Exploring the Cultivable Fraction of the Bacterial Microbiome from Tomato Plants for Growth-Promoting and Biocontrol Traits Toward Bioinput Development

Plant growth-promoting bacteria (PGPB) represent a sustainable alternative to synthetic inputs in horticultural systems; however, their bioprospecting is hindered by the absence of integrative, performance-oriented selection strategies. In this study, a comprehensive collection of 259 bacterial isolates associated with tomato plants was systematically screened to identify strains with biocontrol and plant growth-promoting potential. Isolates were characterized in vitro for potential plant colonization ability, antifungal activity, and multiple plant growth-promoting mechanisms. These traits were integrated into composite indices and analyzed using multivariate approaches to guide the selection of promising isolates. Selected candidates were subsequently evaluated in vivo for biocontrol and plant growth at both seedling and productive stages, and most isolates exhibited consistent effects. Isolates from the genera Stenotrophomonas, Pseudomonas, and Bacillus reduced fungal disease incidence to 2–9% (control disease: 80%). A Bacillus isolate increased seedling biomass by 54% in lettuce and 38% in tomato. Under productive conditions, lettuce marketable weight increased by 21–37%, whereas tomato yield showed positive but non-significant increases (~21–25%) after inoculation with Pseudomonas or Bacillus isolates. Overall, this work provides a structured framework for PGPB bioprospecting and validation, combining laboratory screening, composite indices, multivariate analyses, and multi-stage in vivo assays under realistic horticultural conditions.