The 18S V4 region barcode identified many more algal OTUs than 23S but the two barcodes lacked concordance. The number of identifiable OTUs (identifiable to the genus level) and sequence abundance of the 18S and 23S barcode sequences were compared. Algal estimates include genera within the phyla Chlorophyta, Glaucophyta, Rhodophyta, Charophyta, Cryptophyta, Haptophyta, Ochrophyta, Bacillariophyta and Dinoflagellata. Heterotroph estimates include genera within the phyla Apicomplexa, Intramacronucleata, Postciliodesmatophora, Cercozoa and Oomycota. The y-axis is the number of genera represented by each circle and the circle diameter represents the number of sequence reads detected for those genera. Green circles represent algal genera detected using 18S, blue represent algal genera detected using 23S and maroon represent heterotrophic genera detected using 18S. The ‘all sites’ graph represents all genera and sequence reads from the entire study.