Shared and unique genera
Across the four main phyla studied, a total of 215 genera were identified with both sedDNA and microscopy. Of these genera, 113 (52.6%) were uniquely detected by microscopy, 66 (30.7%) were uniquely detected by sedDNA, and 36 (16.7%) were detected in both the sedDNA and microscopy records (Fig. 4 A-D). More chlorophyte, ochrophyte and bacillariophyte genera were detected by microscopy compared to sedDNA, whereas more dinoflagellate genera were detected by sedDNA.
The majority of genera detected by each method were chlorophytes. There was a total of 128 chlorophyte genera detected by both methods combined, and almost half of these (65 genera) were only detected by microscopy. sedDNA uniquely detected 38 chlorophyte genera, and 25 genera were detected by both methods (Fig. 4A).
Only 4 dinoflagellate genera were uniquely detected by microscopy (Chimonodinium , Glenodiniopsis , Glenodinium andGyrodinium ). sedDNA uniquely detected 16 dinoflagellate genera, and a further 4 genera (Ceratium , Gymnodinium andPeridinium ) were detected in both the sedDNA and microscopy records (Fig. 4B).
Microscopy uniquely detected 21 ochrophyte genera, and 8 genera within this phylum were unique to the sedDNA record. In addition to these, 4 genera (Dinobryon , Mallomonas , Ochromonas andUroglena ) were detected with both methods (Fig. 4C).
sedDNA detected a total of 8 bacillariophyte genera, 4 of these were uniquely detected by sedDNA (Staurosira , Opephora ,Planothidium and Staurosirella ), and 4 were detected with both methods (Aulacoseira , Diatoma , Discostella andStephanodiscus ). In addition to these shared bacillariophyte genera, a further 23 genera were uniquely detected in the microscopy record (Fig. 4D).
Outside of these four phyla, microscopy also detected 15 charophyte genera, 5 cryptophyte genera and 1 haptophyte genus. sedDNA only detected 3 charophyte genera, 2 of which were also detected by microscopy.
A total of 669 phytoplankton ASVs were detected in the sedDNA record, and 410 (61%) of these ASVs were grouped into 105 genera. However, 259 phytoplankton ASVs (39%) had no definitive taxonomic assignment at the genus level, including 108 unassigned chlorophyte ASVs, 109 unassigned dinoflagellate ASVs, 35 unassigned ochrophyte ASVs, 4 unassigned bacillariophyte ASVs and 3 unassigned haptophyte ASVs. Within the microscopy-based monitoring record, there were 928 phytoplankton records, and 407 (44%) of these records were grouped into 170 genera. The remaining 521 records (56%) could not be identified to the genus level. This included 16 records of unassigned chlorophytes, 1 record of an unassigned dinoflagellate, 3 records of unassigned ochrophytes, 500 records of unassigned bacillariophytes and 1 record of an unassigned charophyte.