PCR primers for assessing community structure of aquatic fungi including Chytridiomycota and Cryptomycota

• The FF390W/EF3r primer set was favorable for the detection of aquatic fungi.
• This primer set detected both Chytridiomycota and Cryptomycota from Lake Inba.
• The optimal conditions of DGGE analysis with primer set FF390W/EF3r-GC were determined.
• Community structures of aquatic fungi and their seasonal succession were revealed.

Fungi are diverse and have the potential for material cycling in freshwater ecosystems. Species composition of aquatic fungi and their seasonal dynamics are often key to their role in the functioning of the ecosystems. However, community structure of aquatic fungi, especially of Chytridiomycota (Chytrids) and Cryptomycota, is still limited because few primer sets are available to examine species composition. In this study, we validated six primer sets for the detection of aquatic fungi by denaturing gradient gel electrophoresis (DGGE) analysis and found that FF390W/EF3r showed the highest specificity among the primer sets tested. We detected both Chytrids and Cryptomycota from Lake Inba by DGGE analysis using the FF390W/EF3r-GC primer set. Further study with our established analysis revealed community structures of aquatic fungi and their seasonal succession patterns in the lake. Results of our study are useful for selection of the primer set for studying community structures of aquatic fungi and their seasonal succession.