Shared and unique genera
More genera were detected by microscopy compared to sedDNA within each phylum except dinoflagellates. For chlorophytes, ochrophytes and bacillariophytes, microscopy may have been more sensitive when distinguishing between genera. Only a small proportion of genera occurred in both records. This was highest for chlorophytes, with 19.5% of chlorophyte genera detected by both methods, but only 16.7% for dinoflagellates, 12.1% for ochrophytes, and 12.9% for bacillariophytes. The majority of genera were uniquely detected by each method, and each method may be capable of recording a different component of the phytoplankton community. Genera unique to the sedDNA record could include taxa that occupied deeper layers of the water column or littoral areas and were therefore beyond the scope of the surface water monitoring scheme, or those that were difficult to identify based on morphology. Depositional or degradational processes could explain why a large proportion of the phytoplankton community were missed by sedDNA. Previous studies have shown that the certain groups of eukaryotic algae (Gauthier et al ., 2021) and cyanobacteria (Nwosuet al ., 2021) were differentially represented in surface lake sediments compared to the water column, and this could be because some taxa did not readily deposit. The deposition potential of phytoplankton could be affected by grazing pressure and whether the cells form colonies or aggregate with organic matter which make them heavier and more likely to deposit and could also protect the DNA from degradation (Gauthier et al ., 2021; Mauvisseau et al ., 2022; Nwosuet al ., 2021).
A larger number of dinoflagellate genera were detected in the sedDNA record compared to the microscopy record, and sedDNA may therefore be a particularly valuable method for studying past dinoflagellate communities. Many dinoflagellates form a robust cyst during the resting stage of their lifecycle which may protect their DNA from grazing by zooplankton and other extracellular degradation processes (Bravo and Figueroa, 2014). Dinoflagellates have previously been shown to be well-represented by sedDNA, but it was possible that they were overrepresented due to their large genomes and high 18S rRNA gene copy number (Gong et al ., 2020).
Bacillariophyte DNA could also be expected to be preserved in sediments due to the presence of the protective silica frustule (Aguirre et al ., 2018). However, this group was present at the lowest relative abundance of the four main phyla in the sedDNA record, despite being one of the groups with the highest occurrence in the microscopy record, and a larger number of bacillariophyte genera were detected by microscopy. Another sediment core collected from Esthwaite Water for microfossil analysis found Asterionella , Aulacoseira andFragilaria to be the most dominant genera between 1945 and 2005 (Dong et al ., 2012). These genera were also detected by microscopy in the monitoring record from 1945 to 2010, butAsterionella and Fragilaria were absent from the sedDNA record. Targeted primers may be more capable of distinguishing a larger number of bacillariophyte genera compared to the broad range 18S rRNA amplicon primers selected in the present study, such as primers targeting the rbcL gene (Anslan et al ., 2022; Dulias et al ., 2017; Kang et al ., 2021). Although a substantial number of bacillariophytes were missed by sedDNA, a small number of genera were detected which may have been overlooked in the microscopy-based monitoring and microfossil records. This included Staurosira ,Opephora , Planothidium and Staurosirella .Planothidium are typically benthic taxa (Lange-Bertalot et al ., 2017), and may therefore have been outside of the scope of the surface water monitoring scheme, although Planothidium was only detected by sedDNA after 2010. The bacillariophyte community sequenced in lake surface sediments has previously been compared with microscopy-based methods, and also revealed that while microscopy could detect more genera, each method detected a distinct proportion of the community (Dulias et al ., 2017; Kang et al ., 2021).
A substantial proportion of ASVs detected by sedDNA (39%) and records in the microscopy-based monitoring scheme (56%) were unidentified at the genus level. In the sedDNA record, the majority of ASVs unassigned at the genus level were chlorophytes and dinoflagellates, while in the microscopy record, a significant number of bacillariophytes were unidentified at the genus level. Taxonomy assignment in the sedDNA record may be limited by reference database coverage (Anslan et al ., 2022). Taxonomic identification with microscopy may be limited by microscope resolution and the expertise and time investment of the observers, which may vary throughout the monitoring scheme. Separation of the influence of these variables in long-term monitoring schemes from an environmental response is complex (Straile et al ., 2013). While palaeolimnological tools such as sedDNA typically do not suffer from method changes, they may be subject to other limitations such as DNA degradation. Each method has its own limitations and biases, and multi-proxy analysis is likely the most reliable approach for reconstructing past phytoplankton communities.