A metagenomic view on fungal diversity in freshwater lakes

Fungi are essential components in a wide range of ecosystems and while major efforts have been spent on disentangling the diversity and functional roles of fungi in terrestrial environments, our knowledge about aquatic fungi is lagging. To address this knowledge gap, we explored metagenomes from 25 lakes from the arctic and boreal zone and one tropical reservoir with the aim of describing the community structure of fungi and fungi-like organisms (Oomycota). A second objective was to identify possible environmental factors influencing the composition of the fungal communities. Our results show that the main fungal phyla and orders are the same across all the lakes despite the differences in geographic location and prevailing climate. Still, there was differential distribution of more highly resolved taxa across the lakes that accordingly featured distinct communities, possibly caused by differential availability of carbon substrates in the lakes. A more detailed classification of sequences related to the pathogenic Oomycota genus Phytophthora clearly demonstrated that while technologies now exist for sequencing entire microbial communities in great detail, we are still severely limited by insufficient coverage of eukaryotic sequences and genomes in public databases. ### Competing Interest Statement The authors have declared no competing interest.