Abundance, diversity and metabolomic profiles of soil cyanobacteria-dominated microbial communities under long-term differential management in an olive orchard.

This study assessed the effects of 22 years of sustainable (Smng) versus conventional (Cmng) management on cyanobacteria-enriched microbial communities in a Mediterranean olive orchard. Surface soils were selectively cultivated in nitrogen-free Bristol medium to obtain cultivable cyanobacteria-dominated, nitrogen-fixing assemblages for molecular and metabolomic analyses. Cyanobacteria-enriched assemblages derived from Smng soils showed greater phylogenetic diversity and distinct community clustering under N-free cultivation conditions. At the cyanobacterial genus level, Cmng-derived communities were dominated by Leptolyngbya, whereas Smng assemblages shifted towards Nodosilinea, alongside the consistent presence of heterocystous Nostoc. These patterns suggest that reduced disturbance and organic inputs favour the enrichment of stable cultivable nitrogen-fixing cyanobacteria. Untargeted metabolomics identified 494 features and revealed strong functional divergence. Cmng-derived assemblages showed enhanced lipid and vitamin biosynthesis, consistent with stress-related metabolic investment. In contrast, Smng-derived assemblages displayed increased amino acid biosynthesis and enhanced activity of signalling- and hormone-related metabolic pathways, including cytokinin biosynthesis and ethylene biosynthesis-related pathways. These metabolic signatures suggest a shift towards resource allocation supporting microbial interactions, plant signalling and nitrogen transfer within the soil–plant system. Overall, the results indicate that Smng favours cyanobacteria-dominated communities with metabolic traits linked to ecosystem functioning, underscoring their role in improving soil quality and resilience in semi-arid agroecosystems.