Agricultural soils act as both carbon sinks and sources of emissions. They store more carbon than the atmosphere and all vegetation combined, yet farming practices can also make them release large quantities of greenhouse gases.
With the world's population growing, demand for food and agricultural products is higher than ever. Meeting it has meant converting grassland into farmland, expanding energy-intensive production systems, and applying both chemical and organic inputs more heavily. Greenhouse gas emissions from agriculture have risen accordingly, and agriculture is now the second-largest contributing sector after energy. In India, farming adds substantially to national emissions through carbon dioxide, methane, and nitrous oxide. Methane accounts for the largest share in agriculture, released mainly by ruminants through enteric fermentation and by flooded paddy fields through anaerobic decomposition.
Deep tillage, residue removal, and heavy fertiliser use all accelerate the breakdown of organic matter and release carbon dioxide. Rice fields are a major methane source in their own right, and recent global assessments put emissions from paddy rice at roughly 25 to 40 teragrams of methane per year, accounting for about 6% to 11% of total anthropogenic methane. The Global Methane Budget gives 25.1 to 37.5 teragrams for the decade to 2019, and a recent satellite-based inventory arrives at 39.3 teragrams. Set alongside livestock, fertiliser use, and the conversion of grassland to cropland, this is why forestry, agriculture, and land-use change together account for around a quarter of global greenhouse gas emissions.
Addressing this calls for integrated approaches to soil monitoring, understanding, and management. Metagenomics has changed soil microbiome research by allowing culture-independent profiling of microbial communities, both taxonomically and functionally. It studies microorganisms directly in their natural environment by sequencing functional genes, and instead of depending on culture methods, it gives a comprehensive view of microbial diversity, community composition, genetic relationships, and functional activity. Applied to soils, it can identify the functional genes tied to greenhouse gas emissions within the microbial community. Integrated with chamber-based emission data, the approach shows how nitrogen fertilisers reshape soil microecology, identifies the pathways regulating carbon and nitrogen cycling, and highlights the bacterial groups driving emissions.
Why measuring soil emissions is difficult
The static chamber method is among the most widely used techniques for measuring non-reactive greenhouse gas fluxes from soils, particularly methane and nitrous oxide. A closed chamber is placed over a defined area of soil, and gases accumulate in the chamber headspace. The change in concentration inside the chamber over time is measured and converted to a flux rate, representing the exchange between the soil and the atmosphere.
Spatial heterogeneity: soils within a single farm are never uniform. Some patches are sandy and dry, while others are clay-rich and moist, and those differences shape microbial activity and the amount of carbon released. Certain areas become emission hotspots, giving off far more carbon dioxide or nitrous oxide than others, particularly after fertiliser application or rainfall. Because of that patchiness, a single chamber or sensor reading cannot capture the picture, and multiple measurements across different spots are needed. A multi-year, high-resolution dataset showed that carbon dioxide and nitrous oxide fluxes vary significantly across small spatial scales, requiring dense sampling to capture true emission patterns.
Temporal variability: emissions are not fixed but change with climate and ecological conditions. In forests, temperature largely drives microbial activity and carbon dioxide release, while in grasslands and croplands, moisture plays a larger role, with drought slowing microbes and excess water shifting emissions towards methane. Plant communities add further complexity, since roots and litter feed microbes differently depending on vegetation type. A global meta-analysis drawing on 1,337 paired observations from 150 peer-reviewed publications between 1990 and 2023 evaluated the effects of elevated temperature alone and in combination with elevated carbon dioxide, drought, and increased precipitation on soil nitrous oxide and methane fluxes, microbial functional genes, and extracellular enzyme activity across grassland, cropland, and forest ecosystems.
Linking microbial genes to emission pathways
Combining soil metagenomics with chamber-based measurement allows microbial functional genes to be linked directly to observed emission fluxes. Metagenomic analysis has shown that shifts in microbial community succession are closely tied to changes in the abundance of key functional genes involved in nitrification, denitrification, and methane metabolism. A strong correlation between denitrification genes and nitrous oxide fluxes indicates that denitrification is a dominant pathway driving nitrous oxide emissions in the agro-pastoral ecotone studied. Actinobacteria, Thermoproteota, and Nitrospirota emerged as the core microbial taxa carrying those genes, which places them centrally in mediating emissions.
Together, these findings show how microbial community dynamics and functional gene profiles shape soil greenhouse gas fluxes, and they offer insight into the mechanisms behind fertiliser-driven emissions.
From measurement to mitigation
Agriculture has to feed a growing population from limited land, which demands higher yields per hectare. Traditional practices release methane, nitrous oxide, and carbon dioxide, making agriculture a significant driver of climate change, which calls for a shift towards practices that balance productivity with climate responsibility.
Improved soil management, including residue retention, reduced tillage, crop residue return, and biochar addition, raises soil organic carbon, with increases reported up to 34.3%. In Haryana, India, work through the Climate-Smart Villages programme found that adopting zero tillage raised farm profits by close to USD 97.5 per hectare through savings in labour, fuel, and equipment, while cutting carbon emissions by about 1.5 Mg per hectare per season.
Soils can store carbon and they can release greenhouse gases, and the same management decisions govern both. Metagenomics combined with chamber methods gives a clearer picture of how microbes and fertilisers drive carbon dioxide, methane, and nitrous oxide fluxes. Practices such as residue retention, reduced tillage, crop return, and biochar help soils hold more carbon and cut emissions at the same time. Using the measurement and the management together improves the accuracy of what is tracked and reduces what is emitted, which is what turns soils into sinks serving both food security and climate protection.
Sources
Chataut, G., Bhatta, B., Joshi, D., Subedi, K., and Kafle, K. (2023). Greenhouse gas emissions from agricultural soil: a review—Journal of Agriculture and Food Research, 11, 100533.
Basheer, S., Wang, X., Farooque, A. A., Nawaz, R. A., Pang, T., and Neokye, E. O. (2024). A review of greenhouse gas emissions from agricultural soil: sustainability, 16(11), 4789.
Clagnan, E., et al. (2024). Culturomics and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture—frontiers in Microbiology, 15, 1473666.
Meng, T., Shi, J., Zhang, X., et al. (2026). Mechanistic insights into nitrogen fertiliser regulation of carbon-nitrogen cycling and greenhouse gas emissions, a metagenomics-based investigation. Frontiers in Microbiology, 17, 1808047.
Kim, N., Jang, C., Yang, W. H., Guan, K., DeLucia, E. H., and Lee, D. (2025). Spatial variability of agricultural soil carbon dioxide and nitrous oxide fluxes: agriculture, Ecosystems & Environment, 387, 109636.
Shakoor, A., Pendall, E., and Macdonald, C. A. (2025). Microbial mechanisms of interactive climate-driven changes in soil N2O and CH4 fluxes, a global meta-analysis. Journal of Environmental Management, 376, 124380.
Fan, X., Kong, H., Zhao, Y., Hu, H., Jiang, Z., and Wang, X. (2026). Global synthesis of agricultural practices on crop yield, soil organic carbon and greenhouse gas emissions. Journal of Cleaner Production, 540, 147529.
Singh, S., Kiran, B. R., and Venkata Mohan, S. (2024). Carbon farming, a circular framework to augment CO2 sinks and to combat climate change. Environmental Science Advances, 3(4), 522-542.
Saunois, M., et al. (2025). Global Methane Budget 2000-2020. Earth System Science Data, 17, 1873-1958.
CCAFS-CIMMYT (2014). Climate-Smart Villages in Haryana, India. CGIAR Research Program on Climate Change, Agriculture and Food Security.
Singh, N., Patel, D., and Khalekar, G. (2018). Methanogenesis and methane emission in rice and paddy fields, climate impact on agriculture.
Malik, S., Verma, and Rani, E. (2026). Greenhouse gas emissions from the Indian agricultural sector. International Journal of Current Science, 16, 245-256.
