Transcriptomic and metabolomic profiling reveals early responses of tomato plants elicited by compost-derived bacteria

Compost produced from biowaste has a defined microbiota, and some bacterial species may represent promising resources for low-input crop systems. However, their effects on plant physiology are poorly investigated and remain difficult to predict from standard bacterial traits alone. We isolated several bacterial strains (Bacillus sonorensis, Glutamicibacter arilaitensis, and Kocuria rhizophila) from biowaste compost and examined their early effects on tomato seedlings under controlled in vitro conditions. Responses were assessed by root phenotyping, root and shoot transcriptomics, and mass spectrometry-based profiling of primary metabolites in plant tissues, root exudates and bacterial culture filtrates. B. sonorensis induces the broadest response, reducing primary root length and lateral root number and density and triggering broad transcriptional changes related to metabolism, redox balance, hormone signalling and defence-associated pathways. G. arilaitensis elicits a more selective, tissue-dependent response, whereas K. rhizophila has limited phenotypic and transcriptional effects at this stage. All isolates reshape primary metabolism, with recurrent effects on amino acid-, carbohydrate- and lipid-related pathways, together with isolate-specific changes in root exudate composition. This study characterises the early molecular and metabolic responses of tomato to compost-derived bacteria and identifies common and strain-specific physiological signatures that provide a foundation for future studies under biotic and abiotic stress.