Organic matter degradation by oceanic fungi differs between polar and non-polar waters

Recent discoveries have uncovered pelagic fungi as significant contributors to the recycling of organic matter in the ocean. However, their drivers and whether the environmental filtering on the functional role of prokaryotes also applies to pelagic fungi remain unknown. In this study, we employed the metagenomic and metatranscriptomic approaches to explore the fungi mediated organic matter degradation in the sunlit ocean. Samples were collected from the subtropical Atlantic Ocean (non-polar) to the Southern Ocean (polar), and differentiated between small (0.2 − 3 µm, SF) and large ( >3 µm, LF) size fractions, to study niche partitioning in fungal communities and functions. Fungi accounted for 2–5% of eukaryotic genes and transcripts. Fungi contributed over 3% of eukaryotic carbohydrate-active enzymes (CAZymes) transcripts but less than 0.5% of protease transcripts, highlighting their specialized role in carbohydrate degradation. Non-polar and polar regions exhibited distinct fungal community composition and metabolic functions, potentially disrupting the balance of organic matter storage and cycling in these ecologically sensitive regions. Temperature emerged as a key driver of fungal CAZyme activity, revealing sensitivity to ocean warming. Our findings underscore the active role of pelagic fungi in organic matter degradation while revealing the environmental and ecological factors shaping their functional contributions across global oceanic regions.