Data from: Comparative analysis of environmental DNA metabarcoding and spectro-fluorescence for phytoplankton community assessments

Quantifications of phytoplankton biomass and species composition are
crucial for monitoring biodiversity and population dynamics in aquatic
environments, and both direct microscopic counts and fluorescence-based
methods have been widely used for monitoring. Recent advancements in DNA
metabarcoding offer an alternative way of easily assessing diversity and
species composition. However, a comprehensive comparison of the relative
merits and limitations of DNA- and fluorescence-based methods is currently
lacking. Here, we compare phytoplankton community composition measured via
fluorescence and DNA metabarcoding in an outdoor, replicated mesocosm
experiment. We show that there is a positive correlation between
fluorescence-measured biomass and DNA read and amplicon sequence variants
(ASV) numbers for cyanobacteria, but either weak or no correlation for the
other phytoplankton groups assessed (cryptophytes, chromophytes, green
algae). In addition, DNA metabarcoding was systematically better at
detecting cryptophytes, which were rarely detected via fluorescence.
Hence, while DNA metabarcoding may not provide reliable biomass estimates
for the majority of phytoplankton groups, metabarcoding analysis offers
higher taxonomic resolution and the capability to detect rare
phytoplankton groups. Overall, our findings provide new insights into the
strengths and limitations of each method and highlight the considerable
potential and importance of including DNA barcoding in freshwater
ecosystem assessment and biomonitoring programmes with a focus on
biodiversity assessments.