Data considerations
Differences between the sedDNA and microscopy records may arise from the way the data are collected, and this must be considered when comparing the two temporal records. For example, changes and improvements to the methods used throughout long-term monitoring schemes are to be expected. In the present study, the type of counting chamber used to produce the microscopy record changed from a sedimentation chamber to a Lund chamber in 1994. The way counts were recorded also varied throughout the monitoring scheme as cells were sometimes counted according to size, form or whether they were found in colonies. To alleviate some of the possible biases that may arise from changes to the counting method, the counts were converted to binary presence-absence values as a measure of temporal occurrence. A consequence of converting counts to occurrence is that this measure may not be directly comparable with the relative abundance values used in the sedDNA record, although a positive relationship between species occurrence and abundance has been widely observed (Gaston and He, 2011). Some issues could remain such as the ability of the observer to identify phytoplankton to genus level by microscopy. This may have varied with the counting method used and the expertise and time investment of the observers, and the counts may have been biased towards more easily identifiable taxa or taxa of particular scientific interest.
There are also methodological factors associated with the sedDNA record which must be considered when making comparisons with the microscopy-based record. For example, the chronology of the sediment core was estimated based on the chronology of a separate sediment core collected in 2014 from the same location within Esthwaite Water. Application of this chronology required the assumption that the sedimentation rate remained constant since 2014, but variation in the sedimentation rate could lead to inaccuracies in the estimated chronology and therefore cause a discrepancy between the sedDNA and microscopy records. Only phytoplankton residing in the surface water were examined in the monitoring scheme, but sedDNA had the potential to record taxa originating from deeper within the water column and at the sediment surface. While contribution from active benthic phytoplankton may be relatively low at the depth the sediment core was collected due to low light availability, benthic taxa originating from littoral areas may have been transported to the sediment in the deeper basin during sediment resuspension and focussing (Mackay et al ., 2012). The choice of 18S rRNA amplicon primers influences the composition of the community detected, and the accuracy of taxonomic assignment is limited by completeness of the reference database (Francioli et al ., 2021). The 18S rRNA gene copy number can vary between taxa and lead to over-estimations in relative abundance for some groups (Gong and Marchetti, 2019). Despite these data considerations, there were still remarkable similarities between the sedDNA and microscopy records, but possible explanations for the discrepancies between the records are explored further in the following sections.