Salinity and diatom host community jointly shape chytrid parasite diversity along a natural salinity gradient.

Parasitic fungi of the phylum Chytridiomycota are known parasites of phytoplankton, yet little is known about drivers of their diversity and host interaction dynamics in marine and brackish habitats. This study investigates the diversity and distribution patterns of phytoplankton-chytrid associations during a phytoplankton spring bloom along a natural salinity gradient of the Baltic Sea at a bi-weekly temporal resolution. Direct linking of chytrids to their host species using single-cell picking and sequencing (SCPS), combined with community composition analyses using amplicon sequencing and quantitative imaging flow cytometry, enabled a high-resolution profiling of spatiotemporal patterns of host-chytrid interactions and infection dynamics along the salinity gradient. This showed an increase in the relative abundance of parasitic chytrids coupled with the increase in phytoplankton biomass towards the end of the spring bloom. Moreover, SCPS revealed 5 novel chytrid-phytoplankton associations and aligning their sequences with spatiotemporal amplicon sequencing data showed a greater diversity and relative abundance of parasitic chytrids below a salinity of 8. Above this threshold, chytrid diversity and abundance declined considerably, coinciding with host community turnover and a shift towards marine non-fungal parasites. These results indicate that salinity structures chytrid communities primarily through its effects on host composition and parasite competition rather than through direct physiological limitation alone. Our findings leverage a combination of methods to provide novel insights at single-cell resolution on drivers of parasitic chytrids associated with phytoplankton blooms. Covering a spatial salinity gradient and temporal dynamics, our data highlights the role of phytoplankton blooms in shaping fungal communities.