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.