Diversity and ecology of fungi using multiple metabarcoding primers in the sediments and surface water of brackish and salt marshes Raw sequence reads

Fungi are key drivers of biogeochemical processes in all ecosystems, but marine fungi remain understudied. We performed a metabarcoding survey targeting the small and large subunit rRNA genes and the internal transcribed spacer region of fungi (18S rRNA, 28S rRNA, and ITS2) in the sediment and surface water of a salt marsh and brackish marsh in South Carolina, USA. The 28S primer (LF402 and LR0R) identified more early diverging fungi and was better than ITS at assessing fungal diversity. The universal primer (515F-Y and 926R) targeting the small subunit rRNA gene (18S) identified three fungal operational taxonomic units even at a sequencing depth of about half a million reads per sample, likely because prokaryotes dominated the microbial communities. We found that the 28S primer was better suited to identify early diverging fungi than the ITS2 primer, which could be partially attributed to the ITS region's database limitation (biased towards Dikarya). By using the 28S region, we found that Dikarya fungi were dominant in the salt marsh communities. In contrast, the brackish marsh communities were dominated by early diverging fungi. Early diverging fungi, such as Zoopagomycota, Blastocladiomycota, Chytridiomycota, and Mucoromycota, were key phyla that drove the differences between the brackish and salt marsh. Our study underscores the vast untapped fungal diversity in estuarine and coastal ecosystems.