A sweeping new analysis of a decade of agricultural research suggests that the way we farm may shape not only what grows in our fields, but which microbes thrive beneath them and how much greenhouse gas escapes from the soil. In a study published in Discover Soil, researchers led by Neha Kalonia and Dipti Grover of Kurukshetra University, together with colleagues at the International Rice Research Institute South Asia Regional Centre and Amity University Punjab, combined bibliometric mapping with a targeted synthesis of experimental studies to chart how conventional, organic, and natural farming systems affect soil microbial communities and greenhouse gas emissions. The work offers one of the most structured pictures yet of a research field that has grown rapidly but unevenly across the globe.
The team began by searching the Web of Science database for publications from 2015 to 2024, using search strings for conventional farming, organic farming, and natural farming, and then refining the results with terms related to microbial activity, microbial dynamics, and greenhouse gases. After removing duplicates and screening for relevance, 118 articles remained for detailed analysis: 30 on conventional farming, 50 on organic farming, and 38 on natural farming. The bibliographic data were then visualized using VOSviewer, a software tool that maps keyword co-occurrence, with node size indicating how often a term appears and links between nodes revealing how closely related research themes are. The authors stress that this mapping identifies research trends and thematic structures rather than direct biological effects; the biological conclusions came from a separate comparative synthesis of experimental literature.
The publication trends tell a story of shifting scientific priorities. Research on conventional farming showed a fluctuating pattern, peaking in 2021 and 2022 with five publications each year before declining slightly. Organic farming research also fluctuated, reaching its highest annual output of eight publications in 2022. Natural farming research, by contrast, emerged much more recently, with little or no output in earlier years but a marked surge in 2023 and 2024. This temporal pattern, the authors note, reflects a progressive shift in research attention toward farming systems that emphasize soil biological functioning, resource conservation, and climate-related outcomes, even though the evidence base for natural farming remains considerably smaller and younger than that for its conventional and organic counterparts.
Geography matters too. Conventional farming research was concentrated in North America, Europe, and Asia, with the United States leading at 213 publications, followed by Germany with 203, France with 153, Italy with 147, China with 144, India with 125, Spain with 117, and Brazil with 97. Organic farming research was more decentralized, with France, Germany, and the United States at the top, and contributions spread across every inhabited continent. Natural farming research, however, was strikingly concentrated: India produced 69 of the publications, far exceeding the United States at 22, England at 16, China at 14, and Japan at 10. The authors caution that publication volume measures research productivity rather than scientific impact, but the pattern highlights how strongly natural farming scholarship remains tied to the region where practices such as Zero Budget Natural Farming originated.
Keyword co-occurrence analysis revealed three thematic clusters for each farming system, and the differences are revealing. For conventional farming, the clusters linked microbial activity and biodiversity with agricultural practices such as fertilizer use, residue management, and greenhouse gas emissions; connected soil properties with microbial biomass and enzyme activities; and tied microbial activity to climate themes including carbon sequestration and nitrous oxide. Organic farming research clustered around soil organic carbon, minimum tillage, and residue management; around microbial diversity, compost, manure, and community composition; and around soil fertility, dehydrogenase activity, legumes, and arbuscular mycorrhizal fungi. Natural farming research, meanwhile, was distinguished by the prominence of terms such as Jeevamritha and Beejamrit, the traditional cattle-based biological inputs at the heart of the practice, alongside clusters on microbial networks, soil health, reduced tillage, carbon pools, mulching, and sustainable soil management.
To move beyond keyword maps, the researchers synthesized 21 highly cited experimental studies on soil microbial dynamics, seven for each farming system. Fourteen of these were published between 2019 and 2024, underscoring the field’s recent momentum. The evidence that emerged was consistent in direction: conventional farming, with its intensive tillage, synthetic fertilizers, and pesticides, was repeatedly associated with reduced microbial diversity, lower fungal-to-bacterial ratios, diminished microbial biomass carbon, reduced enzyme activities, and declining soil organic carbon. Crop residue burning emerged as particularly damaging, raising soil temperatures and depleting organic matter, while long-term inorganic nitrogen use was linked to soil acidification and disrupted nutrient cycling. In one comparative study, microbial activity under organic management increased by 61.4 percent for cluster bean and 62.0 percent for tomato during flowering, while natural farming yielded increases of 41.0 and 43.8 percent over standard practices, with organic conditions showing the highest microbial diversity and natural farming second-best.
Organic and natural farming systems, by contrast, generally supported richer and more active soil communities. Organic practices such as green manures, farmyard manure, vermicompost, diverse rotations, and reduced tillage were associated with greater bacterial and fungal diversity, higher enzymatic activity, increased microbial biomass carbon, and enhanced carbon sequestration. Reduced tillage in particular increased the abundance of Glomeromycota, ecologically important fungi that form symbioses with crop roots. Natural farming studies reported greater abundance of saprotrophic fungi and of bacteria involved in carbon and nitrogen cycling, higher microbial network complexity, and more nitrogen-fixing and phosphate-solubilizing bacteria, potentially because the absence of chemical inputs removes stresses that suppress beneficial organisms. Long-term naturally farmed orchards showed greater abundance of beneficial fungal species and nitrogen-cycling bacteria than conventional counterparts.
The greenhouse gas picture is more nuanced. Drawing on 15 highly cited experimental studies, five per system, the synthesis found that conventional agriculture contributes substantially to emissions of carbon dioxide, methane, and nitrous oxide through intensive nitrogen fertilization, tillage, residue burning, and irrigation. In India, emissions from crop residue burning rose from 19.34 teragrams of carbon dioxide equivalent annually in 2011 to 33.83 teragrams in 2020, an increase of nearly 75 percent, averaging roughly 1.3 tonnes of carbon dioxide equivalent per hectare per year. Globally, residue burning releases about 176 teragrams of carbon dioxide, 314 gigagrams of methane, and 8 gigagrams of nitrous oxide each year, adding roughly 30 teragrams of carbon dioxide equivalent annually when non-carbon dioxide gases are converted using standard warming potentials.
Organic farming generally showed lower emissions than conventional management, but with important exceptions. One analysis found that organic systems reduced nitrous oxide emissions per hectare by 40.2 percent compared with nonorganic systems, and organic rotations typically produced fewer nitrous oxide emissions than conventional ones. Yet rice cultivation stands out as a significant caveat: methane emissions from organic rice paddies were sometimes equivalent to or substantially greater than those from conventional paddies, and organic rice systems showed lower carbon efficiency ratios and higher greenhouse gas intensities in some studies. Co-applying biochar with the aquatic fern Azolla, however, improved soil properties and reduced yield-equivalent methane and nitrous oxide emissions. Natural farming studies reported lower methane, nitrous oxide, and carbon dioxide equivalent emissions than both conventional and organic methods, with Zero Budget Natural Farming linked to increased microbial diversity and nutrient cycling, but the authors urge caution because this evidence base is recent and geographically concentrated.
The overarching message is that sustainable agriculture cannot be judged by a single metric. Soil microbial processes appear to be a crucial biological link connecting farming practices to carbon dynamics, nutrient cycling, and greenhouse gas fluxes, but the magnitude and even the direction of these effects depend on crop type, soil properties, water regime, climate, and management duration. The authors identify clear research gaps: long-term experiments that simultaneously measure microbial diversity, soil organic carbon, greenhouse gas fluxes, and crop productivity remain scarce; natural farming needs independent, long-term field trials across diverse agro-climatic regions; and rice systems demand particular attention because methane and nitrous oxide respond differently to management. Future work, they argue, should integrate environmental performance with yield and economic viability, so that farming systems can be designed to enhance soil health, curb emissions, and sustain food production all at once.
Subject of Research: Comparative effects of conventional, organic, and natural farming systems on soil microbiomes and greenhouse gas emissions
Article Title: Mapping global research on interactions of conventional, organic, and natural farming systems and soil health with respect to microbiomes and greenhouse gas emissions
Article References: Kalonia, N., Grover, D., Mishra, A. K., & Singh, R. (2026). Mapping global research on interactions of conventional, organic, and natural farming systems and soil health with respect to microbiomes and greenhouse gas emissions. Discover Soil, 3(1), Article 165. https://doi.org/10.1007/s44378-026-00324-8
Image Credits: AI Generated
DOI: 10.1007/s44378-026-00324-8
Keywords: bibliometric analysis, conventional farming, organic farming, natural farming, soil microbiome, soil health, greenhouse gas emissions, carbon sequestration, nitrous oxide, methane, sustainable agriculture, VOSviewer
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Alan Morgan. (September 27, 2026). Soil Microbes and Emissions Reveal a Clear Divide Between Conventional, Organic, and Natural Farming. Scienmag. https://scienmag.com/soil-microbes-and-emissions-reveal-a-clear-divide-between-conventional-organic-and-natural-farming/
Alan Morgan. “Soil Microbes and Emissions Reveal a Clear Divide Between Conventional, Organic, and Natural Farming.” Scienmag, 27 September 2026, https://scienmag.com/soil-microbes-and-emissions-reveal-a-clear-divide-between-conventional-organic-and-natural-farming/. Accessed 27 September 2026.
Alan Morgan. “Soil Microbes and Emissions Reveal a Clear Divide Between Conventional, Organic, and Natural Farming.” Scienmag. September 27, 2026. https://scienmag.com/soil-microbes-and-emissions-reveal-a-clear-divide-between-conventional-organic-and-natural-farming/
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Tags: agricultural research on soil microbesBibliometric analysiscarbon sequestrationcomparison of farming methods and environmental outcomesconventional farmingconventional farming environmental impactcrop cultivation and greenhouse gasesfarming system effects on soil microbiotaglobal agricultural practices and emissionsgreenhouse gas emissionsgreenhouse gas emissions in agriculturemethanenatural farmingnatural farming practices and sustainabilitynitrous oxideorganic farmingorganic farming soil healthsoil healthsoil microbial communitiessoil microbiology and climate changesoil microbiomesustainable agriculturesustainable agriculture and microbial diversityVOSviewer
