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.