Deciphering the fungal communities occurring in the lower oceanic crust using metabarcoding and culturomics

The lower oceanic crust represents one of the last great frontiers of biology on Earth, as our understanding of the habitability and biological diversity in the deep biosphere is still in its infancy. During IODP (International Ocean Discovery Program) Expedition 360, a drilling leg cored Hole U1473A at ~800 meters below seafloor (mbsf) into Atlantis Bank, on the southwest Indian Ridge (SWIR). iTAG data and Amplicon Sequence Variants (ASVs) were used to describe the fungal diversity in different depth layers and highlighted low-diversity communities heterogeneously distributed along the core depth. iTAGs were complemented by a culture-based approach merging basic culturing and high-throughput culturing using Laser Nephelometry. ~150 fungal isolates were obtained from 10 samples ranging from 10 to 747 mbsf, with a majority of isolates harvested from the first layers. While numerous isolates appear ubiquitous, several previously-uncultured taxa were obtained. High-throughput ecophysiological and metabolic characterizations were then processed on ~80 fungal isolates as a proxy for assessing their adaptation to the deep biosphere. This study gives first hints on the presence and activity of fungi in the lower oceanic crust where they are hypothesized to play roles in organic carbon recycling.