Decoupling Microbial Activity from Metabolite Action: A Comparative Assessment of EM Technology and Its Cell-Free Extract as Nature-Based Solutions for Plant Biostimulation

Soil degradation and climate-driven stress increasingly compromise crop performance by disrupting microbial communities and weakening soil biological functions. Microbial consortia such as Effective Microorganisms (EM) are widely adopted as nature-based solutions to enhance soil health and plant productivity, yet it remains unclear whether their biostimulant effects arise primarily from microbial activity or from the metabolites they release. This study aimed to disentangle these contributions by comparing the effects of EM and its cell-free extract (EM Extract) on zucchini (Cucurbita pepo L.), grown under controlled conditions. Growth parameters and pigment composition were quantified through morphological and spectrophotometric analyses, while soil microbial communities and metabolic profiles were characterized using metabarcoding and high-resolution FTIR-based soil metabolomics. Both EM and EM-derived cell-free extracts significantly enhanced zucchini growth, increasing plant height, biomass, chlorophyll content and root development. Cultural-based microbial analyses showed complementary shifts in rhizosphere communities, yet no major taxonomic differences were detected. Consistently, both treatments induced similar metabolomic changes in bulk and rhizosphere soils, resulting in a shared functional state shaped by plant inputs. These results suggest EM extract as a stable and effective alternative to live microbial inoculants for sustainable crop bio stimulation.