Methane oxidation and the competition for oxygen in the rice rhizosphere

A mechanistic approach is presented to describe oxidation of the greenhouse gas methane in the rice rhizosphere of flooded paddies by obligate methanotrophic bacteria. In flooded rice paddies these methanotrophs compete for available O(2) with other types of bacteria. Soil incubation studies and most-probable-number (MPN) counts of oxygen consumers show that microbial oxygen consumption rates were dominated by heterotrophic and methanotrophic respiration. MPN counts of methanotrophs showed large spatial and temporal variability. The most abundant methanotrophs (a Methylocystis sp.) and heterotrophs (a Pseudomonas sp. and a Rhodococcus sp.) were isolated and characterized. Growth dynamics of these bacteria under carbon and oxygen limitations are presented. Theoretical calculations based on measured growth dynamics show that methanotrophs were only able to outcompete heterotrophs at low oxygen concentrations (frequently < 5 microM). The oxygen concentration at which methanotrophs won the competition from heterotrophs did not depend on methane concentration, but it was highly affected by organic carbon concentrations in the paddy soil. Methane oxidation was severely inhibited at high acetate concentrations. This is in accordance with competition experiments between Pseudomonas spp. and Methylocystis spp. carried out at different oxygen and carbon concentrations. Likely, methane oxidation mainly occurs at microaerophilic and low-acetate conditions and thus not directly at the root surface. Acetate and oxygen concentrations in the rice rhizosphere are in the critical range for methane oxidation, and a high variability in methane oxidation rates is thus expected.     

Prediction of reducible soil iron content from iron extraction data

Soils contain various iron compounds that differ in solubility, reducibility and extractability. Moreover, the contribution of the various iron compounds to total iron (Fe) and total Fe concentrations differs highly among soils. As a result, the total reducible Fe content can also differ among soils, and so does the dynamics of iron reduction. These factors complicate the prediction of reducible Fe based on Fe extraction data and hamper the application of process-based models for reduced or waterlogged soils where redox processes play a key-role. This paper presents a theoretical analysis relating reducible to extractable Fe reported in the literature. Predictions made from this theoretical analysis were evaluated in soil incubations using 18 rice paddy soils from all over the world. The incubation studies and the literature study both show that reducible Fe can be related to Fe from some selected, but not all, iron extractions. The combination of measurements for labile Fe(III)oxides (derived from oxalate-extractable Fe) and stabile Fe(III)oxides (derived from dithionite-citrate-extractable Fe) shows highly significant correlations with reducible Fe with high coefficients of determination (r² = 0.92–0.95 depending on the definition of stabile Fe(III)oxides). Given the high diversity in rice soils used for the incubations, these regression equations will have general applicability. Application of these regression equations in combination with soil database information may improve the predictive ability of process-based models where soil redox processes are important, such as CH₄ emission models derived for rice paddies or wetlands.     

Methane Oxidation and the Competition for Oxygen in the Rice Rhizosphere

A mechanistic approach is presented to describe oxidation of the greenhouse gas methane in the rice rhizosphere of flooded paddies by obligate methanotrophic bacteria. In flooded rice paddies these methanotrophs compete for available O₂ with other types of bacteria. Soil incubation studies and most-probable-number (MPN) counts of oxygen consumers show that microbial oxygen consumption rates were dominated by heterotrophic and methanotrophic respiration. MPN counts of methanotrophs showed large spatial and temporal variability. The most abundant methanotrophs (a Methylocystis sp.) and heterotrophs (a Pseudomonas sp. and a Rhodococcus sp.) were isolated and characterized. Growth dynamics of these bacteria under carbon and oxygen limitations are presented. Theoretical calculations based on measured growth dynamics show that methanotrophs were only able to outcompete heterotrophs at low oxygen concentrations (frequently <5 μM). The oxygen concentration at which methanotrophs won the competition from heterotrophs did not depend on methane concentration, but it was highly affected by organic carbon concentrations in the paddy soil. Methane oxidation was severely inhibited at high acetate concentrations. This is in accordance with competition experiments between Pseudomonas spp. and Methylocystis spp. carried out at different oxygen and carbon concentrations. Likely, methane oxidation mainly occurs at microaerophilic and low-acetate conditions and thus not directly at the root surface. Acetate and oxygen concentrations in the rice rhizosphere are in the critical range for methane oxidation, and a high variability in methane oxidation rates is thus expected.     

Composition of Archaeal Community in a Paddy Field as Affected by Rice Cultivar and N Fertilizer

Methanogenesis in paddy fields is significantly influenced by environmental and field management factors such as rice cultivar and nitrogenous fertilizer. However, it has been unclear whether such effects are reflected in the structure of methanogenic archaeal populations. In the present study, molecular analyses including cloning and sequencing and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of archaeal 16S rRNA genes were used to characterize the methanogenic archaeal assemblages and to identify the effect of environmental variables including rice cultivar and N fertilizer on archaeal community compositions in a Chinese paddy field soil. The correlation between methanogenic archaeal composition and environmental variables was explored by correspondence analysis. The results showed that the spatial or niche factor (rice roots versus rhizosphere, surface, and the deeper layer soils) had the greatest influence on the archaeal community composition. There was an obvious enrichment or selection of hydrogenotrophic as opposed to acetoclastic methanogens by rice roots. The archaeal community also changed, though slightly, between the rhizosphere and bulk soils and between the surface soil and the deeper layer soil. However, rice cultivar and N fertilizer appear to have an effect only on methanogens tightly associated with rice roots.     

稻田甲烷排放模型研究——模型及其修正

在过去十多年内 ,关于稻田甲烷排放的模拟已经进行了不少有益的探索并且开发出了数个有关的模型。模型的成功研制是准确定量估计不同区域范围内稻田甲烷排放的前提。以往大部分模型由于模拟精度不高 ,或者是其要求太多的输入参数 ,因而限制了它在大尺度范围内的广泛应用。在一个比较成熟的模型基础上 ,进行了必要的修正与扩充。增加了稻田甲烷通过气泡方式排放的模拟模块 ,并修正了原模型中关于土壤氧化还原电位变化的模拟 ,使之能适应于多种稻田水管理方式。新修正的模型 (CH4 MOD)不仅保留了原模型输入参数较少和易于获得的优点 ,而且能适应多种水稻耕作方式 ,这为进一步利用模型技术准确估计大尺度区域稻田甲烷排放提供了一种新的科学方法     

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.     

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.     

Greenhouse gas emissions from rice microcosms amended with a plant microbial fuel cell

Methane (CH₄) release from wetlands is an important source of greenhouse gas emissions. Gas exchange occurs mainly through the aerenchyma of plants, and production of greenhouse gases is heavily dependent on rhizosphere biogeochemical conditions (i.e. substrate availability and redox potential). It is hypothesized that by introducing a biocatalyzed anode electrode in the rhizosphere of wetland plants, a competition for carbon and electrons can be invoked between electrical current-generating bacteria and methanogenic Archaea. The anode electrode is part of a bioelectrochemical system (BES) capable of harvesting electrical current from microbial metabolism. In this work, the anode of a BES was introduced in the rhizosphere of rice plants (Oryza sativa), and the impact on methane emissions was monitored. Microbial current generation was able to outcompete methanogenic processes when the bulk matrix contained low concentrations of organic carbon, provided that the electrical circuit with the effective electroactive microorganisms was in place. When interrupting the electrical circuit or supplying an excess of organic carbon, methanogenic metabolism was able to outcompete current generating metabolism. The qPCR results showed hydrogenotrophic methanogens were the most abundant methanogenic group present, while mixotrophic or acetoclastic methanogens were hardly detected in the bulk rhizosphere or on the electrodes. Competition for electron donor and acceptor were likely the main drivers to lower methane emissions. Overall, electrical current generation with BESs is an interesting option to control CH₄ emissions from wetlands but needs to be applied in combination with other mitigation strategies to be successful and feasible in practice.     

Monitoring of root growth and redox conditions in paddy soil rhizotrons by redox electrodes and image analysis

The root-zone of wetland rice was monitored in a paddy soil throughout a vegetation period with the aid of a rhizotron experiment. For this purpose (a) digital images of the root-zone were taken daily, and (b) the redox potential was measured in situ every day. The images were processed by image analysis in order to display areas of oxidation and reduction in the soil. Therefore, thresholds were set to simplify the localization and quantification of discrete areas which were colourized due to the redox potential. Both, images and measured redox potentials, provide the basis for the visualization of the root and redox dynamics in the root-zone. The anaerobic root-zone of flooded paddy soils is significantly influenced by the aerenchymal transport of oxygen to rice roots. The release of oxygen into the rhizosphere, which causes different patterns of oxidized and reduced areas in the course of the vegetation period, also affects microbial communities such as methane producing archaea or methane oxidizing bacteria. The visualization of redox dynamics may, therefore, be useful to localize potential hotspots for the microorganisms in the root-zone of paddy soils. The reduced and oxidized conditions changed spatiotemporally. Oxidized areas were mostly found in the surrounding of active roots and in a distinct layer next to the soil surface. Reduced areas shifted from beneath the oxidized surface layer into sparsely-rooted soil. The ratio of the analyzed oxidized and reduced areas was oscillating with increasing intensity throughout the monitored vegetation period.     

长期不同施肥下水稻土甲烷氧化能力及甲烷氧化菌多样性的变化

稻田内源甲烷的氧化是稻田甲烷减排的重要途径。而甲烷氧化菌是土壤中甲烷氧化的主要施动者,在长期不同施肥条件下,土壤微生物群落的演变是否影响到土壤甲烷氧化菌群落结构及其活性,进而影响到田土壤CH4向大气的实际排放强度还不清楚。为此,选择太湖地区一个长期肥料试验的稻田土壤为研究对象,分析长期不同肥料施用对土壤甲烷氧化能力的影响及其与土壤中甲烷氧化菌群落结构变化的可能关系。结果表明,长期不同的施肥措施下稻田土壤对甲烷的氧化能力产生了明显差异,伴随着土壤中甲烷氧化菌（MOBI和MOBII）的基因群落多样性的显著变化。长期单一施用氮肥为主的化肥显著降低了土壤对甲烷的氧化能力,同时显著降低了稻田土壤甲烷氧化菌的多样性和丰富度;不同施肥下甲烷氧化菌多样性的变化与土壤的甲烷氧化能力的变化趋势相一致。因此,研究显示长期不同施肥处理下甲烷氧化菌群落结构的改变可能是引起水稻土甲烷氧化能力变化的一个主要因素,有机无机配合施用可以明显降低稻田土壤甲烷的大气释放潜能。但长期不同施肥处理下甲烷氧化菌活性的变化还有待于进一步研究。     

Localization of iron-reducing activity in paddy soilby profile studies

Profiles of iron speciations (porewaterFe(II) and Fe(III), solid-phase Fe(II) andFe(III)) have been studied to localize both ironreduction and oxidation in flooded paddy soil. Sulfateand nitrate were determined to analyze interactions ofredox reactions involved in the iron cycle with thoseof the sulfur and nitrogen cycle. The development ofthe iron(II) and iron(III) profiles was observed inmicroscale over a time period of 11 weeks. After 11weeks the profiles were stable and showed lowestconcentrations of solid-phase iron(II) on the soilsurface with increasing concentrations to a soil depthof 10 mm ( 100 µmol/cm³). Profilesof iron(III) showed a maximum of iron(III) at a depthof 2 to 4 mm ( 100--200 µmol/cm³).Porewater iron(II) concentrations were three orders ofmagnitude lower than extracted iron(II) and indicatedthat most iron(II) was adsorbed to the solid-phase orimmobilized as siderite and vivianite. Diffusive lossof iron from the soil was indicated by iron recovery(0.3 µmol gdw^–1) in the flooding water after12 weeks. The organic content of the soil influencedthe concentrations of solid-phase iron(II) in deepersoil layers (> 6 mm); higher Fe(II) concentrationsin soil with limiting amounts of electron donors mayindicate lower consumption of CO₂ by methanogenicbacteria and therefore a higher sideriteprecipitation. Soil planted with rice showed similariron(II) profiles of fresh paddy soil cores. However,maximal iron(III) concentrations ( 350µmol/cm³) were present in planted soil at adepth of 1 to 2.5 mm where oxygen is provided by a matof fine roots. Sulfate and nitrate concentrations inthe porewater were highest on the soil surface (10µM NO₃ ^–, 40 µM SO₄ ^2–) anddecreased with depth. Similar profiles were detectedfor malate, acetate, lactate, and propionate, theconcentrations decreased gradually from the surface toa depth of 4 mm. Profiles of oxygen showed highestconcentrations at the surface due to photosyntheticproduction and a depletion of oxygen below 3 mm depth.Methane production rates measured from soil layersincubated separately in closed vessels were zero atthe soil surface and increased with depth. In soildepths below 4 mm where iron(III) concentrationsdecreased higher methane production rates werefound.     

水稻土中脂肪酸互营氧化的研究进展

水稻田是温室气体甲烷(CH4)的重要释放源之一,有机质在水稻土中通过厌氧分解途径最终产生CH4和CO2.短链脂肪酸互营氧化是水稻土有机质降解的关键环节,但是由于互营微生物独特的生理生态特性,目前人们对于参与该过程的微生物群落及功能了解甚少.稳定同位素探针(SIP)技术被认为是实现环境中参与物质转化微生物种类与功能相耦合的有力工具.本文首先讨论互营过程的热力学基础和互营微生物的种间相互作用模式,然后简要讨论了互营过程的环境影响因子,最后详细综述稳定同位素探针技术在水稻土短链脂肪酸互营氧化过程中的相关研究.目前的研究表明:参与水稻土脂肪酸互营氧化过程的互营细菌种类丰富、多样性高;除已知互营细菌的作用外,大量未培养、功能未知的细菌类型也可能参与短链脂肪酸的互营氧化;对于互营细菌的伙伴而言,新型产甲烷胞菌属(Methanocella)类型的古菌在不同脂肪酸互营降解过程中均起主要作用,揭示了这类产甲烷古菌在水稻土厌氧产甲烷过程中的重要作用.     

Effect of ducks on CH4 emission from paddy soils and its mechanism research in the rice-duck ecosystem

The effect of ducks on CH₄ emission from paddy soils and its mechanism were probed in order to decide the optimum number of ducks in the rice-duck ecosystem. Methane emission fluxes from paddy soils were measured by the static box technique. The correlations between methane emission and soil physical and chemical characteristics were also analyzed. The results showed that significant differences (p < 0.01) existed in the dissolved oxygen content of water body in the treatment fields, and the more the ducks, the higher the dissolved oxygen content. Secondly, the soil redox matter content and methanogenic bacteria population of the rice-duck ecosystem reduced more sharply than those of the no-duck rice farming, resulting in a lower methane production. Thirdly, the amount of methane emission differed between the treatments—the more the ducks, the less the methane emission. Other related analyses showed that the negative correlation was significant (p < 0.001) between the methane emission flux and dissolved oxygen content of water body. However, CH4 emission flux had significantly positive correlation (p < 0.01) with the soil redox matter content and rice field methanogenic population.     

Coupled anaerobic methane oxidation and metal reduction in soil under elevated CO2

Continued current emissions of carbon dioxide (CO₂) and methane (CH₄) by human activities will increase global atmospheric CO₂ and CH₄ concentrations and surface temperature significantly. Fields of paddy rice, the most important form of anthropogenic wetlands, account for about 9% of anthropogenic sources of CH₄. Elevated atmospheric CO₂ may enhance CH₄ production in rice paddies, potentially reinforcing the increase in atmospheric CH₄. However, what is not known is whether and how elevated CO₂ influences CH₄ consumption under anoxic soil conditions in rice paddies, as the net emission of CH₄ is a balance of methanogenesis and methanotrophy. In this study, we used a long-term free-air CO₂ enrichment experiment to examine the impact of elevated CO₂ on the transformation of CH₄ in a paddy rice agroecosystem. We demonstrate that elevated CO₂ substantially increased anaerobic oxidation of methane (AOM) coupled to manganese and/or iron oxides reduction in the calcareous paddy soil. We further show that elevated CO₂ may stimulate the growth and metabolism of Candidatus Methanoperedens nitroreducens, which is actively involved in catalyzing AOM when coupled to metal reduction, mainly through enhancing the availability of soil CH₄. These findings suggest that a thorough evaluation of climate-carbon cycle feedbacks may need to consider the coupling of methane and metal cycles in natural and agricultural wetlands under future climate change scenarios.     

Accumulation of nitrogen and microbial residues during 2000 years of rice paddy and non‐paddy soil development in the Yangtze River Delta,China

Lowland rice paddy soils may accumulate significant amounts of organic matter. Our aim was to investigate the role of prolonged paddy management on the nitrogen (N) status of the soils, and to elucidate the contribution of bacteria and fungi to long‐term N accumulation processes. For this purpose, we sampled a chronosequence of 0–2000 years of rice cropping with adjacent non‐paddy systems in the Bay of Hangzhou, China. The samples were analyzed for bulk density, total, mineral and microbial N (N_mic), and amino sugars as markers for microbial residues. The results showed that during the first 100 years of land embankment, both paddy and non‐paddy soils accumulated N at a rate of up to 61 and 77 kg ha^?1 per annum, reaching steady‐state conditions after 110–172 years, respectively. Final N stocks in paddy fields exceeded those of the non‐paddies by a factor of 1.3. The contribution of amino sugars to total N increased to a maximum of 34 g N kg^?1 N in both land‐use systems, highlighting a significant accumulation of N in microbial residues of the surface soils. Correspondingly, the ratio of N_mic to microbial residue‐N decreased to a constant value. In the paddy subsoils, we found that bacterial residues particularly contributed to the pool of microbial residue‐N. Nevertheless, the absolute contents of amino sugars in paddy subsoils decreased during the last 1700 years of the chronosequence. We conclude that under paddy cultivation, soil microorganisms may accumulate parts of this N in their residues despite low overall N availability. However, this N accumulation is limited to initial stages of paddy soil development and restricted to the surface horizons, thus challenging its sustainability with future land‐use changes.     

The mechanism of reduction in waterlogged paddy soil

Elucidation of the laws governing the reduction process in flooded rice paddy soil is indispensable for developing the lowland rice cultivation system by which the oxidation-reduction conditions for optimum growth can be maintained throughout the growth of the crop. The authors’ efforts have been focussed on the microbial metabolism of the reduction process in paddy soil, using waterlogged soil incubated in closed syringes as a simplified model of rice paddy field soil under flooded conditions. Such conditions can be assumed to occur throughout the plowed layer of field soil under flooding, except for the uppermost layer to which oxygen is supplied. One may conclude from the results of this investigation that the type of microbial metabolism in waterlogged soil changes successively according to the oxidation-reduction state from aerobic respiration in the presence of molecular oxygen, which is the most efficient energy-yielding reaction, to methane fermentation, which appears to be a less efficient energy-yielding reaction.     

稻田水氮氧环境因子对水稻生长发育、光合作用和氮利用的调控研究进展

水分和氮素是影响水稻生长发育的两个重要环境因子。适宜的水氮耦合模式可通过“以水调氮、以水控氧”调控稻田根际氮形态和溶氧量等环境因子,促进良好根系形态构建,提高叶片光合速率和光合产物“源-库”分配平衡,提高水稻群体质量和产量形成。同时,稻田水氮氧环境因子驱动的微生物调控机制在水稻-土壤系统氮高效利用方面也发挥重要作用。本文重点阐述了水氮耦合下水分、氮形态和溶氧量对水稻生长发育、光合作用、碳氮代谢、稻田氮转化过程及其微生物调控机制等方面的研究进展,展望并提出了未来亟待加强的研究方向:1)开展水氮耦合下水稻根际溶氧量时空动态分布特征及氧环境调控关键因子研究;2)明确不同基因型水稻根源信号增氧响应特征及其对水稻生长发育的影响调控机制;3)阐明根际氧环境驱动的关键微生物过程对稻田氮转化和氮素利用的影响。