Algal-derived extracts act as selective ecological filters shaping soil microbiomes, bacterial traits, and tomato performance under biotic stress

Modern agriculture faces the dual challenge of increasing food production while reducing reliance on synthetic inputs that degrade soil ecosystems and compromise long-term sustainability. Algal biomasses have emerged as promising biostimulants, yet their capacity to selectively modulate soil microbiomes and plant growth-promoting bacterial (PGPB) functions remains poorly understood. Here, we evaluated 17 phylogenetically and biochemically diverse macro- and microalgal extracts to determine their effects on soil microbial communities, bacterial functional traits, and tomato (Solanum lycopersicum) performance. Algal supplementation selectively restructured microbial communities without disrupting overall diversity, promoting taxa associated with plant-beneficial functions, including Bacillus, Pseudomonas, and Actinobacteria. In soil microcosms, specific treatments increased culturable bacterial abundance by up to [~]200-fold relative to the initial soil. Functional assays revealed strong extract- and strain-dependent responses. Siderophore production and ACC-associated activity were the most consistently stimulated traits, whereas auxin production, biofilm formation, and proline synthesis showed more variable or context-dependent responses. Notably, Ulva sp. (AP11.2) enhanced siderophore production across the majority of isolates, with over four-fold increases in individual strains, while Arthrospira-derived extracts (NG4.1, N14.1) consistently promoted bacterial growth across multiple taxa. In contrast, extracts such as Nannochloropsis sp. (NG6.1) and Tetraselmis sp. (NG5.1) induced more selective or inhibitory responses, highlighting extract-dependent functional trade-offs. Integration of biochemical and biological datasets identified fatty acid composition as a key axis associated with microbial functional responses, whereas volatile organic compound profiles showed weaker and less consistent associations. These microbiome and functional shifts translated into improved plant performance, with algal treatments increasing tomato growth and reducing mortality by approximately 20% under non-sterile soil conditions characterized by pathogen-associated pressure. Together, these findings demonstrate that algal extracts act as selective modulators of soil microbiomes, enhancing specific bacterial functions and improving plant performance in a context-dependent manner. This work provides a mechanistic framework for the development of targeted algal-based biostimulants aimed at reducing agrochemical inputs and advancing microbiome-informed agriculture.