DNA metabarcoding as a tool to study plankton responses to warming and salinity change in mesocosms

Climate change is transforming marine ecosystems, with rising temperatures and changing salinity patterns expected to reshape plankton communities in the Baltic Sea. As key components of marine food webs and biogeochemical cycles, plankton are highly sensitive to environmental change. Here, we examined the effects of warming and salinity change on plankton communities using a mesocosm experiment at the Tvärminne Zoological Station, Finland. We employed both traditional microscopy-based identification and DNA metabarcoding (18S rRNA and COI markers) to assess shifts in phytoplankton, ciliates, and mesozooplankton. Our findings indicate that salinity primarily affected higher trophic levels, while warming influenced lower ones. Warmer conditions increased community evenness and favoured mixotrophic and heterotrophic taxa, whereas salinity effects were most pronounced in rotifers and copepods, reflecting species-specific tolerances. Interactive effects varied, with salinity sometimes buffe..., Samples were collected from mesocosms at a depth of 1 m. Temperature, salinity, fluorescence, and dissolved oxygen were measured every two days using a calibrated digital water meter (MU 6100 H, VWR). Water samples (4 L) were taken every two days, stored in a 10 L plastic container, and transported to the laboratory for further analysis.
Microscopy-based plankton identification: Phytoplankton, ciliates, and zooplankton samples were preserved with Lugol’s iodine (1%) and counted using Utermöhl chambers under an inverted microscope (Olympus CKx41). Phytoplankton and ciliates were identified to genus level, while zooplankton were identified to genus or species where possible. Enumeration methods followed standard protocols, with abundance reported as cells or individuals per liter. 
Metabarcoding: DNA samples for metabarcoding were collected every two weeks following modified protocols from Minamoto et al. (2019). A 1000 mL water sample was filtered onto 47 mm diameter, 0.7µm pore siz..., , # Data from: DNA metabarcoding as a tool to study plankton responses to warming and salinity change in mesocosms

[https://doi.org/10.5061/dryad.bvq83bkkq](https://doi.org/10.5061/dryad.bvq83bkkq)

## Description of the data and file structure

This dataset contains species abundance data from a mesocosm experiment conducted at Tvärminne Zoological Station, Finland (59.84° N, 23.25° E), between September and October 2022. The experiment investigated the effects of warming and salinity changes on plankton communities using microscopy-based counts, DNA metabarcoding (18S rRNA and COI markers), and associated environmental metadata.

### Files and variables

#### File: new_metadata.tsv

**Description:** This file contains metadata associated with the mesocosm experiment to use with metabarcoding tables, including sample identifiers, environmental conditions, and treatment groups.

##### Variables

* sample_metab: Unique identifier for each sample.
* Treatment: Identifier for the experiment...,