Investigation of Microbial Consortia: From Fundamental to Applied Results, From Established to Novel Production Systems

Soil microbiology has long been a rich source of novel scientific discoveries and continues to be a key contributor to industrial applications. In this regard, fungi have played multifaceted roles, from promoting plant growth to serving as prolific producers of antimicrobial compounds. Despite significant advances, the full potential of fungal–plant interactions remains underexplored, particularly in the case of the aromatic and medicinal plants such as Lavandula, and the microfungal communities associated with its root system. In this work, we demonstrated that the characterization of microfungal community in association with Lavandula led not only to taxonomical advancements by expanding established fungal phylogenies, but also to the discovery and characterization of novel antimicrobial compounds such as antifungal proteins (AFPs). A comprehensive methodological pipeline was employed, beginning with fungal isolation, morpho-molecular species-level identification, biodiversity assessment, and taxonomic classification. These were followed by protein production and purification, biochemical and structural characterization, and genome engineering techniques. This integrative framework enabled the translation of basic mycological discoveries into biotechnologically relevant results. Ecological analyses revealed that climate ecosystems, rather than plant species identity, were the predominant determinants affecting microfungal community composition. Lavander-associated fungal communities displayed strong site-specific variability, with alpha diversity gradually declining from Mediterranean to continental climates while beta diversity revealed complex patterns influenced by agricultural practices, highlighting the need for further research to harness their ecological and agricultural potential. Additionally, two novel fungal species belonging to the genera Rasamsonia and Talaromyces were identified and described for the first time. While the thermophilic Rasamsonia lemurum shares the genus' typical heat tolerance but exhibits rare globose conidia, Talaromyces montemartinii displays unusual thermotolerance and reduced sporulation, together highlighting how thermal adaptation and morphological divergence shape fungal biodiversity. Moreover, we reported the identification, production, and functional characterization of AfAfpC, a novel AFP from the Lavandula soil isolate Aspergillus fischeri. AfAfpC exhibited moderate-to-strong inhibitory activity against filamentous fungi, despite its near-neutral isoelectric point. CRISPR-Cas9-mediated deletion of the afafpC gene revealed that it is dispensable for growth and development. These findings enhance our understanding of AFP diversity and establish A. fischeri as a promising platform for the development of sustainable antifungal applications. Finally, the incorporation of the developed know-how was designed and started to be implemented in an innovative project uniting aquaculture systems with Artificial Intelligence. Potential future research directions might see other, novel species descriptions deriving from similar working guidelines, as well as new antimicrobial compounds discovered and investigated in their biotechnological potential.