Characterisation of Bacillus BacMix-Linked Metabolic Response in Strawberry and Descriptive Leaf Microbiome Signatures

Sustainable indoor growing management requires biological alternatives that protect against pathogens, preserve fruit quality and minimise chemical inputs in strawberries. We compared the impacts of a four-strain Bacillus consortium (BacMix) and chemical fungicides on two cultivars (cv. Elsanta and cv. Sonsation) by evaluating the metabolite outcomes—the free amino acids (FAAs) in the leaves and the sugars in the fruits. Furthermore, the descriptive shotgun metagenomics provides a functional context for these biochemical traits. The BacMix increased the total FAAs in the leaves and stabilised the fruit sugar profiles, maintaining moderate–high sucrose with controlled glucose and fructose. The chemically treated plants showed significant reductions in both FAAs and sugars. The metagenomic data showed BacMix-related shifts in the microbial functional potential in the leaves, but the biological agent did not affect diversity. An increased representation of genes involved in amino acid biosynthesis (aminoacyl tRNA pathway) and secondary metabolite biosynthesis was observed, along with changes in the relative CAZy signals. The direction of these metagenomic trends aligned with the metabolite outcomes, suggesting that BacMix influences the endophytic microbiome in a way that supports nitrogen-related metabolism and carbohydrate stability during the vegetation period. The cultivar-independent metabolic improvements emphasise the benefits of BacMix and highlight microbiome-based interventions as promising tools for sustainable, chemical-reduced strawberry production.