Abstract
Vegetable fermentation represents a globally ubiquitous yet overlooked source of greenhouse gas (GHG) emissions. This study quantified GHG fluxes and integrated 16S rRNA sequencing to elucidate the potential microbial mechanisms using a 90-day cabbage fermentation model. High-salt conditions enhanced cumulative CO₂ emissions 2.1-fold relative to the low-salt treatment. This amplification was driven by salt-induced osmotic dehydration accelerating dissolved organic carbon release from vegetable tissues, which likely fueled heterofermentative guilds (e.g., Leuconostoc) and resulted in elevated CO₂ production. Conversely, low-to-medium salt concentrations favored N₂O generation via nitrification and denitrification by salt-sensitive Proteobacteria (e.g., Enterobacter), whereas high salinity shifted nitrogen flux toward dissimilatory nitrate reduction to ammonium (DNRA), thereby minimizing gaseous losses. Globally, vegetable fermentation is estimated to contribute between 16,483 and 56,872 tonnes of CO₂-equivalent annually. These findings establish vegetable fermentation as an important GHG source, offering new insights for mitigating the food industry’s environmental footprint.
Similar content being viewed by others
Carbon footprint of food production: a systematic review and meta-analysis
Changes in global food consumption increase GHG emissions despite efficiency gains along global supply chains
Integrating degrowth and efficiency perspectives enables an emission-neutral food system by 2100
Data availability
The raw 16S rRNA gene sequencing data generated in this study have been deposited in the NCBI Sequence Read Archive (SRA) under accession number SRP648168. The raw abundance data corresponding to Fig. 6 are provided in Table S8. All other data supporting the findings of this study are available from the corresponding author upon reasonable request.
References
Torres, S., Verón, H., Contreras, L. & Isla, M. I. An overview of plant-autochthonous microorganisms and fermented vegetable foods. Food Sci. Hum. Well. 9, 112–123 (2020).
Tamang, J. P. et al. Fermented foods in a global age: East meets West. Compr. Rev. Food Sci. F. 19, 184–217 (2020).
Yu, Y. et al. Isolation of lactic acid bacteria from Chinese pickle and evaluation of fermentation characteristics. LWT 180, 114627 (2023).
Mi, T. et al. Effects of salt concentration on the quality and microbial diversity of spontaneously fermented radish paocai. Food Res. Int. 160, 111622 (2022).
Li, Y. et al. Fermentation modeling and machine learning for flavor prediction in low-sodium radish paocai with potassium chloride substitution. npj Sci. Food 9, 156 (2025).
Wang, G. & Wu, X. Research on the development of Qiandongnan-flavor pickles. Rural Pract. Technol. 9, 115–116 (2020).
Kim, S. H. et al. Lactic acid bacteria directly degrade N-nitrosodimethylamine and increase the nitrite-scavenging ability in kimchi. Food Control 71, 101–109 (2017).
Cole, J. J. et al. Plumbing the global carbon cycle: integrating inland waters into the terrestrial carbon budget. Ecosystems 10, 172–185 (2007).
Dinsmore, K. J. et al. Role of the aquatic pathway in the carbon and greenhouse gas budgets of a peatland catchment. Glob. Chang. Biol. 16, 2750–2762 (2010).
Liu, L. et al. Residual nitrite and biogenic amines of traditional northeast sauerkraut in China. Int. J. Food Prop. 20, 2448–2455 (2017).
Song, Q. et al. Metagenomic insights into Chinese northeast suancai: Predominance and diversity of genes associated with nitrogen metabolism in traditional household suancai fermentation. Food Res. Int. 139, 109924 (2021).
Kuypers, M. M., Marchant, H. K. & Kartal, B. The microbial nitrogen-cycling network. Nat. Rev. Microbiol. 16, 263–276 (2018).
Tang, J. et al. Effect of salt concentration on the quality and microbial community during pickled peppers fermentation. Food Chem. X 23, 101594 (2024).
Peng, X., Kelly, R. M. & Han, Y. Sequential processing with fermentative Caldicellulosiruptor kronotskyensis and chemolithoautotrophic Cupriavidus necator for converting rice straw and CO2 to polyhydroxybutyrate. Biotechnol. Bioeng. 115, 1624–1629 (2018).
Heyer, R. et al. Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter. Water Res. 250, 121020 (2024).
Chun, B. H. et al. Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation. Sci. Rep. 7, 11504 (2017).
Zhai, Y. & Pérez-Díaz, I. M. Contribution of Leuconostocaceae to CO2-mediated bloater defect in cucumber fermentation. Food Microbiol. 91, 103536 (2020).
Liang, H. et al. Bacterial profiles and volatile flavor compounds in commercial Suancai with varying salt concentration from Northeastern China. Food Res. Int. 137, 109384 (2020).
Lee, D. Y. et al. A comparative study of the physicochemical, microbial, and metabolic profiling of kimchi during long-term fermentation under varying salinity conditions. LWT 196, 115838 (2024).
Bautista-Gallego, J. et al. Salt reduction in vegetable fermentation: reality or desire? J. Food Sci. 78, R1095–R1100 (2013).
Zhao, C. C. et al. Kinetic study of mass transfer in different parts of Chinese cabbage during brining. J. Food Process Eng. 41, e12666 (2018).
Herman-Lara, E. et al. Mass transfer modeling of equilibrium and dynamic periods during osmotic dehydration of radish in NaCl solutions. Food Bioprod. Process 91, 216–224 (2013).
Chen, D. et al. Altering bacterial community: a possible way of lactic acid bacteria inoculants reducing CO2 production and nutrient loss during fermentation. Bioresour. Technol. 329, 124915 (2021).
Kandler, O. Carbohydrate metabolism in lactic acid bacteria. Anton. Leeuw. Int. J. G. 49, 209–224 (1983).
Bouwman, A. F. et al. Global trends and uncertainties in terrestrial denitrification and N2O emissions. Phil. Trans. R. Soc. 368, 20130112 (2013).
Lam, S. K., Suter, H., Mosier, A. R. & Chen, D. Using nitrification inhibitors to mitigate agricultural N2O emission: a double-edged sword?. Glob. Chang. Biol. 23, 485–489 (2017).
Ruser, R. & Schulz, R. The effect of nitrification inhibitors on the nitrous oxide (N2O) release from agricultural soils—a review. J. Plant Nutr. Soil Sci. 178, 171–188 (2015).
Zumft, W. G. Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61, 533–616 (1997).
Mpongwana, N. et al. Isolation of high-salinity-tolerant bacterial strains, Enterobacter sp., Serratia sp., and Yersinia sp., for nitrification and aerobic denitrification under cyanogenic conditions. Water Sci. Technol. 73, 2168–2175 (2016).
Zheng, H. Effects of salinity on nitrogen reduction pathways in estuarine wetland sediments. Mar. Pollut. Bull. 207, 116834 (2024).
Giblin, A. E. et al. The effects of salinity on nitrogen losses from an oligohaline estuarine sediment. Estuar. Coast. 33, 1054–1068 (2021).
Jia, M., Winkler, M. K. & Volcke, E. I. Elucidating the competition between heterotrophic denitrification and DNRA using the resource-ratio theory. Environ. Sci. Technol. 54, 13953–13962 (2020).
Lin, B. & Lei, X. Carbon emissions reduction in China’s food industry. Energy Policy 86, 483–492 (2015).
Boehm, R. et al. A comprehensive life cycle assessment of greenhouse gas emissions from US household food choices. Food Policy 79, 67–76 (2018).
Naresh Kumar, S. & Chakabarti, B. Energy and carbon footprint of food industry. in Energy Footprints of the Food and Textile Sectors. Environmental Footprints and Eco-design of Products and Processes (eds Muthu, S.) Springer 19–44 (Springer, 2019).
McGill, B. M., Hamilton, S. K., Millar, N. & Robertson, G. P. The greenhouse gas cost of agricultural intensification with groundwater irrigation in a Midwest US row cropping system. Glob. Chang. Biol. 24, 5948–5960 (2018).
Huo, P. & Gao, P. Degassing of greenhouse gases from groundwater under different irrigation methods: a neglected carbon source in agriculture. Agric. Water Manag. 301, 108941 (2024).
FAO. Agricultural Production Statistics 2010–2023 (FAO, 2024).
Toensmeier, E., Ferguson, R. & Mehra, M. 2020. Perennial vegetables: a neglected resource for biodiversity, carbon sequestration, and nutrition. PLoS ONE 15, e0234611 (2020).
Sharma, S. et al. Appraisal of carbon capture, storage, and utilization through fruit crops. Front. Environ. Sci. 9, 700768 (2021).
Garrido, A. et al. Fruit photosynthesis: more to know about where, how and why. Plants 12, 2393 (2023).
Liang, H. et al. Synergistic effects of carbon cycle metabolism and photosynthesis in Chinese cabbage under salt stress. Hortic. Plant J. 10, 461–472 (2024).
Huisingh, D. et al. Recent advances in carbon emissions reduction: policies, technologies, monitoring, assessment, and modeling. J. Clean. Prod. 103, 1–12 (2015).
IPCC. Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (eds Masson-Delmotte, V. et al.) 2391 https://doi.org/10.1017/9781009157896 (Cambridge University Press, 2021).
Fowler, D. et al. The global nitrogen cycle in the twenty-first century. Philos. Trans. R. Soc. B Biol. Sci. 368, 20130164 (2013).
Xu, J. et al. A review on fermented vegetables: microbial community and potential upgrading strategy via inoculated fermentation. Compr. Rev. Food Sci. Food Saf. 23, e13362 (2024).
Blandino, A. et al. Cereal-based fermented foods and beverages. Food Res. Int. 36, 527–543 (2003).
Auchtung, J. M., Hallen-Adams, H. E. & Hutkins, R. Microbial interactions and ecology in fermented food ecosystems. Nat. Rev. Microbiol. 23, 622–634 (2025).
De Laurentiis, V., Corrado, S. & Sala, S. Quantifying household waste of fresh fruit and vegetables in the EU. Waste Manage 77, 238–251 (2018).
Pérez-Marroquín, X. A. et al. Agro-food waste as an ingredient in functional beverage processing: sources, functionality, market and regulation. Foods 12, 1583 (2023).
Park, S. E. et al. Effects of different fermentation temperatures on metabolites of Kimchi. Food Biosci. 23, 100–106 (2018).
Kim, J. et al. Controlled fermentation of kimchi using naturally occurring antimicrobial agents. Food Microbiol. 32, 20–31 (2012).
Lee, J. et al. Unravelling the key factors for the dominance of Leuconostoc starters during kimchi fermentation. npj Sci. Food 9, 61 (2025).
Kang, B. K. et al. The influence of red pepper powder on the density of Weissella koreensis during kimchi fermentation. Sci. Rep. 5, 15445 (2015).
Huang, T. T., Wu, Z. Y. & Zhang, W. X. 2020. Effects of garlic addition on bacterial communities and the conversions of nitrate and nitrite in a simulated pickle fermentation system. Food Control 113, 107215 (2020).
Xu, J. et al. Mining of characteristic microbes and qualities in pickled and salted chili peppers through integrated analysis. npj Sci. Food 9, 77 (2025).
Xia, Y., Zhu, W., Su, Y. & Chen, Y. Novel insights into the quality changes and metabolite transfer rules of pickles during fermentation: Pickle versus pickle solution. Food Chem. X 25, 102203 (2025).
Moon, E. W., Yang, J. S., Yoon, S. R. & Ha, J. H. Application of colorimetric indicators to predict the fermentation stage of kimchi. J. Food Sci. 85, 4170–4179 (2020).
Zhao, Z. et al. Metabolites changes of a low-temperature and low-salt fermented Chinese kohlrabi during fermentation based on non-targeted metabolomic analysis. Front. Sustain. Food Syst. 7, 1156173 (2023).
Johnson, K. M., Hughes, J. E., Donaghay, P. L. & Sieburth, J. M. Bottle-calibration static head space method for the determination of methane dissolved in seawater. Anal. Chem. 62, 2408–2412 (1990).
Weiss, R. F. & Price, B. A. Nitrous oxide solubility in water and seawater. Mar. Chem. 8, 347–359 (1980).
National Food Safety Standard: Determination of Nitrite and Nitrate in Foods (China Standards Press, 2016).
Wood, W. W. & Hyndman, D. W. Groundwater depletion: a significant unreported source of atmospheric carbon dioxide. Earth Future 5, 1133–1135 (2017).
World Meteorological Organization. WMO Greenhouse Gas Bulletin (No. 21): The state of greenhouse gases in the atmosphere based on global observations through 2024. https://wmo.int/files/greenhouse-gas-bulletin-no-21 (2025).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272–1277 (2016).
Douglas, G. M. et al. PICRUSt2 for prediction of metagenome functions. Nat. Biotechnol. 38, 685–688 (2020).
Acknowledgements
This study was supported by the Department of Agriculture and Rural Affairs of Shaanxi Province (Grant No. S202101010). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Author information
Authors and Affiliations
Contributions
Pan Huo: Conceptualization, Data curation, Investigation, Visualization, Writing—original draft. Xinyu Zhang: Investigation, Data curation, Visualization. Chunyan Xu: Investigation, Data curation. Tianyi Han: Investigation. Pengcheng Gao: Conceptualization, Supervision, Writing – review & editing.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Supplementary Information (download DOCX )
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
Reprints and permissions
About this article
Cite this article
Huo, P., Zhang, X., Xu, C. et al. Vegetable fermentation as an overlooked source of greenhouse gases: from microbial mechanisms to global budget implications.
npj Sci Food (2026). https://doi.org/10.1038/s41538-026-00825-4
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41538-026-00825-4
Source: Ecology - nature.com
