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 ..., Experimental setup
To compare DNA metabarcoding and a traditional fluorescence method (ALA), we performed a biomonitoring study of the phytoplankton community composition and biomass in an outdoor, large-scale, replicated experiment. The experiment was conducted from April 7th to October 20th, 2020, in a setup consisting of 24 cylindrical polyethylene mesocosms (diameter = 0.7m, height = 1m) situated at Lund University (55.1° N, 13.2° E), in southern Sweden. The sides and base of each mesocosm were insulated, and each mesocosm was filled with 400L unfiltered lake water, i.e., contained organisms naturally occurring in the nearby eutrophic Lake Ringsjön (55.9° N, 13.5° E). Lake sediment was also added to the mesocosms to facilitate the natural succession, recruitment of resting stages and help stabilise water chemistry. The sediment, also collected from Lake Ringsjön, was drained and homogenised before 500g was placed into a plastic tray (14x14x10 cm) and placed at the bottom of each mes..., # Data from: Comparative analysis of environmental DNA metabarcoding and spectro-fluorescence for phytoplankton community assessments

Dataset DOI: [10.5061/dryad.jwstqjqn1](10.5061/dryad.jwstqjqn1)

## Description of the data and file structure

Datasets and R code for the manuscript titled \"Comparative analysis of environmental DNA metabarcoding and spectro-fluorescence for phytoplankton community assessments\" by Romana Salis and Lars-Anders Hansson. DOI: 10.1002/edn3.70097

We conducted a comparative analysis of phytoplankton community composition using fluorescence-based measurements and DNA metabarcoding in a controlled mesocosm experiment.

### Files and variables

#### File: mapping_eDNA1_16S.csv **and** mapping_eDNA1_18S.csv

**Description:** sample data for pre-processing of the 16S and 18S sequence data.

##### Variables

* Sample date: Date the sample was taken
* sampling week: Week of the experiment the sample was taken
* treatment: Experimental treatment (heated and/or inva...,