Phenotypic and omics analyses of the Sordariomycetes <i>Marquandomyces marquandii</i> and <i>Albophoma yamanashiensis</i> isolated from estuarine sediments

Marine environments harbor a vast diversity of microorganisms, which have developed multiple strategies to adapt to challenging conditions and represent a valuable source for new products such as pigments, enzymes, and bioactive compounds. From all microorganisms inhabiting marine environments, fungi have been the least studied, despite their ubiquitous presence and great biotechnological potential. Here, we focused on the isolation and characterization of filamentous fungi from marine sediment samples, which were collected along the Basque coast in Spain. Through phenotypic characterization, we identified isolates potentially able to produce secondary metabolites or grow on minimal culture medium supplemented with recalcitrant algal polysaccharides. Based on this screening, two Sordariomycetes strains were selected for further analyses through genome sequencing and omics techniques: (i) a <i>Marquandomyces marquandii</i> strain (M60) able to stain the culture medium in yellow, indicative of secretion of pigments and secondary metabolites and (ii) an <i>Albophoma yamanashiensis</i> strain (M98) able to grow in minimal culture medium supplemented with the recalcitrant algal polysaccharide fucoidan. Fungal co-culture experiments suggested an inhibitory effect of the secretome of <i>M. marquandii</i> (strain M60) on fungal growth. Under culture conditions inducing pigment secretion, a set of secondary metabolite gene clusters was differentially expressed, as analyzed by RNA-seq. On the other hand, transcriptomic and proteomic experiments on <i>A. yamanashiensis</i> (strain M98) unveiled the enzymatic activities expressed in response to the presence of fucoidan. Overall, our results indicate that the isolated marine fungal strains could serve as a source of new enzymatic activities and secondary metabolites.IMPORTANCECharacterization of the mycobiota of marine and estuarine environments is important for the identification of new potential biotechnological products such as pigments, enzymes, and bioactive compounds. In this work, we describe the phenotypes and genomics, transcriptomics, and proteomics features of the Sordariomycetes <i>Marquandomyces marquandii</i> (strain M60) and <i>Albophoma yamanashiensis</i> (strain M98). The former was selected as a pigment/secondary metabolite producer, and the secondary metabolite gene clusters differentially expressed under conditions inducing pigment production were identified. <i>A. yamanashiensis</i> (strain M98) was characterized as a potential degrader of fucoidan, and the carbohydrate-active enzymes and sulfatases induced in response to the presence of this sulfated, recalcitrant algal polysaccharide were identified.