Metagenomic insights into the fungal assemblages of freshwater ecosystems

Microbial communities contribute to the taxonomic diversity, food web, and biogeochemical interactions of an aquatic ecosystem. The diversity of aquatic microorganisms is enormous, and the fungal community among them plays critical roles in decomposition and nutrient cycling. Freshwater fungal assemblages were first studied by isolating the species from decaying submerged plant and animal material from freshwater sources. But with the rapid development of metagenomic approaches, the field has witnessed an expansion to understand its actual diversity in such ecosystems; it has also aided in linking the dynamics of complex microbial communities to biogeochemical processes. The shift in study methods to metagenome and targeted sequencing has led to big data collection and identification of previously unknown species present in freshwaters. Here, we provide an overview of the freshwater fungi found in different tropical and temperate freshwater sources and discuss their role in aquatic environments. We discuss how metagenomic approaches and the development of eukaryotic pipelines have expanded the scope of studying fungal assemblages in freshwater ecosystems. 18S rRNA marker genes to identify novel species and new generation shotgun sequencing techniques have revealed the need to structure model organisms and interactive systems to better understand community dynamics and identify novel metabolic pathways. Furthermore, some of the recent studies conducted to estimate the spatial distribution of the fungal communities using metabarcoding and phylogenetic markers of the V4, V9, and V3 fungal regions are also discussed here. Apart from the Hyphomycetes, which have been extensively studied in isolated cultures, several ascomycetes and basidiomycetes have been detected with metagenome analysis. It becomes imperative to continue understanding microbial assemblages in the aquatic environment as freshwater biodiversity shows a characteristic change with environmental context and governs ecological and evolutionary functions.