Rhizomicrobiome Transplantation from Mediterranean Aromatic Plants Differentially Shape Lettuce Growth, Resource Allocation, and Chemical Defense

Traditional holobiont research has largely focused on bacterial taxonomy, often overlooking the functional diversity among strains within a taxon. Using a phenotype-first approach, we evaluated the responses of lettuce (Lactuca sativa L.) to culture-enriched rhizosphere microbial communities (transplanted inocula; RMs) derived from three stress-tolerant Mediterranean species: Juniperus phoenicea (JP), Rosmarinus officinalis (RO), and Pistacia lentiscus (PL). Responses were assessed by growth and physiological measurements together with untargeted LC–MS metabolomics on pooled leaf samples. The JP- and PL-derived RMs significantly increased average leaf mass, and all three produced healthy plant phenotypes, whereas only PL-RM significantly enhanced aboveground biomass, with higher leaf mass per area and maintained photosystem II quantum yield despite lower stomatal conductance. Metabolomic analysis revealed a consistent decrease in phenylpropanoids and resistance-associated alkaloids across all inoculated plants, consistent with a shift between primary and defense-related metabolism; PL-RM specifically promoted protective flavonoids, apocarotenoids, and tryptophan-derived alkaloids, whereas JP-RM and RO-RM reduced primary carbohydrates without increasing biomass, possibly reflecting altered carbon allocation. Overall, the three inocula, each from a single donor community, elicited distinct physiological and metabolic responses. By linking plant phenotypes to microbiome-induced metabolic shifts, this host-centered framework offers a scalable strategy for comparing microbiomes and selecting those suited to a given research objective.