bearing on fertility parameters, i.e., filled grains per plant and seedset. Heterosis for grain yield in the two test-cross populations exhibited a sharp maximum when the proportion of Japonica alleles in the male parent was between 50 and 60%, so was the heterosis for fertility parameters correspondingly. Thus fertility parameters were the most sensitive and important factors which were influenced by the extent of parental genotypic divergence. Moreover, our results showed that parents with moderate extent of genotypic divergence played an important role in the use of inter-subspecific rice heterosis.     

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.     

Linkage analysis of the nuclear homologues of mitochondrial plasmid-like DNAs in rice.

A genetical study on the nucleotide sequences of the nuclear DNAs which share homology with rice mitochondrial plasmid-like DNAs, B1, B2, B3 and B4 was carried out. Restriction fragments of the nuclear DNAs hybridized with these plasmid-like DNAs showed polymorphisms in their length between Indica and Japonica rice cultivars. The hybridized signals found specifically in Indica or Japonica cultivars segregated in the F2 population derived from a cross between these two subspecies. The observed ratio of the nuclear homologues in the F2 population demonstrated that they were transmitted according to the Mendelian inheritance. The co-segregation of homologues was examined and the linkage was detected between the B1-nuclear homologue of Japonica and the B4-nuclear homologue of Indica, and also between the nuclear homologues of B2 and B3 of Indica. The linkage between the B1-nuclear homologue of Japonica and the B4-nuclear homologue of Indica was conserved in the different rice cultivars.