Plant species and field site shape root endosphere microbiomes of wild inoculum plants used in traditional cereal‐based fermentation

Societal Impact Statement Traditional fermented foods worldwide depend on naturally occurring microbes, yet the environmental sources shaping these microbes and their effects on food quality remain poorly understood. We investigated bacteria living inside the roots of wild plants used to produce Munkoyo, a widely consumed nonalcoholic fermented cereal beverage in Zambia, to determine how plant species and local growing conditions influence these microbial communities. We found that both plant species identity and soil environment shape the root microbes that seed fermentation. These findings can improve beverage quality, support the cultivation of threatened species, and promote sustainable access to ingredients, helping protect nutrition, livelihoods and cultural heritage. Summary Plants interact with diverse soil microbes through their roots, and these bacterial communities play vital roles in plant health and nutrient acquisition. In some traditional foods, root microbiomes of specific wild plant species act as natural starter cultures for fermentation. Yet, it remains unclear how distinct these root bacterial communities are among plant species and how much variation reflects plant identity versus growing environment. This study examined three wild plant species used as inoculum for producing Munkoyo, a traditional, nonalcoholic fermented cereal beverage in Zambia. Root endosphere, rhizosphere and bulk soil samples were collected from five districts, and bacterial communities were characterised using 16S rRNA gene amplicon sequencing. Bulk soil bacterial communities varied strongly across field sites and were structured by soil physicochemical properties, whereas root endosphere microbiomes were more distinct and differed among plant species and locations. The findings contribute to a better understanding of the bacterial communities involved in traditional fermented beverage production. They highlight the importance of plant species and soil environment in structuring root microbiomes, with implications for fermentation quality, sustainable cultivation of fermentation plants, and cultural heritage preservation.