LABs Fermentation Side-Product Positively Influences Rhizosphere and Plant Growth in Greenhouse Lettuce and Tomatoes

New agronomical policies aim to achieve greener agricultural systems, sustainable fertilizers and fungicides, a reduction in Greenhouse gases (GHG), and an increase in circular economic models. In this context, new solutions are needed for the market, but it is necessary to carefully assess both their efficacy and their ecological impact. Previously, we reported the biostimulatory activity on soil microbiome for a side-product from Lactic Acid Bacteria (LABs) fermentation: a concentrated post-centrifugation eluate. In the present study, we investigated whether this solution could partially substitute mineral N (N70% + N30% from eluate) in a fertigation (N100% vs. N70%) regime for tomato and lettuce under greenhouse conditions. The impact of the application was investigated through plant physiological parameters (number and weight of ripened fruits, shoots, and roots biomass) and biodiversity of the rhizosphere microbial composition of bacteria and fungi (High-Throughput Sequencing—HTS). The eluate (i) enhanced the plant canopy in lettuce; (ii) increased the shoot/root biomass ratio in both tomato and lettuce; and (iii) increased the harvest and delayed fruit ripening in tomato. Moreover, we found a strong correlation between the eluate and the enrichment for OTUs of plant-growth-promoting microbes (PGPMs) such as <i>Sphingomonas sediminicola</i>, <i>Knoellia subterranean</i>, and <i>Funneliformis mosseae</i>. These findings suggest that integrating the eluate was beneficial for the plant growth, performance, and yield in both tomato and lettuce, and additionally, it enriched specialized functional microbial communities in the rhizosphere. Further studies will investigate the underlying mechanisms regulating the selective activity of the eluate toward PGPMs and its biostimulatory activity towards target crops.