By using Blast against the nucleotide database of NCBI most fungal sequences could only be classified as “fungi” or “environmental samples” (mean: 70.2% of sequences; range: 36.5–89.7% of sequences in a given habitat; see Suppl. material 7). Then by processing the sequences by SILVA NGS we obtained a classification on the order level. Hence, we will use RDP to discuss the fine scale resolution and the SILVA classification for overall comparisons on the order or phyla level (Figure 3, 5). The orders Spizellomycetales and Rhizophydiales (both Chytridiomycetes) comprised the majority of fungal sequences in the four pelagic habitats and the Littoral water sample, with a greater proportion of Spizellomycetales in the three types of water samples compared to more Rhizophydiales in the Plankton and Sediment habitats (Figure 5).