Diversity and ecology of fungi in the sediments and surface water of brackish and salt marshes

Fungi are key drivers of biogeochemical processes, yet marine fungi remain understudied. While various regions of fungal ribosomal RNA have been targeted to study fungal diversity, the ITS region has been the most prevalent region in the literature since 2012. However, ITS metabarcoding has limitations in marine environments, partly due to database biases. We conducted a metabarcoding survey targeting the small and large subunit rRNA genes and the internal transcribed spacer region of fungi (18S, 28S, and ITS2) in the sediment and surface water of salt and brackish marshes in South Carolina, USA. The 28S primer set (LR0R and LF402) excelled at identifying early diverging fungal lineages, including Chytridiomycota, Mucoromycota, Zoopagomycota, and Blastocladiomycota; however, only the ITS2 primer set amplified Cryptomycota and Olpidiomycota. The universal 18S/16S primer set (515F-Y and 926R) identified few fungal taxa because most reads were prokaryotic. The results based on 28S rRNA amplicons revealed that Dikarya fungi dominated salt marshes, whereas early diverging fungi dominated brackish marshes, suggesting Dikarya are more salt-tolerant. Over half of the fungal OTUs identified by the 28S primer set were from early diverging lineages. A FUNGuild analysis found that saprotrophic fungi are the function of most lineages, but in the brackish marsh, saprotrophic fungi from Zoopagomycota, Blastocladiomycota, and Chytridiomycota were more prevalent. Differential abundance analysis revealed that early diverging fungi were key drivers of community composition between the various marsh types. This study advances our understanding of marine fungal diversity by identifying early diverging lineages that were previously overlooked in marine environments. Our study highlights the vast, unexplored fungal diversity in marine environments.