Please wait a minute...
Journal of Integrative Agriculture  2026, Vol. 25 Issue (10): 4339-4350    DOI: 10.1016/j.jia.2025.12.049
Agro-ecosystem & Environment Advanced Online Publication | Current Issue | Archive | Adv Search |
Soil texture drives rice methane emissions at tillering stage via carbon fractions, nutrients and microbial abundance

Deshun Xiao, Chang Ye, Hengyu Ma, Yanan Xu, Yi Tao, Junlin Zhu, Wenli Liao, Song Chen, Guang Chu, Yuanhui Liu, Kai Yu, Chunmei Xu#, Danying Wang#

State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China

 Highlights 

● Soil texture was a core factor influencing CH4 emissions in paddy fields.

● Clay content exhibited the highest degree and closeness centrality.

● Clay content affected SOC composition, nutrients level, and microbial abundance.

● POC and MAOC showed contrasting effects on CH4 emissions.

● AVP and AVK correlate positively with mcrA and pmoA abundance.

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
摘要  

本研究从稻田土壤质地切入,探讨了稻田甲烷(CH4)排放的复杂机制。通过分析中国主要稻作区31份稻田土壤样品,研究了水稻分蘖期土壤质地、有机碳组成、土壤养分和微生物丰度调控稻田CH4排放的复杂相互作用。结果表明,不同土壤间CH4排放存在显著差异,并与土壤质地、有机碳、养分水平及微生物丰度显著相关。土壤质地,尤其是黏粒含量,是影响有机碳组成的关键因素,与矿物结合态有机碳(MAOC)呈显著正相关。有机碳组分显著促进CH4排放,但其影响并不一致:颗粒态有机碳(POC)与CH4排放呈负相关,而MAOC则呈正相关。土壤质地还影响养分有效性,其中黏粒含量与土壤氮、磷含量显著相关。养分含量与产甲烷菌(mcrA)和甲烷氧化菌(pmoA)功能基因丰度密切相关。mcrA丰度与速效钾呈正相关,pmoA丰度与速效磷呈正相关。此外,pmoA的丰度受到溶解性有机碳的促进,但被黏土含量所抑制。网络分析进一步突显了土壤质地的核心地位,土壤黏粒含量表现出最高的度中心性和接近中心性。综上所述,土壤质地是影响水稻分蘖期CH4排放的基础核心因素,其作用通过多条途径实现,包括调控有机碳组成、养分有效性和产甲烷菌与甲烷氧化菌的丰度。该结果为针对不同土壤质地特征制定低碳栽培策略提供了理论基础。



Abstract  

This study explored the complex mechanisms of methane (CH4) emissions in paddy fields, focusing on the often-overlooked role of soil texture.  Through the analysis of 31 paddy soil samples, the research investigated the complex interactions among soil texture, organic carbon composition, soil nutrients, and microbial abundance in regulating CH4 emissions during the tillering stage of rice.  The results revealed significant variations in CH4 emissions among different soils, which were notably associated with soil texture, organic carbon, nutrients levels, and microbial abundance.  Soil texture, particularly clay content, emerged as a key factor influencing the composition of organic carbon, showing a significant positive correlation with mineral-associated organic carbon (MAOC).  While organic carbon components significantly enhanced CH4 emissions, their effects were not uniform: particulate organic carbon correlated negatively with emissions, whereas MAOC showed a positive association.  Soil texture also influenced nutrients availability, with clay content significantly correlated with soil nitrogen and phosphorus content, which in turn affects the abundance of functional genes.  Specifically, mcrA abundance was positively correlated with available potassium, while pmoA abundance was positively correlated with available phosphorus.  Additionally, dissolved organic carbon promoted pmoA abundance, although this effect was mitigated by higher clay content.  Network analysis further emphasized the central role of soil texture, with clay exhibiting the highest degree and closeness centrality.  In conclusion, soil texture is a fundamental and core factor influencing CH4 emissions at tillering of rice, exerting its influence through multiple pathways including modulating the composition of organic carbon, nutrient availability, and the abundance of methanogens and methanotrophs.  These findings provide theoretical foundations for developing low-carbon cultivation strategies tailored to different soil textural characteristics.

Keywords:  soil texture       organic carbon composition       nutrient       microbial abundance  
Received: 30 September 2025   Accepted: 10 November 2025 Online: 26 December 2025  
Fund: 

This study was supported by the Major Special Project of Zhejiang Province, China (2024C02001), the National Rice Industry Technology System, China (CARS-01-29), and the Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences.

About author:  #Correspondence Danying Wang, E-mail: wangdanying@caas.cn; Chunmei Xu, E-mail: xuchunmei@caas.cn

Cite this article: 

Deshun Xiao, Chang Ye, Hengyu Ma, Yanan Xu, Yi Tao, Junlin Zhu, Wenli Liao, Song Chen, Guang Chu, Yuanhui Liu, Kai Yu, Chunmei Xu, Danying Wang. 2026. Soil texture drives rice methane emissions at tillering stage via carbon fractions, nutrients and microbial abundance. Journal of Integrative Agriculture, 25(10): 4339-4350.

Alpana S, Vishwakarma P, Adhya T K, Inubushi K, Dubey S K. 2017. Molecular ecological perspective of methanogenic archaeal community in rice agroecosystem. Science of the Total Environment, 596, 136–146.

Angst G, Mueller K E, Castellano M J, Vogel C, Wiesmeier M, Mueller C W. 2023. Unlocking complex soil systems as carbon sinks: Multi-pool management as the key. Nature Communications, 14, 2967.

Ariani M, Hanudin E, Haryono E. 2022. The effect of contrasting soil textures on the efficiency of alternate wetting-drying to reduce water use and global warming potential. Agricultural Water Management, 274, 13.

Baldock J A, Skjemstad J O. 2000. Role of the soil matrix and minerals in protecting natural organic materials against biological attack. Organic Geochemistry, 31, 697–710.

Bhattacharyya P, Dash P K, Swain C K, Padhy S R, Roy K S, Neogi S, Berliner J, Adak T, Pokhare S S, Baig M J, Mohapatra T. 2019. Mechanism of plant mediated methane emission in tropical lowland rice. Science of the Total Environment, 651, 84–92.

Cai A D, Feng W T, Zhang W J, Xu M G. 2016. Climate, soil texture, and soil types affect the contributions of fine-fraction-stabilized carbon to total soil organic carbon in different land uses across China. Journal of Environmental Management, 172, 2–9.

Cai S, Sun L, Wang W, Li Y, Ding J, Jin L, Li Y, Zhang J, Wang J, Wei D. 2024. Straw mulching alters the composition and loss of dissolved organic matter in farmland surface runoff by inhibiting the fragmentation of soil small macroaggregates. Journal of Integrative Agriculture, 23, 1703–1717.

Chen H T, Qin Y, Zhong X H, Lin C Y, Qin J H, Yang J C, Zhang W Y. 2024. Research progress on the relationship between rice root, soil properties and methane emissions in paddy fields. Chinese Journal of Rice Science, 38, 233–245. (in Chinese)

Cong W W, Meng J, Ying S C. 2018. Impact of soil properties on the soil methane flux response to biochar addition: A meta-analysis. Environmental Science (Processes & Impacts), 20, 1202–1209.

Cotrufo M F, Ranalli M G, Haddix M L, Six J, Lugato E. 2019. Soil carbon storage informed by particulate and mineral-associated organic matter. Nature Geoscience, 12, 989–994.

Creamer C A, Jones D L, Baldock J A, Rui Y, Murphy D V, Hoyle F C, Farrell M. 2016. Is the fate of glucose-derived carbon more strongly driven by nutrient availability, soil texture, or microbial biomass size? Soil Biology and Biochemistry, 103, 201–212.

Cui Y, Luo F L, Chen Y H, Zhang M X, Yu F H. 2022. Rhizodeposition and litter decomposition of Phragmites australis play important roles in composition and properties of soil dissolved organic matter. Ecological Indicators, 142, 109275.

Denier Van Der Gon H A C, Kropff M J, Van Breemen N, Wassmann R, Lantin R S, Aduna E, Corton T M, Van Laar H H. 2002. Optimizing grain yields reduces CH4 emissions from rice paddy fields. Proceedings of the National Academy of Sciencesof the United States of America, 99, 12021–12024.

Dungait J A J, Hopkins D W, Gregory A S, Whitmore A P. 2012. Soil organic matter turnover is governed by accessibility not recalcitrance. Global Change Biology, 18, 1781–1796.

Gao D D, Sheng R, Moreira-Grez B, Liu S G, Xu R S, Li K, Wei W X. 2022. Influences of phosphorus and potassium deficiencies on the methanotrophic communities in rice rhizosphere. Applied Soil Ecology, 170, 9.

Guan S, Qi Z J, Li S R, Du S C, Xu D. 2024. Effects of rice root development and rhizosphere soil on methane emission in paddy fields. Plants-Basel, 13, 19.

Hassan W, Bashir S, Ahmed N, Tanveer M, Shah A N, Bano R, David J. 2016. Labile organic carbon fractions, regulator of CO2 emission: Effect of plant residues and water regimes. Clean-Soil Air Water, 44, 1358–1367.

He Z, Xue L H, Yang L Z, Xu C. 2021. Effects of phosphorus on methane emissions from rice fields and its possible mechanisms. Journal of Agro-Environment Science, 40, 445–450.

Hu H, Chen J, Zhou F, Nie M, Hou D Y, Liu H, Delgado-Baquerizo M, Ni H W, Huang W G, Zhou J Z, Song X W, Cao X F, Sun B, Zhang J B, Crowther T W, Liang Y T. 2024. Relative increases in CH4 and CO2 emissions from wetlands under global warming dependent on soil carbon substrates. Nature Geoscience, 17, 26–31.

IPCC (Intergovernmental Panel on Climate Change). 2022. Summary for policymakers. In: Global Warming of 1.5°C: Intergovernmental Panel on Climate Change Special Report on Impacts of Global Warming of 1.5°C above Pre-industrial Levels in Context of Strengthening Response to Climate Change, Sustainable Development, and Efforts to Eradicate Poverty. Cambridge University Press, Cambridge.

Jiang Y, Guan D H, Zhang W J. 2018. The effect of rice plant traits on methane emissions from paddy fields: A review. Chinese Journal of Eco-Agriculture, 26, 175–181. (in Chinese)

Kimura M, Murase J, Lu Y H. 2004. Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO2 and CH4). Soil Biology & Biochemistry, 36, 1399–1416.

Kögel-Knabner I, Amelung W, Cao Z H, Fiedler S, Frenzel P, Jahn R, Kalbitz K, Kölbl A, Schloter M. 2010. Biogeochemistry of paddy soils. Geoderma, 157, 1–14.

Liu D Q, Chen M W, Liu H, Qi J C, Yang J W, Lv M, Li C, Li C J, Li C Z. 2025. The conversion of tropical natural forests alters soil carbon fractions in aggregates and reduces aggregates stability. Journal of Environmental Management, 376, 10.

Liu S G, García-Palacios P, Tedersoo L, Guirado E, Van Der Heijden M G A, Wagg C, Chen D M, Wang Q K, Wang J T, Singh B K, Delgado-Baquerizo M. 2022. Phylotype diversity within soil fungal functional groups drives ecosystem stability. Nature Ecology & Evolution, 6, 900–909.

Liu X Y, Peñuelas J, Sardans J, Fang Y Y, Wiesmeier M, Wu L Q, Chen X X, Chen Y Y, Jin Q, Wang W Q. 2021. Response of soil nutrient concentrations and stoichiometry, and greenhouse gas carbon emissions linked to change in land-use of paddy fields in China. Catena, 203, 13.

Malyan S K, Bhatia A, Kumar A, Gupta D K, Singh R, Kumar S S, Tomer R, Kumar O, Jain N. 2016. Methane production, oxidation and mitigation: A mechanistic understanding and comprehensive evaluation of influencing factors. Science of the Total Environment, 572, 874–896.

Mao H R, Cotrufo M F, Hart S C, Sullivan B W, Zhu X F, Zhang J C, Liang C, Zhu M Q. 2024. Dual role of silt and clay in the formation and accrual of stabilized soil organic carbon. Soil Biology and Biochemistry, 192, 109390.

Miao J, Ji M Y, Xiao L R, Liu F H, Wu M, Sang W J. 2023. Unraveling the fascinating connection between hydrochar feedstock and methane emissions in rice paddy soil: Insights from microorganisms and organic matter. Chemical Engineering Journal, 472, 13.

Nijman T P A, Amado A M, Bodelier P L E, Veraart A J. 2022. Relief of phosphate limitation stimulates methane oxidation. Frontiers in Environmental Science, 10, 1–8.

Niu Y, Li Y, Lou M, Cheng Z, Ma R, Guo H, Zhou J, Jia H, Fan L, Wang T. 2024. Microbial transformation mechanisms of particulate organic carbon to mineral-associated organic carbon at the chemical molecular level: Highlighting the effects of ambient temperature and soil moisture. Soil Biology and Biochemistry, 195, 109454.

Nwokolo N L, Enebe M C. 2025. Methane production and oxidation - A review on the pmoA and mcrA gene abundances for understanding the functional potentials of agricultural soils. Pedosphere, 35, 161–181.

Qian H Y, Zhu X C, Huang S, Linquist B, Kuzyakov Y, Wassmann R, Minamikawa K, Martinez-Eixarch M, Yan X Y, Zhou F, Sander B O, Zhang W J, Shang Z Y, Zou J W, Zheng X H, Li G H, Liu Z H, Wang S H, Ding Y F, Van Groenigen K J, et al. 2023. Greenhouse gas emissions and mitigation in rice agriculture. Nature Reviews Earth & Environment, 4, 716–732.

Rakhsh F, Golchin A, Al Agha A B, Nelson P N. 2020. Mineralization of organic carbon and formation of microbial biomass in soil: Effects of clay content and composition and the mechanisms involved. Soil Biology and Biochemistry, 151, 108036.

Ren G C, Zhang X F, Xin X L, Yang W L, Zhu A N, Yang J, Li M R. 2023. Soil organic carbon and nitrogen fractions as affected by straw and nitrogen management on the North China Plain. Agriculture, Ecosystems & Environment, 342, 108248.

De Ros A, Piccoli I, Sartori L, Portelli B, Serra G, Dal Ferro N, Morari F. 2025. Advancing soil texture and organic carbon spatial variability assessment: Integrating proximal γ-ray spectroscopy and electromagnetic induction via data fusion for site-independent analysis. Catena, 254, 108980.

Su J, Hu C, Yan X, Jin Y, Chen Z, Guan Q, Wang Y, Zhong D, Jansson C, Wang F, Schnürer A, Sun C. 2015. Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice. Nature, 523, 602–606.

Tan W F, Xu Y, Shi Z H, Cai P, Huang Q Y. 2023. The formation process and stabilization mechanism of soil aggregates driven by binding materials. Acta Pedologica Sinica, 60, 1297–1308. (in Chinese)

Wang L, Wei C F, Xie D T. 2002. Research advances on methane emission from rice paddy. Soil and Environmental Sciences, 11, 158–162.

Wang M J, Feng X Q, Zhou Z Y, Ma H Y, Ge T D, Tang C X, Wang D Y, Chen S. 2024. Labile organic carbon fractions in the rhizosphere contribute to nitrogen and phosphorus uptake in rice under long-term crop rotations and nitrogen application. Applied Soil Ecology, 200, 105459.

Wang M X, Li J. 2002. CH4 emission and oxidation in Chinese rice paddies. Nutrient Cycling in Agroecosystems, 64, 43–55.

Yan Y, Zhang X, Xu C, Liu J, Hu F, Geng Z. 2025. Effect of colloidal particle size on physicochemical properties and aggregation behaviors of two alkaline soils. Soil, 11, 85–94.

Yang C, Sainju U M, Li C, Fu X, Zhao F, Wang J. 2023. Long-term chemical and organic fertilization differently affect soil aggregates and associated carbon and nitrogen in the Loess Plateau of China. Agronomy, 13, 1466.

Yao Z Y, Hu H L, Wang T, Wang X G, Li Y L, Sun X M, Adl S, Yan F F, Zhang Y J, Zhu B. 2025. Key functional guilds with high trophic level organisms in soil are vital contributors to greenhouse gas emissions from cropland. Agriculture, Ecosystems & Environment, 381, 109441.

Ye C, Zheng G J, Tao Y, Xu Y N, Chu G, Xu C M, Chen S, Liu Y H, Zhang X F, Wang D Y. 2024. Effect of soil texture on soil nutrient status and rice nutrient absorption in paddy soils. Agronomy, 14, 1339.

You X X, Wang S, Du L N, Wu H, Wei Y. 2022. Effects of organic fertilization on functional microbial communities associated with greenhouse gas emissions in paddy soils. Environmental Research, 213, 113706.

Zare Abyaneh H, Khodabandehlo Z, Bayat H, Jovzi M. 2022. The effect of a superabsorbent and biochar on some physical and hydraulic properties of two arable sandy loam and clay loam soils. Journal of Soil Science and Plant Nutrition, 22, 2557–2569.

Zhou Z H, Ren C J, Wang C K, Delgado-Baquerizo M, Luo Y Q, Luo Z K, Du Z G, Zhu B, Yang Y H, Jiao S, Zhao F Z, Cai A D, Yang G H, Wei G H. 2024. Global turnover of soil mineral-associated and particulate organic carbon. Nature Communications, 15, 5329.

[1] Yingpeng Wang, Yifan Hua, Lanxin Mei, Yixuan Meng, Yongtao Guo, Jian Cai, Mei Huang, Yingxin Zhong, Xiao Wang, Dong Jiang, Qin Zhou. An application strategy of combined controlled-release fertilizers can balance the yield and quality of soft wheat while meeting its nutrient requirements[J]. >Journal of Integrative Agriculture, 2026, 25(7): 2783-2795.
[2] Yang Gao, Zhihao Zheng, Ning Li. Is intra-household nutrient allocation equitable?  Evidence from asymmetric expenditure responses in rural China[J]. >Journal of Integrative Agriculture, 2026, 25(7): 3074-3085.
[3] Yufeng Wang, Zixuan Chang, Jiayu Wang, Tingliang Li, Zhiping Yang. Residual nitrogen exhibits lower stability and greater influence on wheat yield formation compared to phosphorus and potassium in drylands of the Loess Plateau[J]. >Journal of Integrative Agriculture, 2026, 25(5): 2063-2076.
[4] Junwei Wang, Qi Zou, Huimin Yuan. Improved selected soil properties predictions using MIR and pXRF sensor fusion[J]. >Journal of Integrative Agriculture, 2026, 25(4): 1687-1699.
[5] Yi Zhou, Shenghua Chang, Xiaojuan Huang, Wenjun Wang, Fujiang Hou, Yanrong Wang, Zhibiao Nan . Plant community micronutrients mediate the soil carbon stock by altering plant growth, reproduction and survival trade-offs[J]. >Journal of Integrative Agriculture, 2026, 25(4): 1675-1686.
[6] Li Han, Qiyu Tian, Qi Han, Yulong Yin, Jie Yin, Xingguo Huang. Methyl donor micronutrients orchestrate lipid metabolism: The role of DNA methylation modification[J]. >Journal of Integrative Agriculture, 2026, 25(4): 1343-1358.
[7] Jili Xu, Shuo Liu, Zhiyuan Gao, Qingdong Zeng, Xiaowen Zhang, Dejun Han, Hui Tian. Genome-wide association study reveals genomic regions for nitrogen, phosphorus and potassium use efficiency in bread wheat[J]. >Journal of Integrative Agriculture, 2026, 25(3): 847-863.
[8] Zhihao Pang, Nina Nikolic, Miroslav Nikolic, Alexander Lux, Yongchao Liang. Where is plant beneficial element research heading?[J]. >Journal of Integrative Agriculture, 2026, 25(3): 829-846.
[9] Miaomiao Wang, Hongsong Chen, Wei Zhang, Kelin Wang. Variations and major driving factors for soil nutrients in a typical karst region in Southwest China[J]. >Journal of Integrative Agriculture, 2026, 25(2): 424-435.
[10] Haobo Fan, Farman Wali, Pengjuan Hu, Haixia Dong, Haiqiang Li, Dan Liang, Jingru Shen, Mingxia Gao, Hao Feng, Benhua Sun. Sustainable phosphorus (P) management: Impact of low P input with enhancement measures on soil P fractions and crop yield performance on a calcareous soil[J]. >Journal of Integrative Agriculture, 2026, 25(1): 290-301.
[11] Yuheng Wang, Furong Kang, Bo Yu, Quan Long, Huaye Xiong, Jiawei Xie, Dong Li, Xiaojun Shi, Prakash Lakshmanan, Yueqiang Zhang, Fusuo Zhang. Magnesium supply is vital for improving fruit yield, fruit quality and magnesium balance in citrus orchards with increasingly acidic soil[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3641-3655.
[12] Vicente José Laamon Pinto Simões, Lóren Pacheco Duarte, Rafaela Dulcieli Daneluz Rintzel, Amanda Posselt Martins, Tales Tiecher, Leonardo Dallabrida Mori, Carolina Bremm, Marco Aurélio Carbone Carneiro, Paulo César de Faccio Carvalho. System fertilization improves soil quality and increases primary production in an integrated crop-livestock system[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3671-3688.
[13] Yongshui Hao, Xueying Liu, Qianqian Wang, Shuxin Wang, Qingqing Li, Yaqing Wang, Zhongni Guo, Tiantian Wu, Qing Yang, Yuting Bai, Yuru Cui, Peng Yang, Wenwen Wang, Zhonghua Teng, Dexin Liu, Kai Guo, Dajun Liu, Jian Zhang, Zhengsheng Zhang. Mapping QTLs for fiber- and seed-related traits in Gossypium tomentosum CSSLs with a G. hirsutum background [J]. >Journal of Integrative Agriculture, 2025, 24(2): 467-479.
[14] Guanghao Li, Qijian Zhang, Weiping Lu, Dalei Lu. Response of nutrient accumulation, remobilization and yield to combined application of nitrogen and potassium in waxy maize[J]. >Journal of Integrative Agriculture, 2025, 24(12): 4561-4572.
[15] Jinfeng Wang, Xueyun Yang, Shaomin Huang, Lei Wu, Zejiang Cai, Minggang Xu. Long-term combined application of organic and inorganic fertilizers increases crop yield sustainability by improving soil fertility in maize–wheat cropping systems[J]. >Journal of Integrative Agriculture, 2025, 24(1): 290-305.
No Suggested Reading articles found!