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<\/small><\/p>\nFigure 1. <\/span>Microbial functions in soil<\/span><\/strong>The three plant macronutrients are nitrogen, potassium, and phosphorus, but plants cannot absorb nutrients in organic form. In addition to transforming macronutrients from organic to inorganic forms, microorganisms serve as microbial biomass by storing and supplying nutrients.<\/p>\n<\/div>\n Rice plants need not only sunlight and water from irrigation and\/or rain, but also nutrients from fertilizers to thrive in paddy fields. Almost all the nutrients that rice and all other plants can absorb are in inorganic forms. Microorganisms in the soil decompose organic matter, such as animal and plant residues, as well as compost, and transform them into inorganic forms.<\/p>\n The three major macronutrients for plants are nitrogen, potassium, and phosphorus, which are the primary elements of fertilizer. Nitrogen is particularly important; plants absorb ammonium and nitrate as nitrogen sources which are transformed from nitrogen in soil organic matter (organic nitrogen) by microorganisms. Rice plants absorb mainly ammonium as the nitrogen source which is derived from not only fertilizer but also organic nitrogen in the soil. Ammonium derived from organic nitrogen accounts for around half of the total nitrogen uptake by rice plants. The role of microorganisms in converting organic nitrogen to inorganic forms is therefore crucial.<\/p>\n Microbial cells as well as human cells contain various nutrients. This role of nutrient reservoir is called “microbial biomass” and has been regarded as important in recent years. After the death of microorganisms in the soil, nitrogen, phosphorus, potassium, and other substances stored in their cells are released (Figure 2). Ammonium is mainly produced via amino acids by the decomposition of proteinaceous nitrogen derived from microbial cells and then absorbed by rice plants. Bacterial members in the genus Bacillus<\/i>—to which Bacillus subtilis<\/i> and the variant used for making fermented soybeans, Bacillus subtilis<\/i> var. natto<\/i>, also belong—contribute to this mineralization process in paddy field soil. Although the content of microbial biomass nitrogen is low, accounting for just a few percent of the total nitrogen content in soil, it turns over actively and therefore plays a key role as a source of inorganic nitrogen.<\/p>\n Figure 2. <\/span>The role of microbial biomass<\/span><\/strong>Nitrogen (N), phosphorus (P), and potassium (K) are released following the death of microorganisms in the soil. Nitrogen and phosphorus are then transformed into inorganic forms by microorganisms.<\/p>\n<\/div>\n As potassium does not form organic compounds, unlike nitrogen and phosphorus, it has long been believed that rice plants absorb water-soluble potassium via a mechanism that does not involve microorganisms. However, our research has revealed that potassium in microbial cells is also released after they die, like nitrogen and phosphorus. In addition, in the paddy fields without application of potassium fertilizer, we observed that the amount of potassium derived from microorganisms was higher than the amount of potassium attributed to the mechanism in which microorganisms were not involved. This indicates that microbial biomass plays an important role as a source of potassium in the fields.<\/p>\n Paddy fields are flooded and rice transplanting begins around May. The flooded conditions last for about 100 days and then the paddy fields are drained before harvest. Functions and activities of microorganisms change during this cycle, which contribute to maintaining paddy field soil suitable for rice growth (Figure 3).<\/p>\n Figure 3. <\/span>Microbial reduction of soil<\/span><\/strong>Anaerobic microorganisms cause various substance transformations in the anoxic soil after being covered with floodwater. In addition, cyanobacteria inhabiting floodwater synthesize nitrogen compounds such as ammonia from atmospheric nitrogen (nitrogen fixation).<\/p>\n<\/div>\n When the paddy fields are covered with floodwater, less oxygen enters the soil from the atmosphere. As aerobic microorganisms that use oxygen for metabolism consume oxygen by respiration, the soil other than the surface layer beneath the floodwater gradually becomes anoxic (lacking in oxygen).<\/p>\n As a result, microorganisms carry out metabolism by fermentation and anaerobic respiration, which uses oxygen-containing substances such as nitrate, manganese and iron oxides, sulfate, and CO2<\/sub> instead of molecular oxygen. Since less energy is obtained from the fermentation and anaerobic respiration than from the aerobic respiration, the decomposition rate of organic matter decreases, which causes accumulation of organic nitrogen in the soil, and consequently the content of organic nitrogen increases. The findings that the organic nitrogen content in soil is higher in paddy fields than in upland fields indicate the high fertility of paddy fields, although the amount varies depending on the type of soil.<\/p>\n Removal of oxygen from oxides (reduction) through the fermentation or metabolism by microorganisms leads to positive changes in the soil. For example, iron is present as ferric (trivalent) iron in oxic soils such as in upland fields. Phosphorus, an important nutrient, is combined with ferric iron to form ferric phosphate, which does not readily dissolve in water and therefore can hardly be absorbed by plants. However, as ferric iron is reduced to ferrous (divalent) iron in paddy fields, the bound phosphate dissolves in water and can be absorbed by rice plants.<\/p>\n Reduction of soil also influences the concentration of hydrogen ions (pH) in the soil. The optimal pH for paddy rice is weakly acidic to neutral. It was reported that production of hydrogen ions associated with decomposition of organic matter and consumption of hydrogen ions through iron reduction are balanced and pH settles to neutral as the reduction process progresses, even in highly acidic or alkaline soils.<\/p>\n Furthermore, the reduction of soil has been believed to be involved in the mechanisms that enable continuous cropping of rice in paddy fields, unlike upland rice cultivation. This has been mainly because of the suppression of aerobic pathogens such as filamentous fungi, but questions remain. This is because lotus root and arrowhead suffer continuous cropping disorder due to filamentous fungi, though these crops are also grown in flooded fields.<\/p>\n So, why paddy rice does not suffer continuous cropping disorder? To prevent root rot, rice plants transport oxygen taken up from the leaves and stems of rice plants above the ground to roots and a small amount of oxygen leaks out through the roots. Based on this phenomenon, we are studying to test two hypotheses: either free radicals<\/span> produced by the oxidation of ferrous iron have a fungicidal effect, or aerobic protozoa prey on pathogens around rice roots.<\/p>\n Aside from reduction of soil, there is another microbial function unique to flooded paddy fields, for which cyanobacteria, blue-green algae, inhabiting floodwater are responsible. Cyanobacteria grow photosynthetically and synthesize nitrogen compounds such as ammonia from atmospheric nitrogen (nitrogen fixation). The amount of nitrogen fixed by cyanobacteria in a single cropping season of rice was estimated to be 26 kg\/ha in an experiment. Given that rice plants require about 100 kg\/ha nitrogen from fertilizers, it can be said that the role of cyanobacteria is large.<\/p>\n On the other hand, microorganisms do not necessarily always have a positive effect on rice plants. Japanese soil scientists have found solutions for the problems that negatively impact the growth of rice plants by elucidating dynamics of the components and microbial functions in the soil over the years. For example, in the late 1920s and early 1930s, when commercial fertilizers were still expensive, the poor efficacy of ammonium sulfate as a nitrogen fertilizer became a problem. As described above, oxygen consumption by microorganisms in the soil was active just after flooding paddy fields, but it stabilizes after a while; the uppermost surface layer of the soil is oxidized with the oxygen diffused from floodwater. When a nitrogen fertilizer such as ammonium sulfate is applied to the surface layer, microorganisms called nitrifying bacteria oxidize the ammonium to nitrate. As soil particles are negatively charged, also negatively charged nitrate cannot be absorbed to soil particles and immediately moves to the lower, reduced layer of the soil. In the reduced layer, denitrifying bacteria immediately use the nitrate for anaerobic respiration to obtain energy by oxidizing organic matter and transform nitrate to nitrogen gas. In other words, the expensive nitrogen fertilizer is applied with effort, but it is converted into nitrogen gas and escapes into the atmosphere.<\/p>\n Once this mechanism has been clarified, a method for incorporating the fertilizer into the reduced lower layer or all layers has been developed to retain ammonia and nitrogen fertilizer can be applied effectively.<\/p>\n In addition, sulfate-reducing bacteria produce hydrogen sulfide, which is potentially harmful to the growth of rice plants, by reducing sulfate ion of ammonium sulfate. However, hydrogen sulfide is combined with ferrous iron produced by iron reduction and detoxified as iron sulfide. Therefore, paddy fields with sufficient iron are not a problem, but a phenomenon called “autumn decline” occurs in paddy fields, where the content of iron in the soil is originally low or iron levels have greatly decreased by heavy leaching as in degraded paddy fields. A representative symptom of autumn decline is that rice plants thrive through the summer and deteriorate in autumn before harvest. Autumn decline can be remedied by applying a soil amendment containing iron, deep plowing to put the iron from the bottom layer back to the upper layer, and oxidizing the soil by drainage.<\/p>\n Conversely, if there is too much iron in soil, the rice plants absorb an excessive amount of ferrous iron, causing poor growth. This phenomenon is rarely seen in Japan and occurs in paddy fields with a high iron content in soil such as the fields located in tropical basins; in some cases, the entire harvest is lost. The countermeasures are to oxidize the soil by drainage, but large-scale agricultural infrastructure work such as the laying of culverts to manage water flow is required.<\/p>\n Application of rice and wheat\/barley straw as fertilizer has been employed for a long time. If a large amount of fresh, unfermented straw is applied, the decomposition process of organic matter by microorganisms fails to progress smoothly, and organic acids, intermediate metabolite products, may accumulate in the soil, causing rice growth inhibition. Organic matter is quickly degraded to CO2<\/sub> by microorganisms under oxic conditions, but under anoxic conditions, it is ultimately metabolized into CO2<\/sub> and methane via intermediate metabolites including fatty acids such as acetic acid, propionic acid, and butyric acid, as well as aromatic carboxylic acids. In particular, it has been reported that aromatic carboxylic acids have a major impact on rice plant growth, even at low concentrations, and are often produced in paddy fields in warm regions. Currently, to prevent these metabolites from accumulating, straw is composted before use or it is incorporated into the soil before flooding of the field for allowing decomposition.<\/p>\n Methane is the final decomposition product in the metabolic process described above and becomes a problem. While methane does not affect growth of rice plants, it has a stronger greenhouse effect than CO2<\/sub> and has therefore emerged as a major environmental problem in recent years. In particular, in Japan, methane emissions from rice cultivation account for the largest share of total emissions derived from human activities, at 44%. Methane is produced by anaerobic microorganisms called methanogens inhabiting paddy field soil and is emitted via aerenchyma in rice plants. To suppress activities of methanogens, the following countermeasures are being implemented: oxidizing the soil by the midseason drainage with temporary draining paddy fields around at the maximum tillering stage of rice or the intermittent irrigation with repeated flooding and draining every few days, and application of composted straw.<\/p>\n In addition, the oxidized part of paddy field soil is also inhabited by methane-oxidizing bacteria that oxidize methane to CO2<\/sub>. We are conducting a collaborative research project with research institutions to identify highly active methane-oxidizing bacteria and utilize them to mitigate methane emission. One might wonder whether this approach will increase CO2<\/sub> emissions. In fact, most of the methane comes from CO2<\/sub> taken up by rice plants during photosynthesis. Therefore, even if methane-oxidizing bacteria convert methane to CO2<\/sub>, the balance comes out even and it is unlikely to lead to an increase in CO2<\/sub> emissions.<\/p>\n Interestingly, microorganisms inhabiting paddy field soil, as mentioned above, are stably present without large fluctuation in the composition and abundance even when paddy fields are drained and the soil is oxidized. When the drained paddy fields are flooded again in the following year, microorganisms start to work again. However, if paddy fields are converted to upland fields and oxic soil conditions sustain for more than a year or two, microorganisms specific to paddy field soil decrease in the abundance and the composition also changes. Therefore, it is necessary to consider the changes in microorganisms when paddy-upland rotation, interconversion between paddy fields and upland fields for certain periods, is implemented to reduce rice production.<\/p>\n While we have already made progress in unraveling the mechanisms behind various phenomena caused by microorganisms in paddy field soil, there still remain many unknowns, including the functions of individual microorganisms. In order to sustain stable production of rice, a staple food in not only Japan but also the rest of Asia, it is important to identify microorganisms and elucidate the more detailed mechanisms. We will continue to undertake basic research using DNA\/RNA analysis in addition to conventional culture techniques, and work on environmental conservation such as mitigation of methane emission as well as improving growth of rice plants.<\/p>\n Rice is a wetland plant. Growing rice in paddy fields can suppress growth of upland weeds and facilitates soil managements. Paddy field soil generally shows higher fertility than upland field soil, supporting stable rice yields under low fertilization conditions. A combination of several factors resulted in the development of rice cultivation in paddy fields in Japan. The high fertility of paddy fields is supported by various functions of microorganisms in the soil. They decompose organic matter in the soil and produce inorganic nutrients requisite for growth of rice plants. On the other hand, emission of methane, one of the decomposition products of organic matter, has become an environmental problem. Mitigation of methane emission is a pressing issue since the gas has a stronger greenhouse effect than CO2<\/sub>.<\/p>\n","protected":false},"author":2,"featured_media":2664,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[18],"tags":[],"class_list":["post-2658","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-nature"],"acf":{"author":"composition by Yumi Ohuchi Rice is a wetland plant. Growing rice in paddy fields can suppress growth of upland weeds and facilitates soil management. Paddy field soil generally shows higher fertility than upland field soil, supporting stable rice yields under low fertilization conditions. A combination of several factors resulted in the development of rice cultivation in paddy fields in Japan. The high fertility of paddy fields is supported by various functions of microorganisms in the soil. They decompose organic matter in the soil and produce inorganic nutrients requisite for growth of rice plants. On the other hand, emission of methane, one of the decomposition products of organic matter, has become an environmental problem. Mitigation of methane emission is a pressing issue since the gas has a stronger greenhouse effect than CO2<\/sub>.<\/p>","person":[{"acf_fc_layout":"personcontent","personimg":2650,"personsholder":"Professor, Graduate School of Bioagricultural Sciences, Nagoya University","personname":"Susumu Asakawa","persondetail":"Holds a Ph.D. in agriculture. Graduated from the Department of Agricultural Chemistry, Faculty of Agriculture, the University of Tokyo in 1985. After working as a researcher at the Kyushu National Agricultural Experiment Station, Ministry of Agriculture, Forestry and Fisheries, he became an associate professor at the Graduate School of Bioagricultural Sciences, Nagoya University in 2001 and took up his current post in 2013. In 2021, he was also appointed to Vice Director of Nagoya University Library. He specializes in the ecology of microorganisms inhabiting paddy field soil ecosystems, methanogenic archaea, methane-oxidizing bacteria, etc."}],"issue":2638,"custom_css":""},"_links":{"self":[{"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/posts\/2658","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/comments?post=2658"}],"version-history":[{"count":0,"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/posts\/2658\/revisions"}],"acf:post":[{"embeddable":true,"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/issue\/2638"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/media\/2664"}],"wp:attachment":[{"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/media?parent=2658"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/categories?post=2658"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/healthist.net\/en\/wp-json\/wp\/v2\/tags?post=2658"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}![\"\"](\"https:\/\/healthist.net\/en\/wp-content\/uploads\/sites\/3\/2026\/04\/296_en_feature01_03_fig02-1.png\")
<\/small><\/p>\nFunctions of microorganisms change due to flooding of paddy fields<\/h2>\n
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Modified from Asakawa S. in Nigiyaka na Tanbo: Inago ga Hane, Tori wa Mai, Sakana no Oyogu Shōuchū<\/i> [Paddy fields teeming with life: A microcosm where grasshoppers leap, birds flutter, and fish swim], ed. Natsuhara Y., p. 74, Information Design Associates Kyoto, 2015.<\/small><\/p>\n\n
Microorganisms do not necessarily always have a positive effect<\/h2>\n
Methane emissions from rice cultivation account for 44% of total emissions<\/h2>\n
illustration by Rokuhisa Chino","intro":"