Environmental DNA (eDNA) relative abundances of eukaryotic plankton at the Western English Channel coastal station ‘L4’ from 2001 to 2023

Environmental DNA (eDNA) relative abundances of eukaryotic plankton at the Western English Channel coastal station ‘L4’ (in the Western Channel Observatory: https://www.westernchannelobservatory.org.uk/index.php) from June 2001 to February 2023 (excluding July 2018 to January 2021). Proportions (i.e. relative abundance) of plankton DNA (metabarcoding) sequences per AphiaID are relative to the total abundance of DNA sequences whose assigned AphiaID appears on the plankton lifeform traits master list (v7:2024-06) (https://doi.mba.ac.uk/data/3260/1).

Samples were collected approximately once per week from the surface (≤5 m depth) and stored at −80°C. Inconsistencies in eDNA sampling method are conveyed by the code in the ‘Comment’ column of the data file as follows: ‘TMS’ (years 2001-2018): Seawater was collected via CTD Niskin-rosette’; 1 L per sample was filtered onto 0.45 µm cellulose-nitrate filters (503 samples) or polycarbonate filters (31 samples); ‘TRN_A’ – ‘TRN_K’ and ‘TIDAL’: Seawater was collected via CTD Niskin-rosette; 2 L per sample was filtered on to 0.22 µm cellulose-nitrate filters; ‘CNL’: Seawater was collected via an under-way sampling system; 1 L per sample was filtered on to 0.22 µm cellulose-nitrate filters. DNA was extracted from filters (using ZymoBIOMICS Miniprep Kits; Zymo Research) within a 12-month campaign. Metabarcoding of eukaryotic plankton was conducted via amplification of the18S rRNA gene-V9 region (PCR primers: 1391F and EukB; based on Amaral-Zettler et al, 2009, and Stoeck et al, 2010), according to the Earth Microbiome Project (EMP) protocol (https://earthmicrobiome.org/protocols-and-standards/18s/; including reference to Caporaso et al., 2012), excepting the use of KAPA2G Robust Master Mix (Roche Diagnostics), and sequenced as 250 bp paired-end reads (via Illumina Miseq).

Metabarcoding sequences (reads) were trimmed to remove sequencing adapters and primers and were further processed with nf-core/ampliseq (version 2.8.0; Straub et al., 2020, including DADA2; Callahan et al., 2016) to: remove low quality reads and PCR chimeras, merge read pairs, dereplicate reads and determine individual biological sequences (i.e. Amplicon Sequence Variants: ASVs). Taxonomic classification utilised the Protist Ribosomal Reference (PR2) database (‘PR2 - Protist Reference Ribosomal Database - Version 5.0.0’) (Guillou et al., 2013). Taxonomy and abundance of ASVs were primarily interrogated using the R (R Core Team, 2004) package Phyloseq (McMurdie and Holmes, 2013). ASVs identified as prokaryotes, likely contamination and/or as very rare (identified in <2 samples and <3 reads) were removed, as were ASVs not characterised beyond domain level. Per-sample read abundance was assessed and samples with <1000 reads (n = 41) were discarded. Using PR2 classifications and the R package Worrms (Chamberlain and Vanhoorne, 2023), AphiaIDs were assigned to ASVs at each resolvable taxonomic level (i.e. the lowest level classified and those above).

Here, only ASVs assigned an AphiaID that appears on the plankton lifeform traits master list (v7:2024-06) were retained. For each such ASV, the lowest taxonomic rank of matching AphiaID was utilised for calculating per-AphiaID abundances. Due to inherent biases of PCR amplification and differences in sequencing depth between samples, ASV abundance data (sequence counts) were transformed to proportional values (i.e. relative abundance). This dataset contains the relative abundance values of ASVs pooled by AphiaID, as proportions of the total abundance of ASVs with AphiaIDs on the master list.

References:

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