Biogeography of wetland rice methanotrophs

We focused on the functional guild of methane oxidizing bacteria (MOB) as model organisms to get deeper insights into microbial biogeography. The pmoA gene was used as a functional and phylogenetic marker for MOB in two approaches: (i) a pmoA database (> 4000 sequences) was evaluated to obtain insights into MOB diversity in Italian rice paddies, and paddy fields worldwide. The results show a wide geographical distribution of pmoA genotypes that seem to be specifically adapted to paddy fields (e.g. Rice Paddy Cluster 1 and Rice Paddy Cluster 2). (ii) On the smaller geographical scale, we designed a factorial experiment including three different locations, two rice varieties and two habitats (soil and roots) within each of three rice fields. Multivariate analysis of terminal restriction fragment analysis profiles revealed different community patterns at the three field sites, located 10–20 km apart. Root samples were characterized by high abundance of type I MOB whereas the rice variety had no effect. With the agronomical practice being nearly identical, historical contingencies might be responsible for the field site differences. Considering a large reservoir of viable yet inactive MOB cells acting as a microbial seed bank, environmental conditions might have selected and activated a different subset at a time thereby shaping the community.     

Rice field ecology and fish culture — an overview

Rice fields are an integral part of the landscape throughout most of the tropics. Rice is also grown widely in higher latitudes. Most rice cultivation is done in flooded fields where a temporary aquatic fauna is generated. Rice cultivation has sustained some of the oldest civilizations but the use of the aquatic phase for raising a crop of fish has not been practiced widely although fragmentary records indicate that rice and fish have been cultivated concurrently but rarely over 2 or 3 millennia. We have more reliable records of rice and fish culture in rice fields during the past 150 years.Rice cultivation is now very highly mechanized and uses high fertilizer and pesticide inputs and extensive irrigation facilities have been constructed to increase the area of rice cultivation and enhance yields. Rice cultivation also provides a suitable habitat for the breeding of mosquitoes, some of which are vectors for diseases. It appears that in regions outside the tropics aquatic pests of rice are also encountered. In the tropics indigenous fishes and other organisms including copepods act as biological control agents for mosquitoes and aquatic rice pests.The rice field is usually a successor of shallow marshes or a lowland area which can be supplied with adequate water. In addition deep water rice is grown in permanent marshes and rice is also grown in terraced hillsides, not to mention relatively dry localities where dry-land rice is cultivated. The marsh habitat is usually rich in plant and animal species. Some of these survive in rice fields. The water supplied to rice fields come via irrigation systems which bring a complement of plants, animals, and other organisms seasonally to colonize the rice field. The rice field is thus a new habitat, like a reservoir, with some similarities to a marsh but manipulated for cultivation of rice. This creates a unique, temporary and rapidly changing habitat which is often very productive and can be used to raise fish on an artisanal or intensive scale.Fish culture in rice fields has had a checkered history during the past 150 years when records are available. Its earlier history is obscure. Long-term records of fish culture activities are not available from any part of the world although apparently thriving enterprises seem to have existed in Japan, Italy, USSR and China. Attempts to culture fish in rice fields have been made on all continents except Australasia and Antarctica of course. At the present time the focus of rice-cultivation seems to have shifted to China, Indonesia, and Thailand. Whether this enterprise will endure even in these countries cannot be predicted with any degree of certainty.     

A semi-empirical model of methane emission from flooded rice paddy soils

Reliable regional or global estimates of methane emissions from flooded rice paddy soils depend on an examination of methodologies by which the current high variability in the estimates might be reduced. One potential way to do this is the development of predictive models. With an understanding of the processes of methane production, oxidation and emission, a semi-empirical model, focused on the contributions of rice plants to the processes and also the influence of environmental factors, was developed to predict methane emission from flooded rice fields. A simplified version of the model was also derived to predict methane emission in a more practical manner. In this study, it was hypothesized that methanogenic substrates are primarily derived from rice plants and added organic matter. Rates of methane production in flooded rice soils are determined by the availability of methanogenic substrates and the influence of environmental factors. Rice growth and development control the fraction of methane emitted. The amount of methane transported from the soil to the atmosphere is determined by the rates of production and the emitted fraction. Model validation against observations from single rice growing seasons in Texas, USA demonstrated that the seasonal variation of methane emission is regulated by rice growth and development. A further validation of the model against measurements from irrigated rice paddy soils in various regions of the world, including Italy, China, Indonesia, Philippines and the United States, suggests that methane emission can be predicted from rice net productivity, cultivar character, soil texture and temperature, and organic matter amendments.     

水稻植株对稻田甲烷排放的影响

稻田CH4排放是稻田土壤中CH4产生、氧化和传输不同过程的净效应,水稻植株强烈影响稻田CH4的产生、氧化和传输过程,是导致稻田CH4排放季节性变化规律的一个重要因素,本文综述了水稻植株对稻田CH4排放过程的不同影响,水稻植株根系分泌物和脱落物作为产甲烷前体促进稻田土壤中CH4的产生,在水稻生长后期,植株根系分泌物和脱落物被认为是稻田土壤甲烷产生的主要基质,是导致这一时期稻田CH4高排放通量的主要原因;水稻植株根系泌氧在根际环境形成一个微氧区域氧化稻田甲烷,整个水稻生长季稻田土壤中产生的CH4大约36％～90％在植株根际环境中被氧化;约80％甚至更多的稻田CH4通过水稻植株的通气组织进入大气圈,植株对稻田CH4的传输具有十分重要的意义。     

Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses

The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related to Methanomicrobiales and Rice cluster I. Methanomicrobiales, Rice cluster I and Methanosarcinales were major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related to Methanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off-crop season.     

Soil type links microbial colonization of rice roots to methane emission

Most of the methane (CH₄) emission from rice fields is derived from plant photosynthates, which are converted to CH₄. Rice cluster I (RC-1) archaea colonizing the rhizosphere were found to be the methanogens responsible for this process. Hence, RC-1 methanogens seem to play a crucial role in emission of the greenhouse gas CH₄. We determined the community composition and activity of methanogens colonizing the roots of eight different rice cultivars after growth on both Italian rice soil and river bank soil, which contained different communities of methanogenic archaea. The community composition was analyzed by terminal restriction fragment length polymorphism and cloning/sequencing of the archaeal 16S rRNA gene and the mcrA gene coding for a subunit of the methyl coenzyme M reductase. When grown on rice field soil, the methanogenic community of the different rice cultivars was always dominated by RC-1 methanogens. In contrast, roots were colonized by Methanomicrobiales when grown on river bank soil, in which RC-1 methanogens were initially not detectable. Roots colonized with Methanomicrobiales compared with RC-1 exhibited lower CH₄ production and CH₄ emission rates. The results show that the type of methanogens colonizing rice roots has a potentially important impact on the global CH₄ cycle.     

Does flooding of rice fields after cultivation contribute to wetland plant conservation in southern Brazil?

Question: Does flooding of rice fields after cultivation contribute to wetland plant conservation in southern Brazil? Location: Rice fields in the coastal plain of southern Brazil. Methods: Six rice fields with different management practices were randomly selected (three dry rice fields and three flooded rice fields). Six collections were carried out over the rice cultivation cycle. Richness and biomass were measured using the quadrat method. Results: A total of 88 macrophyte species was recorded. There was no statistical interaction between management practices and rice cultivation phases for macrophyte richness and biomass. Macrophyte species richness and biomass changed over time, but were similar between flooded and dry rice fields. The first three axes generated by detrended correspondence analysis explained 29% of the variation in species composition and the multivariate analysis of variance showed that there was a statistical interaction between management practices and agricultural periods. Conclusions: Rice fields may help to conserve an important fraction of the aquatic macrophyte diversity of wetlands of southern Brazil by providing the setting up of a greater number of species within the agricultural landscape. However, rice fields must not be viewed as surrogate systems for natural wetlands. The difference in species composition between flooded and dry rice fields is interesting in terms of biodiversity conservation. If rice producers could keep part of their agricultural land flooded during the fallow phase, this management practice could be an important strategy for the conservation of biodiversity in areas where natural wetlands have been converted to rice fields.     

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     

Statistical analysis of the major variables controlling methane emission from rice fields

Rice cultivation is an important anthropogenic source of atmospheric methane (CH₄), the emission of which is affected by management practices. Many field measurements have been conducted in major rice‐producing countries in Asia. We compiled a database of CH₄ emissions from rice fields in Asia from peer‐reviewed journals. We developed a statistical model to relate CH₄ flux in the rice‐growing season to soil properties, water regime in the rice‐growing season, water status in the previous season, organic amendment and climate. The statistical results showed that all these variables significantly affected CH₄ flux, and explained 68% of the variability. Organic amendment and water regime in the rice‐growing season were the top two controlling variables; climate was the least critical variable. The average CH₄ fluxes from rice fields with single and multiple drainages were 60% and 52% of that from continuously flooded rice fields. The flux from fields that were flooded in the previous season was 2.8 times that from fields previously drained for a long season and 1.9 times that from fields previously drained for a short season. In contrast to the previously reported optimum soil pH of around neutrality, soils with pH of 5.0–5.5 gave the maximum CH₄ emission. The model results demonstrate that application of rice straw at 6 t ha^?1 before rice transplanting can increase CH₄ emission by 2.1 times; when applied in the previous season, however, it increases CH₄ emission by only 0.8 times. Default emission factors and scaling factors for different water regimes and organic amendments derived from this work can be used to develop national or regional emission inventories.     

稻田不同耕作制下有机质和氮磷钾的变化研究

６ａ定位研究的结果表明,在东洞庭湖地区土壤,气候及施肥等条件下,４种主要耕作制中,稻－稻－冬闲耕作制不仅产量较低,而且经济效益也较差,并有可能导致土壤肥力的下降和退化,稻－稻－肥（紫云英）耕作制由具有一定的增产效果,并且有较高的经济效益,土壤肥力亦呈现出上升和进化的趋势,稻－稻－麦（大麦）和稻－稻－油（油菜）耕作制则不仅使土地的得用率提高,增加了单位的产量,且土壤肥力也同样得到了上升和进化,但其经     

Agronomic aspects of wetland rice cultivation and associated methane emissions

Wetland rice cultivation is one of the major sources of atmospheric methane (CH₄). Global rice production may increase by 65% between 1990 and 2025, causing an increase of methane emissions from a 92 Tg CH₄ y^–1 now to 131 Tg in 2025.Methane production depends strongly on the ratio oxidizing: reducing capacity of the soil. It can be influenced by e.g. addition of sulphate, which inhibits methanogenesis. The type and application mode of mineral fertilizers may also affect methane emissions. Addition of organic matter in the form of compost or straw causes an increase of methane emissions, but methane production is lower for materials with a low C/N ratio.High percolation rates in wetland rice soils and occasional drying up of the soil during the cultivation period depresses methane release. Water management practices aimed at reducing emissions are only feasible during specific periods in the rice growing season in flat lowland irrigated areas with high security of water availability and good control of the water supply. Intermittent drying of soils may not be possible on terraced rice lands.Assuming a 10 to 30% reduction in emission rates per unit harvested area, the global emission may amount to 93 Tg CH₄ y^– in 2025. A reduction of global emissions seems very difficult. To develop techniques for reducing CH₄ emissions from wetland rice fields, research is required concerning interactions between soil chemical and physical properties, and soil, water and crop management and methanogenesis. Such techniques should not adversely affect rice yields.     

Role of rice in mediating methane emission

Methane emitted at different plant conditions through the different organs of rice plants was studied using a closed chamber technique under the laboratory, phytotron, and greenhouse conditions in order to clarify and quantify the role of different organs of rice plant as methane emission sites. Rice plants grown in flooded soils emit methane to the atmosphere via the aerenchyma of leaves, nodes and panicles. Emission through the rice plants is controlled by diffusion. No methane is emitted via the transpiration stream. Leaves are the major release sites at the early growth stage while nodes become more important later. Cracks and porous structure were found in the nodes. Panicles generally contribute little to methane emission. Increasing water depth temporarily reduces methane emission while concentration gradients in rice plants readjust to unsubmerged emission sites. Methane emissions in rice plants cease only when the plants become totally submerged.     

Methane production from rice straw pretreated by a mixture of acetic–propionic acid

Rice straw was treated with a mixed solution of acetic acid and propionic acid to enhance its biodegradability. The effect of acid concentration, pretreatment time, and the ratio of solid to liquid on the delignification performance of rice straw were investigated. It was found that the optimal conditions for hydrolysis were 0.75 mol/L acid concentration, 2 h pretreatment time and 1:20 solid to liquid ratio. Batch methane fermentation of untreated rice straw, pretreated rice straw, and the hydrolysates (the liquid fraction) of pretreatment were conducted at 35 °C for 30 days, and the results indicated that methane production of rice straw can be enhanced by dilute organic acid pretreatment. Moreover, most of the acid in hydrolysates can also be converted into methane gas.     

Patterns of bird abundance and habitat use in rice fields of the Kanto Plain, central Japan

Rice fields, the most widespread cropland in Japan, provide important habitat for birds, but few studies have examined bird communities that are influenced by agriculture in rice fields. I studied the seasonal pattern of bird abundance and their habitat preferences in terms of agricultural habitats in the rice fields of the central Kanto Plain, central Japan. In total, 19 waterbird species and 31 landbird species were recorded over the study year. Waterbird occurrence was largely restricted to the cultivation season (i.e. the flooded season, May–August), with maximum abundance in August. Rice fields dried up during winter and supported few waterbirds except for irregular occurrences of little egrets (Egretta garzetta) and common snipes (Gallinago gallinago), which selectively used ditches with shallow water. Landbird abundance increased after the start of cultivation (May) to August, but more birds were attracted to the rice fields in midwinter (around January). For both waterbirds and landbirds, most species preferred levees and fallow grass fields, but avoided fields with rice vegetation. Unplowed fields after harvest were preferred by several species including skylarks (Alauda arvensis), while plowed fields were less attractive to most species. These results suggest the need for advanced agricultural practices to include improvement in habitat quality for birds.     

Integrated mosquito management in rice field in China

Wetlands Ecology and Management - Rice cultivation is important in China with over 29.33 million hm2 of rice fields, producing 28.9% of rice yields worldwide. Rice fields are mass breeding sites...     

UV-B辐射增强对抗除草剂转基因水稻 CH4排放的影响

在大田条件下,研究了UV-B(ultraviolet-B)辐射增强对抗除草剂转基因水稻及亲本常规水稻甲烷(CH4)排放的影响。UV-B辐射设2水平,即对照(CK,自然光),增强(Elevated,14.4 kJ·m-·2d-1),相当于南京地区大气臭氧耗损25%的辐射剂量。结果表明,UV-B辐射增强并没有改变稻田CH4排放通量的季节性变化规律。与对照相比,UV-B辐射增强显著提高CH4排放通量和累积排放量。水稻分蘖期CH4累积排放量最高,占全生育累积排放量的51.55%—61.01%;其次是拔节至孕穗期,占20.00%—26.64%。抗除草剂转基因水稻的CH4排放通量和累积排放量显著低于亲本常规水稻。研究说明,UV-B辐射增强下种植抗除草剂转基因水稻对于减缓稻田甲烷排放有积极意义。     

Application of Silicon and Selenium in Rice for Reducing Cadmium Stress

Rice is an essential part of the human diet in most parts of the world; On the other hand, the industrialization of societies has led to pollution of the environment, including heavy metal contamination of soil and water, which negatively affects rice production and quality. Therefore, finding ways to increase the yield and quality of this strategic crop seems essential. Several studies have been conducted in recent decades to find effective and inexpensive solutions to reduce the adverse effects of heavy metals in rice fields. Due to the negative effect of cadmium pollution on rice quality and yield, the current study aimed to investigate cadmium absorption and transfer mechanisms in rice (from absorption by roots to loading in grains), and its effects on rice morphology, physiology, and biochemistry (such as biomass, nutrient absorption, antioxidant defenses). Also, rice’s natural mechanisms for detoxifying cadmium were discussed. This study also intended to identify the absorption and transfer pathways of silicon and selenium in rice, their roles in improving rice structures, and their antagonistic effects on reducing cadmium stress (absorption, transport, and toxicity of cadmium).     

东北黑土地区稻田甲烷排放时空演变及排放潜力分析

稻田甲烷排放是农业源甲烷排放的主要来源。东北黑土地区是我国最大的粮食生产基地,农业温室气体减排是实现黑土地永续利用的关键议题之一。运用稻田甲烷排放模型(CH4MOD)核算并分析了2009-2018年东北黑土地区稻田甲烷排放的时空演变特征,结合GOSAT卫星遥感数据探究了水稻生产与区域甲烷排放的时空动态联系,进一步量化了稻田甲烷对区域甲烷排放的贡献程度及不同情景下的排放潜力。结果表明,受水稻生产面积扩张和排放强度提高的影响,东北黑土地区稻田甲烷排放总量从2009年的39.05万t增加到2018年的79.53万t。东北黑土地区区域甲烷排放在季节变化和栅格单元上表现出与稻田甲烷排放较为一致的时空动态,大规模的稻田耕作可能会增加水稻生产与区域甲烷排放直接相关的可能性。随着水稻持续扩种稳产,2018年东北黑土地区水稻生产贡献了区域甲烷排放总量的15.04%,其中黑龙江省的贡献率高达31.06%。在基准发展情景下,预计2035年东北黑土地区稻田CH₄排放量较2018年增加19.5%;在粮食供给保障情景下,维持当前稻田耕作面积,水稻生产集约化程度提高,预计其稻田CH₄排放量较2018年减少0.88%;在此基础上,采取促进秸秆还田、增施有机肥、实施节水间歇灌溉等稻田管理措施将使稻田CH₄排放量增加17.8%-63.6%。以满足膳食需求和供给保障为导向,优化水稻种植结构、控制稻田耕作面积,推动技术进步、品种改良以提升单产水平,采取化肥和有机肥搭配施用、节水间歇灌溉等途径能够缓解稻田甲烷排放。研究综合运用自上而下的遥感数据和自下而上的模型运算,刻画了水稻生产与区域甲烷排放的时空联系,进一步评估了稻田甲烷的排放潜力及减排措施的减排效果,为促进东北黑土地区农业甲烷减排和生产布局优化提供了理论依据和决策参考。     

Impact of gas transport through rice cultivars on methane emission from rice paddy fields

Two Italian rice (Oryza sativa var. japonica) cultivars, Lido and Roma, were tested in the field for methane production, oxidation and emission. In two consecutive years, fields planted with the rice cultivar Lido showed methane emissions 24–31% lower than fields planted with the cultivar Roma. This difference was observed irrespective of fertilizer treatment. In contrast to methane emissions, differences in methane production or oxidation were not observed between fields planted with the two cultivars. Plant-mediated transport of methane from the sediment to the atmosphere was the dominating pathway of methane emission. During the entire vegetation period, the contribution of this pathway to total methane emission amounted to c. 90%, whereas the contribution of gas bubble release and of diffusion through the water column to total methane emission was of minor significance. Results obtained from transport studies of tracer gas through the aerenchyma system of rice plants demonstrated that the root–shoot transition zone is the main site of resistance to plant-mediated gas exchange between the soil and the atmosphere. The cultivar Lido, showing relatively low methane emissions in the field, had a significantly lower gas transport capacity through the aerenchyma system than the cultivar Roma. Thus, the observed differences in methane emissions in the field between the cultivars Lido and Roma can be explained by different gas transport capacities. Apparently, these differences in gas transport capacities are a consequence of differences in morphology of the aerenchyma systems, especially in the root–shoot transition zone. It is, therefore, concluded that identification and use of high-yielding rice cultivars which have a low gas transport capacity represent an economically feasible, environmentally sound and promising approach to mitigating methane emissons from rice paddy fields.     

Bacterial populations colonizing and degrading rice straw in anoxic paddy soil

Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera Bacillus (3 clones), Nitrosospira (1 clone), Fluoribacter (1 clones), and Acidobacterium (2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes) Bacteria detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus Clostridium, mainly to clostridial clusters I (24%), III (6%), and XIVa (24%). An additional 5% belonged to the Cytophaga-Flavobacterium cluster of the Cytophaga-Flavobacterium-Bacteroides phylum, 4% belonged to the alpha, beta, and gamma Proteobacteria, and 1.3% belonged to the Bacillus subbranch of the gram-positive bacteria with a low G+C content. The results show that the bacterial community colonizing and decomposing rice straw developed during the first 15 days of incubation and was dominated by members of different clostridial clusters, especially clusters I, III, and XIVa.