From diversity to dominance: how salt and CO₂ shape LAB-dominated ecosystems in vegetable fermentations.

UNLABELLED: Research on microbial ecosystems is often challenging due to the high diversity of microbial taxa present and the complexity of controlling environmental variables. Fermented foods offer simpler and more reproducible model ecosystems in which both community composition and environmental factors can be more precisely controlled and manipulated. In this study, we focused on fermented vegetables, which are typically dominated by lactic acid bacteria (LAB). However, it remains unclear why LAB consistently drive the spontaneous fermentation of vegetables and how factors such as vegetable substrates, salt addition, and carbon dioxide levels shape microbial community dynamics. We characterized the temporal microbial succession in standardized spontaneous fermentations of 11 different vegetables (including beetroot, bell pepper, cabbage, carrot, cucumber, fennel, green asparagus, leek, parsnip, sunroot, and tomato), revealing a robust and recurrent dominance of Leuconostoc and other LAB across substrates. Additionally, we investigated the impact of varying salt concentrations and found that lower salt levels delayed the establishment of the typically LAB-dominated community, while promoting a higher abundance of Weissella and multiple Enterobacterales taxa. Notably, these salt reduction-induced effects were mitigated by CO2 injection, which reduced Enterobacterales levels and increased the overall abundance of Lactobacillales. Together, these findings demonstrate how targeted manipulation of environmental parameters, such as salinity and gas composition, can be used to uncover ecological principles governing microbial succession and community assembly in reproducible fermentation-based model ecosystems.

IMPORTANCE: Understanding the ecological principles that shape microbial community assembly is essential for advancing our knowledge of microbial ecosystems. Fermented vegetables, which are increasingly popular among the general population, provide a tractable and reproducible model system to study microbial succession. By systematically manipulating variables such as vegetable substrate, salinity, and gas composition, we identified the effects of these factors on microbial dynamics throughout the fermentation. These insights not only enhance our understanding of the microbial ecology of these man-made food systems but also suggest directions for novel strategies to optimize fermentation processes for the production of faster, safer, and more flavorful foods.