Abstract

BACKGROUND:

Global warming is one of the most pressing environmental issues which concomitantly complicates global climate change. Methane emission is a balance between methanogenesis and methane consumption, both of which are driven by microbial actions in different ecosystems producing methane, one of the major greenhouse gases. Paddy fields are major sources of anthropogenic methane emissions and could be compounded by organic fertilization.

METHODS AND RESULTS:

Literature reviews were conducted to give an overview of the global warming conditions and to present the relationship of carbon and methane to greenhouse gas emissions, and the need to understand the underlying processes of methane emission. A more extensive review was done from studies on methane emission in paddy fields under organic fertilization with greater emphasis on long term amendments. Changes in paddy soils due to organic fertilization include alterations of the physicochemical properties and changes in biological components. There are diverse phylogenetic groups of methanogens and methane oxidizing bacteria involved in methane emission. Also, multiple factors influence methanogenesis and methane oxidation in rice paddy fields under organic fertilization and they should be greatly considered when developing mitigating steps in methane emission in paddy fields especially under long term organic fertilization.

CONCLUSION(S):

This review showed that organic fertilization, particularly for long term management practices, influenced both physicochemical and biological components of the paddy fields which could ultimately affect methanogenesis, methane oxidation, and methane emission. Understanding interrelated factors affecting methane emission helps create ways to mitigate their impact on global warming and climate change.

Keyword

Methane emission,Methane oxidation,Methanogenesis,Organic fertilization,Paddy fields

Introduction

Global warming and climate change due to industrialization, fossil fuel utilization, forest destruction, and other anthropogenic activities bring environmental issues. The agricultural sector could not be an exception and soil management systems and indices aligned with sustainable development are to be considered with great importance[1]. Methane is a potent greenhouse gas with 28 times global warming potential compared to carbon dioxide with atmospheric methane concentration continuously increasing[2]. The average global concentration continues to rise with 600 Tg CH₄ yr^-1 for global methane emissions, of which, 61% is attributed to anthropogenic sources recorded in the year 2020[3]. Methane emission varies under different soil types particularly those under aerobic and anaerobic conditions. It is dictated by the balance of methane production through methanogenesis and methane consumption through methanotrophy or methane oxidation and is influenced by multiple dynamic factors potentially compounded or stabilized under long term fertilization[4].

The implementation of organic and compost applications has been driven by interrelated environmental issues including soil degradation, unsustainable land use, and contamination of natural resources. The goal is to attain environmental beneficial impacts such as improved carbon sequestration, soil biological diversity, biogeochemical functions, soil fertility, and crop yield[5]. Organic fertilization plays a positive role in climate change mitigation via soil carbon sequestration but its application in paddy fields under submerged conditions becomes a potential source of methane emission[6, 7].

Rice paddies generate approximately 60 Tg CH₄ year^-1 of global methane emissions[8, 9]. In addition, fertilization with inorganic and organic fertilizers affects the physicochemical and biological components of soil paddy fields which ultimately reflect on the soil biogeochemical processes[10]. Therefore, agricultural input of compost or a combination of compost and inorganic fertilizers as short or long term fertilization in paddy fields influences methane-related processes mainly attributed to archaeal or bacterial paddy field communities. Methane emission is mainly mediated by methanogenic archaeal groups[2, 11, 12]. However, methanotrophy is carried out by type I and type II methanotrophs[2, 13], belonging mainly to γ-Proteobacteria and α-Proteobacteria, respectively. Additionally, the effects of fertilization on the soil properties, biotic components, and biologically-driven ecological processes are compounded by differing results[7, 11, 14]. These opposing studies could be linked and mechanistically be attributed to the composition, community structure, diversity, abundance, and functional activity of microbial communities thriving in the paddy soils as they dynamically respond to the effects of fertilization regimes[11, 14].

Intensified global fertilizer application will be necessary to increase rice production but it is known that increased organic fertilization can enhance methane emission from rice agriculture. Long term compost fertilization can also lead to changes in soil factors and biotic components of the paddy fields related to methanogenesis, methane oxidation, and methanol oxidation[15-17]. Assessing contributing factors associated with methane production and consumption is essential to understand and formulate mitigating mechanisms to combat global warming.

This review gives an overview of global warming as a critical environmental issue and the goal of mitigating its impacts, along with the relationship of carbon and methane to greenhouse gas emissions potentially affecting not just agriculture but multiple aspects of human society. This review then focuses on the effects of organic fertilization, with emphasis on long term amendments, on the soil chemical properties and biological components related to methanogenesis and methane oxidation, the microbial diversity of methanogens and methanotrophs, and on the factors affecting the processes of methanogenesis and methane oxidation in paddy field agroecosystems. The scope of this review also extends to the mitigating steps that could be employed to regulate methane emission in paddy fields.

GlobalWarming

Global warming is the increase in the Earth’s overall temperature causing climate change and environmental issues. Carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) are the most important greenhouse gases which could be emitted from direct agricultural production but can be significantly reduced by improving soil management[1]. If the Earth's temperature rises above 2°C, more natural disasters will occur and disastrously lead to significantly reduced various risk factors such as biodiversity and food security[18]. The additive effects of global warming and climate change could also increase multifactorial stress combinations in plants, soils, and microbial communities driving a crucial decline in plant growth, soil conditions, and overall agricultural productivity[19].

The world's population will reach 9.8 billion by 2050, and more food production is needed up to 60%. If global warming continues due to abnormal climates such as unusually high temperatures, the range and number of environmental stresses that can have serious consequences to agricultural production will increase significantly[20]. Various stresses, including nutritional deficiencies and abnormal climates such as temperature and drought, reduce the average productivity and quality of crops, and these problems will become more serious in the future[21-23]. Current agriculture is facing the task of increasing production without further increasing agricultural land and is trying to reduce the damage to climate change by reducing environmental soil issues.

Active management of soil agriculture is essential to achieve the goal of decreasing global warming. Crops absorb CO₂ in the atmosphere to produce energy, and residues after harvest are decomposed by microorganisms and remain in the soil, making soils play important role in absorbing carbon. Therefore, soil microorganisms and plants can partially reduce CO₂ and methane in the atmosphere increasing the effectiveness of soil, including paddy soils, as an absorption sink of greenhouse gases[24]. Effective soil management can reduce greenhouse gases and strengthen soil carbon absorption functions, as well as enhance soil ecosystem diversity, soil fertility, and productivity as organic matter increases[25-28]. To cope with climate change and solve global warming, cost-effective methods are necessary such as optimizing compost fertilization and minimizing energy use while being feasible and eco-friendly.

CarbonandMethaneinRelationtoAgricultureandGreenhouseGasEmission

Organic carbon and total nitrogen in the soil directly control the availability of soil carbon and nitrogen and play an important role in soil productivity indirectly by affecting the physicochemical conditions and biological properties of the soil[29]. In the agricultural environment, the carbon (C) sequestration of soil plays a very important role in alleviating emissions of carbon dioxide (CO₂) into the atmosphere and improving soil fertility[30, 31]. Carbon compounds in the soil not only improve productivity by making the soil fertile but also store billions of tons of carbon each year to reduce greenhouse gas concentrations in the atmosphere[32].

Carbon in the forms of CO₂ and CH₄ causes global warming. The global average methane concentration in the atmosphere reached 1,875 ppb at the end of 2019, which increased more than 2.5 times than the pre-industrial level. Therefore, continuous and long term monitoring of methane circulation is required to prepare for climate change and to confirm the reduction in methane emissions[33]. In the last decade, the global methane emission is 576 Tg CH₄ yr^-1, of which 60% or 358 Tg CH₄ yr^-1 has been caused by human activity. In the agricultural field, intestinal fermentation and manure of livestock are the largest sources of emissions along with rice paddies. Rice is mostly grown in freshwater paddies under anaerobic conditions and accounts for about 10% of total methane emissions[3, 34, 35]. During the flooding period of the paddy soil, various organic matter is decomposed by methane generating archaea in an anaerobic state producing methane[36, 37]. It was reported that the main absorption source of methane was 90% of the oxidation reaction by hydroxyl radical (OH^-1) in the atmosphere, and the rest were absorbed into the soil within the range of 27~45 Tg CH₄ yr^-1 by methane oxidizing bacteria[38]. Regionally, Mainland China and the Middle East saw a significant increase in methane emissions from 2000 to 2017, mainly due to coal mines, waste, and livestock. Europe, South Korea, and Japan decreased methane emissions due to reduced waste and fossil fuel use[39].

Studies related to methane production and emission [33, 39, 40] as well as methanogens and methanotrophic bacteria[41-46] and methane transformations in various environments such as wetlands are actively conducted[47-51]. To reduce greenhouse gas emissions, the carbon sequestration ability of the soil itself and CO₂ fixing and carbon sequestration in grassland or rice paddies have recently attracted attention[24, 52-54]. Paddy fields play the role of a carbon reservoir [55, 56] and are one of the best ways to prevent climate change.

TheImportanceofUnderstandingLongTermOrganicFertilizationandMethaneEmissiononRicePaddyFieldAgroecosystems

The adoption of an organic management system in the rice agroecosystems influences rice grain yields and global greenhouse gas emissions, including carbon dioxide, methane, and nitrous oxide[57]. The connections between methanogenesis, the process producing methane, and methane consumption or methanotrophy through methane oxidation then followed by methanol oxidation are controlled by microbial communities containing the mcrA, pmoA, and mxaF genes encoding their respective enzymes (Fig. 1). Recent uncertainties in global methane budgets push the need for research in the controls of sources and sinks of atmospheric methane. The production of methane by methanogenic archaea in wetlands and rice paddies is a major source while the consumption by methane oxidizing bacteria (MOB) in upland soils is a major sink [11]. It is essential then to evaluate methane emission from paddy fields, to further understand its impact on the greenhouse gas budget while optimizing organic fertilization as an efficient method to maintain rice yield and reduce fertilizer losses[12]. In addition, how nitrogen controls methane emission, consumption and underlying microbial processes have been designated as one of the key knowledge gaps in soil carbon–nitrogen interactions[11]. The dynamics of soil C and N also often vary with different rates of fertilization, hence, the change of soil labile C and N contents in relation to greenhouse gas emissions would be worth investigating under long term organic fertilization[10]. In order to estimate the contribution of paddy fields as a source of CH₄, it is important to understand the long term effects of fertilizer applications which are targets in strategies to combat global climate change [58]. Methane-consuming microbes play a vital role in global warming issues, as they are the only biological sinks for methane[14]. These specific functional microbial populations play important roles in nutrient transformations in paddy ecosystems, revealing the composition and expression characteristics of specific functional genes concerning methanogenesis and methane oxidation[59].

LongTermOrganicFertilizationandItsImpactsontheSoilChemicalPropertiesandBiologicalComponentsinRelationtoMethanogenesisandMethaneOxidation

Long-term organic and N fertilization affect both edaphic and microbial communities in paddy fields involved in methane emission and consumption (Table 1). Studying how soil chemical parameters change as well as methanogenic (methanogens and methanogenesis) and methanotrophic communities respond to long term application of fertilizers could help us mitigate methane emission in paddy fields while allowing optimized fertilization and rice yields. Employing linear regression analysis based on the study of Zhang et al.[60], there is a predicted methane production potential based on the population sizes of methanogenic archaea population. This potential increases with the increase in the copy number of mcrA genes found in the soils of paddy fields.

In general, organic fertilization in the paddy fields involves the use of composted or fresh manure (human, livestock, pigs, poultry) and plant residues (mainly rice straw). The input of different types of fertilization especially organic fertilizers changed the chemical properties of soils including organic matter content (OM) / soil organic carbon (SOC), total nitrogen (TN) content, macro and micronutrient content which in turn also influenced soluble and available levels of carbon, nitrogen, and other nutrients[10, 57, 61, 62]. Soil microbial biomass carbon and soil microbial biomass nitrogen also increased under manure fertilization[63]. Under organic manure and straw fertilization, the combined humus in the forms of humic acid and fulvic acid, also significantly increased with long term fertilization[62]. The labile forms of these soil nutrients became major components that drove soil biochemical transformations generally involving soil microorganisms[10]. Under organic fertilization, there was an increase in the available P, K, N, and DOC which accelerated methane emission[58, 60, 64]. Aside from the general increase in the nutritional content of the soil, other chemical parameters may also change under long term organic fertilization including pH, CEC, EC, and C:N[60, 64].

Long term fertilization not only modifies soil physicochemical properties but may also influence microbial population, community structure, and diversity (Table 1). These in turn change the potential functional attributes found in the paddy soils including enzyme activities and biogeochemical processes such as carbon mineralization, decomposition, methanogenesis, and methane oxidation. In general, the effects of fertilization resulted in changes in the microbial communities and related biological attributes of paddy soils which may stabilize under long term fertilization management schemes. The most usual change observed is in the abundance of the population measured directly or through molecular markers most commonly the 16S rRNA gene. On the other hand, primers for functional genes were also developed to assess gene abundance and indirectly, the abundance of microorganisms related to them[65-69]. Long term organic fertilization or in combination with inorganic fertilizers generally causes changes in community dynamics. In paddy fields, the abundance of cultivable microorganisms has generally increased significantly[10, 70]. This increase in the general population of bacteria was also observed in the 16S rRNA gene universal markers[71]. In terms of specific communities of microorganisms related to the methane cycle, the methanogens or the mcrA gene abundance generally increased under organic fertilization[60, 72, 73]. The abundance of pmoA genes or methanotrophic communities generally increased under compost fertilization or in combination with NPK[58, 72]. However, the effect of compost fertilization especially in combination with different nitrogen fertilizers could have varying effects on specific communities of methanotrophic bacteria. These differences created varying results across studies even in similar soil types or environmental conditions[4]. However, patterns could still be seen especially when looking at more specific groups of methanotrophs. The changes in community abundance, structure, and diversity could also influence the functionality of the soils. Islam et al.[74] showed that substrate evenness, community level functional diversity, and soil enzyme activities increased under long term compost fertilization. Soil enzyme activities, as well as microbial populations, also increased under long term farmyard fertilization[10]. In some cases, predicted functional activities in compost fertilization treatment were deduced to significantly contain higher functional genes related to plant growth promotion, development, and decomposition[71].

MicrobialEcologyofMethanogensandMethanotrophsinPaddyFields:Phylogeny,Diversity,andEcologicalNiches

Culture-independent analyses of archaeal and bacterial genes involved in methane emission and consumption allow robust studies of diverse yet specific microbial communities[65-69] in rice paddies. The difficulty of isolating methanogens resulted in the development of primers amplifying the mcrA gene that codes for the α-subunit of the methyl coenzyme M reductase. It catalyzes the final step in the production of methane and is conserved among all methanogens. The particulate methane monooxygenase is an important enzyme for the conversion of methane to methanol and could be detected by primers designed for pmoA gene amplification[66]. Methanol dehydrogenase is also an important enzyme found in methylotrophic bacteria that catalyzes the conversion of methanol to formaldehyde. Primers designed to amplify the mxaF gene that codes for methanol dehydrogenase allow the detection of diverse methylotrophic communities[65, 67]. Microorganisms involved in methanogenesis and methanotrophy in paddy fields under different fertilization are presented below(Table 2).

Methanogenesis is modulated by the enzyme methyl-CoM reductase, which is coded by the mcrA gene, a highly conserved gene found in all methanogens [76]. In addition, methanotrophy through the enzyme methane monooxygenase is coded by the pmoA gene, while methylotrophy through the enzyme methanol dehydrogenase is coded by the mxaF gene[77]. All methanogens belong to the domain Archaea[2]. A summary of the most dominant groups of methanogens in paddy fields was presented by Yuan et al.[37]. The most dominant families are represented by Methanobacteriaceae, Methanocellaceae, Methanomicrobiaceae, Methanosaetaceae, and Methanosarcinaceae. In addition, the most dominant groups of methanogens at the genus level include Methanobacterium, Methanobrevibacter, Methanocella, Methanoculleus, Methanoregula, Methanosaeta, Methanosarcina, and Methanothrix.

The methanotrophic communities usually detected in paddy fields are grouped into type I and type II MOB. They come from phylogenetically different classes under Proteobacteria and show different biochemical characteristics. Type I belongs to the Gammaproteobacteria employing the ribulose monophosphate pathway for carbon assimilation, while type II belongs to the Alphaproteobacteria and assimilates carbon through the serine pathway[4]. Type I MOB generally observed in rice paddies include Methylobacter, Methylocaldum, Methylococcus, Methylomicrobium, Methylomonas, Methylosphaera, and Methylosarcina[14, 58, 60, 67, 73, 78-81]. Type II MOB generally observed in rice paddies belong to the genus Methylocapsa, Methylocella, Methylocystis, and Methylosinus [14, 58, 73, 78-82]. Aside from the phylogenetic and biochemical differences of type I and type II MOB, it seems that there are some general deductions on their responses and ecological microniches in paddy fields under long term organic. Under long term fertilization, type I MOB was generally stimulated while type II was generally inhibited or with a slower response[14, 58, 78]. In flooded conditions with NPK+manure, type I was enriched on the surface layers while type II was more dominant in the deeper layers[81]. MOB populations on roots were dominated by type I methanotrophs, whereas populations in the rhizosphere soils were dominated by type II, irrespective of growth stages and fertilizer treatment. Type I predominated in both phosphorus-potassium treatment (PK), UreaPK, and the rhizosphere soils while Type II was relatively more dominant under unfavorable conditions such as AmmoniaPK treatment[79]. Type I MOB displayed an increased abundance in soil amended with fertilizers, whereas type II MOB dominated the native soil[80]. In general, type I MOB responds more positively through increased dominance under fertilization while type II MOB responds less, neutral, or inhibited under fertilization.

MethanogenesisandMethaneOxidationandFactorsAffectingtheProcessesinPaddyFields

Along with potential alteration of the soil physicochemical properties of paddy fields, complex microbial responses were also observed due to different fertilization. These responses are categorized as either stimulation, inhibition, or no response[84]. The changes in physicochemical and biological components of the paddy soils concurrently affect soil biochemistry and function. Methanogenesis and methane oxidation, are influenced by multiple factors which are potentially facilitated when paddy soils undergo long term organic fertilization. However, in general, the most important variables that control methane production include soil type, rice variety, temperature, soil redox potential (E_h), water management, and fertilization with organic carbon and nitrogen[4]. The factors affecting methane oxidation include concentrations of acetate, CH₄, O₂, type of fertilization, the availability of nitrogen and copper, pH, and temperature[4]. Since methane emission is a balance between production and consumption, factors that affect methane diffusion, microbial activities in general, methanogenesis, and methane monooxygenase activity all integrate into the equation [2]. Effects of long term organic fertilization on methanogenesis, methane oxidation, and related processes are presented in Table 3.

Long term compost fertilization in paddy field agroecosystems is a critical scenario in relation to methane source, methane sink, methane emission, and global warming potential. In most studies, methane emission seemed to increase as the amount of organic or compost increased especially observed in treatments with low, moderate, and high manure[59, 60]. This was also observed when organic or compost is in combination with any other chemical fertilization[10, 37, 59, 64, 75]. All of these studies unify to present that organic fertilization, in any form, generally enhances methane emission in paddy fields. However, differences in the degree of methane emission can be observed in different types of organic fertilization, with a generalization that manure usually enhances a greater methane flux than crop residues, with the same generalization for fresh manure or crop residue against composted fertilizers[59, 87]. In a wider perspective, different types of N can also impact methane production, albeit, with different effects. Complete chemical fertilizer in combination with compost generally has positive effects on methanogen abundance or the mcrA gene abundance, and in turn, methanogenesis.[37, 59, 64]. Other forms of N such as urea, ammonium, or nitrate, and their concentration, when used as chemical fertilizers may stimulate or inhibit methanogenesis[6, 7, 12, 78].

Another central feature of methanogenesis is its usual correlation with the abundance of methanogens, mcrA gene, or the transcriptional activities of methanogens[10, 12, 60, 73, 88]. In extension, the ratio between the abundance of mcrA and pmoA (mcrA/pmoA) also generally positively correlated with methanogenesis[37, 73]. Other prominent features of the paddy field agroecosystems related to methane emission are the effects of submergence and drainage and rice-stage-related fluxes in methane emissions. Methanogenesis by methanogenic archaea mainly occurs under anoxic conditions favored during submergence and flooding, or even in water-saturated soils[2, 4]. Paddy fields are flooded throughout most of the rice-growing season. Methane emission was promoted when the paddy fields were flooded and inhibited when drained, similar to the effects of wet and dry seasons[10, 73, 89]. Methane flux was also observed in the different rice growing stages. Production of methane was higher during the booting stage[64] and tillering to jointing and at the filling stage[37].

One of the major drivers of methanogenesis, exemplified by long term organic or compost fertilization, is the direct or indirect increase in the substrates necessary for the production of methane. Organic fertilization directly provides the carbon compounds or indirectly enhances plant growth that will eventually release carbon in the paddy soils. The increase in SOC, DOC, labile and soluble C, readily mineralizable C, and other forms of carbon are major factors enhancing methane production[10-12, 60, 73, 75].

Other factors driving methanogenesis in the paddy field provide interesting areas of research. Perhaps one of the most complicated, yet still understudied, are the responses of different groups of methanogens and how these affect methane emission on a global scale. Interactions of methanogens with other competing or synergistic microbial communities add to the complications. A glimpse of such complexity has been shown where interacting microorganisms were crucial factors to methane emission[11, 86, 87].

Under long term organic fertilization, some generalizations could be drawn in relation to methane consumption. Overall, the high concentration of methane in paddy field soils generally enhanced the population, pmoA gene abundance, or the activity of MOB [37, 67, 78, 85]. Aerobic environmental condition is also generally essential for methane oxidation. Flooding enhanced methanogenesis while drainage promoted methane oxidation[10, 64, 73, 85]. The presence of oxygen explained the differences observed between the root rhizosphere and the bulk paddy soils[78, 81]. When organic or compost fertilization were in combination with different inorganic nitrogen fertilizers, there were differences in the results owing to the responses of the specific groups of MOB to different forms of nitrogen[11, 78, 79]. High and low levels of nitrogen, as well as the rate of application, can also be an important factor in methane consumption[6, 7, 80].

To understand methane consumption through methane oxidation, we have to greatly consider the different responses of Type I and II MOB. Type I generally responded well to fertilization[78]. For organic fertilization, Type I tended to increase while type II decreased[14, 58, 73]. Type I predominated in normal conditions in paddy soils while type II is generally dominant in unfavorable conditions such as APK treatment[79]. As a generalization, type I MOB seems to flourish under fertilization, especially surrounding the roots and the rhizosphere while type II MOB seems to favor unfertilized bulk paddy fields.

Ultimately, changes in soil physicochemical and microbial components of the rice agroecosystems also lead to alteration of the microbial functions[10, 90] which could affect global-scale processes such as greenhouse gas methane emission, carbon, and nitrogen cycling. Different fertilization schemes should be assessed in order to optimize potential yield while maintaining soil health and function and mitigating environmental issues such as greenhouse gas emissions especially in long term and on the global scale.

MitigatingMethaneEmissioninPaddyFieldAgroecosystemsunderLongTermOrganicFertilization

Paddy field, with rice as a major crop, is a distinct agroecosystem as it mainly needs soil submergence for at least part of the growing season. This leads to potential enhanced methane emissions. However, rice is a major commodity that is consumed by many people around the world, and rice production is in parallel with the increasing world population. In addition, long term compost fertilization or in combination with chemical fertilizers try to mitigate the unsustainable rice farming system but are also faced with potential issues including enhanced methane emission. As methane emission is a balance between methanogenesis and methane consumption, factors and processes that affect these two interacting processes would also affect the net methane emission and could be exploited for mitigating steps (Fig. 2).

Fertilization, especially forms of nitrogen, has been one of the most studied areas concerning methane emission. However, conflicting results even in paddy fields with the same physicochemical soil occur across studies [78]. For long term organic fertilization, the different types, doses, and rates are crucial factors and need to be investigated in order to optimize rice production while limiting environmental problems. Across studies, the addition of organic fertilizers has always increased methane emission, especially in higher dosages[59, 64]. Thus, the input of the optimized dosage of the required organic fertilizer is essential. Organic fertilization should also concentrate on composted material rather than fresh materials as enhancement of methane emission is greater in uncomposted materials [87]. Combination of organic and chemical fertilizers should also be optimized as some studies showed synergistic enhancement of methane emission with NPK and organic/compost fertilization[6, 12, 59, 75] or reduction of methane emission[37, 64].

Water regime is also one of the most important factors that could enhance or reduce methane emission. Flooding generally enhances methane emission as it provides an ideal anoxic condition especially in the deeper layers of paddy soils. Draining, on the other hand, oxygenates soils and allows methane oxidation [64, 73]. Therefore, repeated or controlled paddy field drainage without affecting rice yield should be applied. Activation of high-affinity methane oxidation has also been observed in drained paddies enhancing them as methane sinks[85]. However, nitrous oxide emission when paddy fields are drained should also be considered.

Crops used in paddy fields also directly and indirectly affect methane emission through enhancement of methane production or methane oxidation. Monocrop systems using rice as the only crop or in alternation with other crops in a multicrop system could affect methane emission, with rice monocrop showing a lower response to methane emission compared to different rice multicrop system[7]. The plant type (genotype, cultivar, diversity, etc.) could directly affect methane emission through root exudations or when they are left in the paddy fields after harvest[11]. Rice plants also act as transport systems for methane through the aerenchyma system. The root and the rhizosphere are also the major sites of methane oxidation as the rice aerates the paddy soils[4]. Thus, rice varieties that provide maximum yield with minimal impact on methanogenesis could be used over other rice varieties.

Theoretically, anything that affects the activity of methanogens or methane oxidizing bacteria could also affect methane emission. Competing and supporting microbes, such as fermenting microorganisms for methanogens and competing nitrifiers for methane oxidation have also complicated the process but are equally important. On the microbial level, stress tolerance, substrate affinity, growth rate, diversity, temperature, pH, soil redox potential, presence of salts, and other interacting factors cumulatively interact to either enhance or reduce methane emission through methanogenesis and methane oxidation[11, 86, 87]. This is greatly observed in the different responses between type I and type II MOB which also influenced the overall methane emission process[14, 58, 67, 73, 78-81].

ConclusionandFuturePerspective

This review mainly focused on the effects of long term compost fertilization on the soil chemical properties and biotic components especially related to methane cycling in the paddy field agroecosystems. Organic fertilization alters soil physicochemical properties and biotic components of the soil potentially influencing the dynamics of methane cycling through the balance between methanogenesis and methane consumption. These processes are affected by multiple factors in paddy fields under organic fertilization which could be assessed and targeted to develop mitigating steps in the contribution of methane to global warming and climate change.

However, to fully comprehend methane emission, there are some other interacting variables and processes that need to be considered and an overall global study and consensus should be elucidated. For instance, there are many other types of organic matter amendments. Temporal fluxes related to rice growth responses and management practices should also be considered together with short-term perturbation and long-term estimation of their contributions to methane emission. Most of the studies on methane emission were also conducted during the rice/crop growing period but changes observed during the fallow period potentially dictate the responses and processes during the rice growing period.

Although paddy fields could be a major source of methane emission, it is also a major sink for methane consumption. Therefore, it is necessary to incorporate the trade-offs under short and long-term organic fertilization. For example, compost fertilization may increase methane emission, but beneficial effects such as enhanced soil fertility, soil productivity, and sustainability are equally important. Furthermore, long term fertilization trials could help us understand the effects of such management systems, assessing and balancing positive and negative impacts which help up design and implement better mitigating steps to reduce agricultural environmental impacts.

Note

The authors declare no conflict of interest.

ACKNOWLEDGEMENT

This study was carried out with the support of "PJ015584042021", Rural Development Administration, Republic of Korea.

Tables & Figures

Fig. 1.

Methanogenesis as modulated by the enzyme methyl-CoM reductase [76] and methane oxidation followed by methylotrophy as mainly controlled by methane monooxygenase and methanol dehydrogenase enzymes, respectively [77]. The functional genes mcrA, pmoA, and mxaF are molecular markers commonly employed to study methanogenesis, methane oxidation, and methanol oxidation, respectively.

Table 1.

Effects of long term organic and compost fertilization on the soil chemical properties and biological components in paddy field agroecosystem

Table 2.

Microbial ecology of methanogens and methanotrophs in paddy soils: phylogeny, diversity, and ecological niches

Table 3.

Methanogenesis, methane oxidation and factors affecting the processes in paddy fields

Table 3.

Fig. 2.

Potential and hypothetical mitigation schemes of methane emission from paddy fields in combination with long term organic fertilization.

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