Freshwater ecosystems are among the most impacted on Earth, having high rates of biodiversity loss due to ongoing climate change and anthropogenic pollution, such as industrial wastewater effluents and urban and agricultural runoff, among others. The current rates of species loss across many organism groups imperils the maintenance of the ecosystem services they provide, including nutrient recycling, carbon sequestration and water purification. Microbial decomposers, particularly aquatic fungi, are known to play a vital role in ecosystem dynamics in freshwater forested streams, relying on the energy input from allochthonous sources, such as leaf litter. This group is the main contributor to carbon and nutrient cycling, by producing and secreting extracellular enzymes that: (i) break down polymeric and recalcitrant organic matter into smaller, assimilable molecules and (ii) cycle nutrients, such as nitrogen and phosphorus. Despite their pivotal role in freshwater ecosystem functioning, the taxonomic and functional diversity of these fungi is currently poorly understood and characterized. The lack of knowledge on this group is even more striking when considering their genetic diversity, particularly their potential to remove recalcitrant compounds and pollutants. In order to help fill in these knowledge gaps, this project aims to: (I) develop strategies for identification and characterization of unknown aquatic fungi in different aquatic environments, (II) gain insight into aquatic fungal diversity and functioning in pristine and impacted aquatic environments , across distinct alpine zonations and (III) Understand the community dynamics of genetic expression during the degradation process, using a model system. To enable these analyses, the development and optimization of standardized workflows for rapid characterization and isolation of fungal isolates (single cells and pure cultures), (meta-)barcoding, and metatranscriptomics of aquatic fungi are sought.