Arctic nekton uncovered by eDNA metabarcoding: diversity, potential range expansions and benthopelagic coupling
Merten, Véronique et al. (2023), Arctic nekton uncovered by eDNA metabarcoding: diversity, potential range expansions and benthopelagic coupling, Dryad, Dataset, https://doi.org/10.5061/dryad.5qfttdz92
The Arctic Ocean is home to a unique fauna that is disproportionately affected by global warming but that remains under-studied. Due to their high mobility and responsiveness to global warming, cephalopods and fishes are good indicators of the reshuffling of Arctic communities. Here, we established a nekton biodiversity baseline for the Fram Strait, the only deep connection between the North Atlantic and Arctic Ocean. Using universal primers for fishes (12S) and cephalopods (18S), we amplified environmental DNA (eDNA) from seawater (50–2700 m) and deep-sea sediment samples collected at the LTER HAUSGARTEN observatory. We detected twelve cephalopod and 31 fish taxa in the seawater and seven cephalopod and 28 fish taxa in the sediment, including the elusive Greenland shark (Somniosus microcephalus). Our data suggest three fish (Mallotus villosus, Thunnus sp. and Micromesistius poutassou) and one squid (Histioteuthis sp.) range expansions. The detection of eDNA of pelagic origin in the sediment also suggests that M. villosus, Arctozenus risso and M. poutassou as well as gonatid squids are potential contributors to the carbon flux. Continuous nekton monitoring is needed to understand the ecosystem impacts of rapid warming in the Arctic and eDNA proves to be a suitable tool for this endeavor.
Sample collection, filtration and DNA extraction
Seawater samples for eDNA metabarcoding were collected during the cruises PS121 in August/September 2019, MSM95 in October/November 2020 and PS126 in May/June 2021 in the Fram Strait (Fig. 1C). Samples were taken in triplicate between 50 m and above the bottom (between 2250 and 2705 m deep) at three stations (S3, HG4, N4) in 2020 and four stations (S3, HG4, N4, EG4) in 2019 and 2021, resulting in a total of 282 samples (Fig. 2).
Sampling was conducted using 12-liter Niskin bottles mounted on a CTD rosette. During the cruises PS121 and PS126, six liters were filled from one Niskin bottle into either three 2 L bottles or one 10 L bottle that were previously cleaned with bleach and flushed with MilliQ water. On cruise MSM95, we had the opportunity to directly filter the water from the Niskin bottles by attaching the tubing needed for filtration. In each case, two liters of water were filtered with a peristaltic pump using 0.22 µm Sterivex-GP filters (Merck Millipore). For filtration controls, MilliQ water was filtered instead of seawater at every station. The Sterivex filters were sealed with caps and stored at -80°C until further processing in the lab. DNA was extracted from the filters using the DNeasy Blood and Tissue Kit (Qiagen) with a modified protocol (Supplement, Methods). DNA extracts were stored at -20°C until further processing.
Sediment samples were collected with a multicorer during the cruises PS121 and PS126 at 16 stations (Fig. 1C). Sediment samples were taken from three cores from the multicorer by scooping the first three cm during PS121 and one cm during PS126 of surface sediment into sterile Falcon tubes. The sediment samples were stored at -20°C until further processing. DNA from the sediment was extracted using a DNeasy Power Soil Kit (Qiagen) in combination with a QIAvac 24 Plus Vaccum Manifold and the updated DNeasy Power Soil Pro Kit (Qiagen) in combination with a Tissue Lyser II, following the manufacturer's protocol. Sediment DNA was eluted in 2x30 µl Solution C6 (10 mM Tris) and stored at -20°C.
For both seawater and sediment extractions, a DNA extraction control was included consisting of MilliQ instead of samples and PCR-negative controls to check for potential contamination in the laboratory. Rigorous precautions were taken to reduce contamination (see Supplement, Methods).
Library preparation and sequencing
The seawater and sediment eDNA was amplified with two universal primer sets, one targeting the nuclear 18S rRNA gene of cephalopods (Ceph18S_forward 5’‑CGCGGCGCTACATATTAGAC and Ceph18S_reverse, 5’‑GCACTTAACCGACCGTCGAC; amplicon length 140 – 190 bp) (de Jonge et al., 2021) and the other one targeting the mitochondrial 12S rRNA gene of fishes (teleo_F: 5'‑ACACCGCCCGTCACTCT and teleo_R: 5'‑CTTCCGGTACACTTACCATG; amplicon length 80 – 100 bp) (Valentini et al., 2016). All samples were amplified in PCR triplicates via a 1-Step PCR (Supplement table S1), resulting in nine PCR products per sampling depth and site. Positive (DNA extract of two fish or cephalopod species that do not occur in the Arctic or Atlantic Ocean and a mock control including 50% of each species) and negative PCR controls (PCR-grade water instead of DNA extract) were added to every PCR plate (Supplement, Methods). After PCR, all samples were pooled with equimolar concentrations resulting in a total of five libraries that were sequenced in five sequencing runs (Table 1). The sequencing runs targeting cephalopods were processed on an Illumina MiSeq with the MiSeq Reagent Kit v3, 600 cycles (PE), 2x 300 bp (Illumina) and the sequencing runs targeting fish were processed on an Illumina MiSeq with the MiSeq Reagent Kit v2, 300 cycles (PE), 2x 150 bp (Illumina). The sequencing runs targeting fish eDNA in sediment were processed in collaboration with the Alfred-Wegener Institute (AWI) in Bremerhaven, Germany, and the remaining sequencing runs were conducted at the Institute of Clinical Molecular Biology (IKMB) in Kiel, Germany.
GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel