Ecological drivers shaping freshwater biodiversity and community dynamics: a multitrophic perspective based on an environmental DNA approach

This dataset contains environmental DNA (eDNA) metabarcoding data from a factorial experiment investigating freshwater eukaryotic community responses to manipulations of trophic structure and nutrient availability in experimental lake ecosystems. The study was conducted at the CNRS-ENS artificial lake platform in Nemours, France, using twelve experimental lakes (15x30 m, 700 m3 volume each) in a replicated factorial design. Water samples (4 L per lake) were collected monthly from April 2022 to April 2023 on the following dates: 21 April 2022, 19 May 2022, 23 June 2022, 21 July 2022, 18 August 2022, 20 September 2022, 21 October 2022, 18 November 2022, 16 December 2022, 19 January 2023, 16 February 2023, 16 March 2023, and 20 April 2023. Samples were collected at multiple depths and filtered through 0.45 micrometer pore size filters. A total of 195 samples were collected, including technical replicates and negative controls. DNA was extracted and amplified using a multiplex PCR approach targeting two 18S rDNA regions (V7 and V9) with primer pairs Euka01 and Euka03. Samples were distributed across four PCR plates for amplification. Libraries were sequenced using 150 bp paired-end sequencing on an Illumina MiniSeq Sequencing System with a High-Output Kit (Illumina).