Abstract
Climate-driven shifts in seasonal frost patterns raise important questions about their impact on food quality and resilience. Here, we show that a single 12-h frost event at harvest can enhance both the microbial and nutritional properties of fermented cabbage and carrots, two cold-tolerant crops widely grown in the U.S. Northeast. Using microbial amplicon and metagenomic sequencing, we found that frost exposure led to subtle but consistent changes in microbial composition, including greater abundance of cold-adapted taxa such as Leuconostoc and Debaryomyces. These changes corresponded to increased abundance of genes involved in vitamin biosynthesis, particularly menaquinone (K₂), cobalamin (B₁₂), and threonine pathways. Nutritional assays confirmed higher concentrations of vitamins A and E in frost-conditioned carrot ferments and increased vitamin K₁ in cabbage. Our findings suggest that exposure to seasonal frost can enhance the health-promoting and sensory qualities of fermented vegetables, offering a novel strategy for value-added, climate-resilient food production in temperate regions.
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Data availability
Raw data (i.e., fastq files) of “16S rRNA” and “ITS” amplicon sequencing and whole-genome sequencing are available on the NCBI’s SRA database using accession number PRJNA1281670. Other data and R scripts for data analysis are included as supplementary materials.
References
Gliessman, S. R. Agroecology: The Ecology of Sustainable Food Systems (CRC Press, 2021).
Duffy, M. Economies of size in production agriculture. J. Hunger Environ. Nutr. 4, 375–392 (2009).
Muna, A. F. The global food crisis: How geopolitical conflicts and climate change are disrupting food security. Preprint at https://doi.org/10.13140/RG.2.2.33878.66889 (2024).
Cicarelli, S., Parera, P. & Wong, E. “Climate change, geopolitics and food security: Event summary” (Center for Climate Security, 2024). https://councilonstrategicrisks.org/wp-content/uploads/2024/01/FR-CCGeopolitics.pdf/.
Beyer, R. M., Hua, F., Martin, P. A., Manica, A. & Rademacher, T. Relocating croplands could drastically reduce the environmental impacts of global food production. Commun. Earth Environ. 3, 1–11 (2022).
Sala, O. E. et al. Global biodiversity scenarios for the year 2100. Science 287, 1770–1774 (2000).
Dudley, N. & Alexander, S. Agriculture and biodiversity: a review. Biodiversity 18, 45–49 (2017).
Crippa, M. et al. Food systems are responsible for a third of global anthropogenic GHG emissions. Nat. Food 2, 198–209 (2021).
California Department of Water Resources. Agricultural Water Use Efficiency. State of California (2025). Available at: https://water.ca.gov/Programs/Water-Use-And-Efficiency/Agricultural-Water-Use-Efficiency.
Visser, M. A., Kumetat, G. & Scott, G. Drought, water management, and agricultural livelihoods: Understanding human-ecological system management and livelihood strategies of farmer’s in rural California. J. Rural Stud. 109, 103339 (2024).
Medellín-Azuara, J., Escriva-Bou, A., Gaudin, A. C. M., Schwabe, K. A. & Sumner, D. A. Cultivating climate resilience in California agriculture: adaptations to an increasingly volatile water future. Proc. Natl. Acad. Sci. USA. 121, e2310079121 (2024)..
USDA/NASS. 2024 State Agriculture Overview for California. USDA National Agriculture Statistics Services (2024).
Edwards, D., Batley, J., Parkin, I. & Kole, C. Genetics, Genomics and Breeding of Oilseed Brassicas (Genetics, Genomics and Breeding of Crop Plants) (CRC Press, 2011).
Iorizzo, M. et al. Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae). Am. J. Bot. 100, 930–938 (2013).
Daugovish, O. et al. Cabbage Production in California. University of California Agriculture and Natural Resources, https://anrcatalog.ucanr.edu/pdf/7208.pdf (2008).
Doulis, M., Stouffer, J., Simons, J. & Arzoumanian, M. A Profile of Agriculture in New York State. Office of the New York State Comptroller, https://www.osc.ny.gov/files/reports/pdf/profile-of-agriculture-in-nys.pdf (2024).
Land Degradation. https://www.ipcc.ch/srccl/chapter/chapter-4/.
Belete, T. & Yadete, E. Effect of mono cropping on soil health and fertility management for sustainable agriculture practices: a review. J. Plant Sci. https://doi.org/10.11648/j.jps.20231106.13 (2023).
Kopittke, P. M. et al. Soil is a major contributor to global greenhouse gas emissions and climate change. Soil 10, 873–885 (2024).
Menegat, S., Ledo, A. & Tirado, R. Greenhouse gas emissions from global production and use of nitrogen synthetic fertilisers in agriculture. Sci. Rep. 12, 14490 (2022).
Vega, A. J., Rohli, R. V. & Wright, E. Changes in growing season in the Northeastern United States. Phys. Geogr. 41, 343–364 (2020).
Wolfe, D. W. et al. Unique challenges and opportunities for northeastern US crop production in a changing climate. Clim. Chang. 146, 231–245 (2018).
Wu, S. et al. Rapid flips between warm and cold extremes in a warming world. Nat. Commun. 16, 3543 (2025).
Soualiou, S., Duan, F., Li, X. & Zhou, W. Crop production under cold stress: an understanding of plant responses, acclimation processes, and management strategies. Plant Physiol. Biochem. 190, 47–61 (2022).
Lindow, S. E., Arny, D. C. & Upper, C. D. Bacterial ice nucleation: a factor in frost injury to plants. Plant Physiol. 70, 1084–1089 (1982).
Evans, W. B. Season Extension in Organic Systems. In Sustainable Development and Biodiversity 293–314 (Springer International Publishing, 2016).
Badji, A., Benseddik, A., Bensaha, H., Boukhelifa, A. & Hasrane, I. Design, technology, and management of greenhouse: a review. J. Clean. Prod. 373, 133753 (2022).
Lamont, W. J. Overview of the use of high tunnels worldwide. Horttechnology 19, 25–29 (2009).
Janke, R. R., Altamimi, M. E. & Khan, M. The use of high tunnels to produce fruit and vegetable crops in North America. Agric. Sci. 08, 692–715 (2017).
Thivierge, M.-N. et al. Perennial forages in cold-humid areas: adaptation and resilience-building strategies toward climate change. Agron. J. https://doi.org/10.1002/agj2.21354 (2023).
Kistner, E., Kellner, O., Andresen, J., Todey, D. & Morton, L. W. Vulnerability of specialty crops to short-term climatic variability and adaptation strategies in the Midwestern USA. Clim. Chang. 146, 145–158 (2018).
Suojala, T. Variation in sugar content and composition of carrot storage roots at harvest and during storage. Sci. Hortic. 85, 1–19 (2000).
Gómez Galindo, F. et al. On the induction of cold acclimation in carrots (Daucus carota L.) and its influence on storage performance. Food Res. Int. 38, 29–36 (2005).
Ljubej, V. et al. Chilling and freezing temperature stress differently influence glucosinolates content in Brassica oleracea var. acephala. Plants 10, 1305 (2021).
Market.us. Global fermented foods market size, share and business benefits (Report ID: 144151). Market.us https://market.us/report/fermented-foods-market/ (2025).
Peraza, R. & Perron, G. G. Investigating the microbial terroir of fermented foods produced in a professional kitchen. Int. J. Gastron. Food Sci. 28, 100509 (2022).
Redzepi, R. & Zilber, D. The Noma Guide to Fermentation (Foundations of Flavor). (Artisan, 2018).
Zheng, J. et al. A taxonomic note on the genus Lactobacillus: description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int. J. Syst. Evol. Microbiol. 70, 2782–2858 (2020).
Jung, J. Y., Lee, S. H. & Jeon, C. O. Kimchi microflora: history, current status, and perspectives for industrial kimchi production. Appl. Microbiol. Biotechnol. 98, 2385–2393 (2014).
Liu, A. et al. Use of psychrotolerant lactic acid bacteria (Lactobacillus spp. and Leuconostoc spp.) isolated from Chinese traditional Paocai for the quality improvement of Paocai products. J. Agric. Food Chem. 65, 2580–2587 (2017).
Lee, K. W. et al. Isolation and characterization of kimchi starters Leuconostoc mesenteroides PBio03 and Leuconostoc mesenteroides PBio104 for manufacture of commercial kimchi. J. Microbiol. Biotechnol. 30, 1060–1066 (2020).
Li, L., Yan, Y., Ding, W., Gong, J. & Xiao, G. Improvement in the Quality of Kimchi by Fermentation with Leuconostoc mesenteroides ATCC 8293 as Starter Culture. Microbiol. Biotechnol. Lett. 48, 533–538 (2020).
Fusco, V. et al. Opportunistic foodborne pathogens. In Food Safety and Preservation (eds Grumezescu, A. M. & Holban, A. M.) 269–306 (Elsevier, 2018).
Birmeta, G., Bakeeva, A. & Passoth, V. Yeasts and bacteria associated with kocho, an Ethiopian fermented food produced from enset (Ensete ventricosum). Antonie Van. Leeuwenhoek 112, 651–659 (2019).
Sugimori, D., Watanabe, M. & Utsue, T. Isolation and lipid degradation profile of Raoultella planticola strain 232-2 capable of efficiently catabolizing edible oils under acidic conditions. Appl. Microbiol. Biotechnol. 97, 871–880 (2013).
Keuth, S. & Bisping, B. Vitamin B12 production by Citrobacter freundii or Klebsiella pneumoniae during tempeh fermentation and proof of enterotoxin absence by PCR. Appl. Environ. Microbiol. 60, 1495–1499 (1994).
DeMilo, A. B., Lee, C.-J., Moreno, D. S. & Martinez, A. J. Identification of volatiles derived from Citrobacter freundii fermentation of a trypticase soy broth. J. Agric. Food Chem. 44, 607–612 (1996).
Raposo, A., Pérez, E., de Faria, C. T., Ferrús, M. A. & Carrascosa, C. Food spoilage by Pseudomonasspp.—an overview. in Foodborne Pathogens and Antibiotic Resistance 41–71 (John Wiley & Sons, Inc., 2017).
Bloomfield, S. J., Palau, R., Holden, E. R., Webber, M. A. & Mather, A. E. Genomic characterization of Pseudomonas spp. on food: implications for spoilage, antimicrobial resistance and human infection. BMC Microbiol. 24, 20 (2024).
Walterson, A. M. & Stavrinides, J. Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae. FEMS Microbiol. Rev. 39, 968–984 (2015).
Tucker, W. G. Freezing injury in carrots. J. Hortic. Sci. 49, 29–35 (1974).
Kidmose, U. & Martens, H. J. Changes in texture, microstructure and nutritional quality of carrot slices during blanching and freezing. J. Sci. Food Agric. 79, 1747–1753 (1999).
Aggarwal, M. & Mondal, A. K. Debaryomyces hansenii: an osmotolerant and halotolerant yeast. In Yeast Biotechnology: Diversity and Applications 65–84 (Springer Netherlands, 2009).
Breuer, U. & Harms, H. Debaryomyces hansenii-an extremophilic yeast with biotechnological potential. Yeast 23, 415–437 (2006).
Zhao, C. J., Schieber, A. & Gänzle, M. G. Formation of taste-active amino acids, amino acid derivatives and peptides in food fermentations—a review. Food Res. Int. 89, 39–47 (2016).
Fang, H., Kang, J. & Zhang, D. Microbial production of vitamin B12: a review and future perspectives. Microb. Cell Fact. 16, 15 (2017).
Walther, B., Karl, J. P., Booth, S. L. & Boyaval, P. Menaquinones, bacteria, and the food supply: The relevance of dairy and fermented food products to vitamin K requirements. Adv. Nutr. 4, 463–473 (2013).
da Silva Dias, J. C. Nutritional and health benefits of carrots and their seed extracts. Food Nutr. Sci. 05, 2147–2156 (2014).
Moreb, N., Murphy, A., Jaiswal, S. & Jaiswal, A. K. Cabbage. in Nutritional Composition and Antioxidant Properties of Fruits and Vegetables 33–54 (Elsevier, 2020).
Hrncirik, K. Stability of fat-soluble vitamins and PUFA in simulated shallow-frying. Lipid Technol. 22, 107–109 (2010).
Reddy, M. B. & Love, M. The impact of food processing on the nutritional quality of vitamins and minerals. Adv. Exp. Med. Biol. 459, 99–106 (1999).
Berry Ottaway, P. Stability of vitamins during food processing and storage. In Chemical Deterioration and Physical Instability of Food and Beverages (eds Skibsted, L. H., Risbo, J. & Andersen, M. L.) 539–560 (Elsevier, 2010).
Lim, S.-D., Kim, K.-S. & Do, J.-R. Physiological characteristics and production of vitamin K2by Lactobacillus fermentum LC272 isolated from raw milk. Korean J. Food Sci. Anim. Resour. 31, 513–520 (2011).
Fulton, J., Norton, M. & Shilling, F. Water-indexed benefits and impacts of California almonds. Ecol. Indic. 96, 711–717 (2019).
Le Gall, H. et al. Cell wall metabolism in response to abiotic stress. Plants 4, 112–166 (2015).
Sharma, V., Hudspeth, M. E. & Meganathan, R. Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menE gene from Escherichia coli. Gene 168, 43–48 (1996).
Liu, Y. et al. Physiological roles of short-chain and long-chain menaquinones (Vitamin K2) in Lactococcus cremoris.Front. Microbiol 13, 823623 (2022).
Slager, J., Kjos, M., Attaiech, L. & Veening, J.-W. Antibiotic-induced replication stress triggers bacterial competence by increasing gene dosage near the origin. Cell 157, 395–406 (2014).
Hanselman, E. & Breslin, P. The taste of fermentation: propionic acid is judged more pleasant than other short chain fatty acids. Curr. Dev. Nutr. 5, 585 (2021).
Hosseini, E., Grootaert, C., Verstraete, W. & Van de Wiele, T. Propionate as a health-promoting microbial metabolite in the human gut. Nutr. Rev. 69, 245–258 (2011).
Mann, E. R., Lam, Y. K. & Uhlig, H. H. Short-chain fatty acids: linking diet, the microbiome and immunity. Nat. Rev. Immunol. 24, 577–595 (2024).
Walther, B. & Schmid, A. Effect of fermentation on vitamin content in food. in Fermented Foods in Health and Disease Prevention (eds Frias, J., Martinez-Villaluenga, C. & Peñas, E.) 131–157 (Elsevier, 2017).
Piñeiro, V. et al. A scoping review on incentives for adoption of sustainable agricultural practices and their outcomes. Nat. Sustain. 3, 809–820 (2020).
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).
White, T. J., Bruns, T., Lee, S. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols 315–322 (Elsevier, 1990).
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–6 (2013).
Glöckner, F. O. et al. 25 years of serving the community with ribosomal RNA gene reference databases and tools. J. Biotechnol. 261, 169–176 (2017).
Abarenkov, K. et al. UNITE general FASTA release for Fungi. UNITE Community https://doi.org/10.15156/BIO/2959332 (2024).
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Pielou, E. C. The measurement of diversity in different types of biological collections. J. Theor. Biol. 13, 131–144 (1966).
Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228–8235 (2005).
Oksanen, J. et al. Vegan: community ecology package. CRAN: Contributed Packages The R Foundation https://doi.org/10.32614/cran.package.vegan (2001).
Wickham, H. et al. Ggplot2: create elegant data visualisations using the grammar of graphics. CRAN: Contributed Packages The R Foundation https://doi.org/10.32614/cran.package.ggplot2 (2007).
Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC Genom. 9, 75 (2008).
Overbeek, R. et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691–5702 (2005).
Acknowledgements
This work was funded in part by the Stone Barns Center for Food and Agriculture (Pocantico Hills, NY, USA) and the Office of Undergraduate Research and the Bard Summer Research Institute of Bard College (Annandale-on-Hudson, NY, USA). This work was also supported in part through the NYU IT High Performance Computing resources, services, and staff expertise (New York, NY, USA). The authors would like to thank Daniel Bartush and Shannon Ryan for their assistance in the fi eld and the lab, respectively, Susi Lu and Kamryn McKenna for their help with the vegetables illustrations in Fig. 1, as well as Ani Alpert and Pia Sörensen for their comments and suggestions on the manuscript.
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The study was designed by A.L., J.G., D.B., S.J., and G.G.P. A.L. and J.G. collected samples. S.J. and G.G.P. processed samples and analyzed data. A.L., J.G., S.J., and G.G.P. wrote the manuscript. S.J. and G.G.P. made final revisions on the manuscript.
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The authors declare that they have no conflicts of interest. J.G., farm manager at Stone Barns Center for Food and Agriculture, as well as A.L. and D.B., both associated with the same center, are involved in the sale of farm products; however, this is not a primary objective of the organization. All authors, including corresponding author G.G.P., were free to write and conclude the paper independently, without influence from any of the organizations involved.
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Luzmore, A., Grauer, J., Barber, D. et al. Seasonal frost improves probiotic and nutrient availability in fermented vegetables. npj Sci Food (2026). https://doi.org/10.1038/s41538-026-00776-w
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DOI: https://doi.org/10.1038/s41538-026-00776-w
