Sector · Mardyck basin
12 species
- Sampling
- 25 November 2025
- Access
- Support vessel
- Salinity (PSU)
- 32
- Turbidity (NTU)
- —
- Mean filtered volume (L)
- 13.7
Environmental DNA
Reading the biodiversity of ports and estuaries.
A fish survey for the Artois-Picardie Water Agency.
The study, along the coast
Environmental DNA · Case study
Reading the biodiversity of ports and estuaries.
A fish survey for the Artois-Picardie Water Agency.
- Client
- Artois-Picardie Water Agency
- Carried out by
- Qualyse, LDgenX and Prelevmar consortium
Reading the biodiversity of ports and estuaries.
A fish survey for the Artois-Picardie Water Agency. Client: Artois-Picardie Water Agency. Carried out by: Qualyse, LDgenX and Prelevmar consortium.
The question asked
How can knowledge of fish communities be improved, and how does eDNA compare with conventional data collection methods?
The eight sampled sites
- Dunkirk East (Port, Nord)
- Dunkirk West (Port, Nord)
- Calais (Port, Pas-de-Calais)
- Slack (Estuary, Pas-de-Calais)
- Boulogne (Port, Pas-de-Calais)
- Canche bay (Bay, Pas-de-Calais)
- Authie bay (Bay, Pas-de-Calais and Somme)
- Somme estuary (Estuary, Somme)
The approach
- Sample: In late November and early December 2025, three water replicates filtered simultaneously at 15 stations across eight ports and estuaries.
- Analyse: Two genetic markers, Teleo for bony fish and Elas02 for elasmobranchs: 23 and 13 taxa identified.
- Compare: In the Somme estuary, eDNA finds the four key species of the beam trawl monitoring (herring, whiting, common goby, sea bass) and detects species the trawl did not catch.
Constraints of the setting highlighted by the publication
- Currents: Currents move water, and with it the traces of DNA it carries.
- Turbidity: Abundant in estuaries, suspended particles cloud the water.
- Tides: The tide changes the water level and how waters mix through the day.
What the study brings
Median richness close between ports and estuaries, except for the Slack, but a different distribution of species; assemblages consistent with the expected ecological guilds. The study feeds the discussion on eDNA for monitoring aquatic environments.
The published results
What the official documents show.
The Artois-Picardie Water Agency published the article, the final report and the restitution presentation of the study, in French. The information below restates their content, with their figures.
- sites, from the ports of Dunkirk to the Somme estuary
- 8
- stations (sectors) sampled
- 15
- filters: three replicates per station
- 45
- genetic markers, Teleo and Elas02
- 2
The objectives
- Improve knowledge of biodiversity in ports and estuaries.
- Compare eDNA with the conventional methods used in estuaries under the Water Framework Directive (WFD).
What the Agency highlights
- The median number of species is fairly similar between estuaries and ports, except for the Slack estuary.
- Species are not distributed in the same way between ports and estuaries.
- Juvenile marine species dominate the downstream part of the sites; upstream, the estuaries and the port of Boulogne-sur-Mer show a large proportion of diadromous species.
- A large share of freshwater species is found at all sites, most likely reflecting rivers carrying DNA from upstream.
Figure (opens in a new tab)The most recurrent core of species
In the estuaries
- Clupea harengus (herring)
- Dicentrarchus labrax (sea bass)
- Pomatoschistus microps (common goby)
- Merlangius merlangus (whiting)
- Pollachius virens (saithe)
In the ports
- Clupea harengus (herring)
- Merlangius merlangus (whiting)
- Dicentrarchus labrax (sea bass)
Frequent in several port sectors:
- Sardina pilchardus (sardine)
- Pollachius virens (saithe)
- Pomatoschistus microps (common goby)
Detections to interpret with caution
Six species detected with Teleo have never been reported in the area (Asterias amurensis, Macrobrachium nipponense, Oncorhynchus keta, Oncorhynchus tshawytscha, Sardinops sagax, Squalius lepidus), nor has one species detected with Elas02 (Atherina hepsetus). The report attributes them to assignment errors, close sequences, contamination or DNA transport; doubtful taxa are excluded from the guild analysis.
Figure (opens in a new tab)Port of Dunkirk East
A contrast between the Mardyck basin, marked by the unusual detection of freshwater species (bream, roach, perch, zander), and the Évolution basin, dominated by coastal marine and estuarine species. These freshwater detections must be interpreted with caution: continental water inputs, indirect DNA transfer or contamination.
Sector · Évolution basin
10 species
- Sampling
- 25 November 2025
- Access
- Support vessel
- Salinity (PSU)
- 36
- Turbidity (NTU)
- —
- Mean filtered volume (L)
- 55
Species totals per site vary with the marker and filters applied between the presentation and the report. The richness shown here is that of each sector in the final report; validated data tables are needed for an interactive dashboard.
Figure (opens in a new tab)
Figure (opens in a new tab)The protocol
In the field
From 25 November to 3 December 2025, three replicates filtered simultaneously at each station with three pumps in parallel, on sterile 0.45 µm Waterra capsules, then preserved in Longmire buffer. Filtered volumes ranged from 2 to 90 L, averaging about 29 L, because of high turbidity.
In the laboratory
DNA extraction (ZymoBIOMICS kit), amplification of two markers: Teleo (teleost 12S gene) and Elas02 (elasmobranchs), five PCR replicates per sample, Ion Torrent S5 Prime sequencing. The sequenced negative controls contain no sequences.
In bioinformatics
Demultiplexing with scripts developed by LDgenX, SAMBA v4.0 pipeline (QIIME2, DADA2), taxonomic assignment against the MIDORI2 database. Of 356 ASVs detected, 96 were assigned to a fish species: 23 taxa with Teleo, 13 with Elas02.
The ecological guilds
- MJ Marine juveniles
- Marine species using the estuary as a nursery.
- ER Estuarine residents
- Species completing all or a major part of their life cycle in the estuary.
- MA Marine adventitious
- Marine species occasionally visiting the estuary or port areas.
- DIA Diadromous migrants
- Species linking marine and freshwater environments, such as salmon or eel.
- FW Freshwater
- Species reflecting continental influence and river inputs.
Figure (opens in a new tab)eDNA and beam trawl
- The comparison with the beam trawl could only be carried out in the Somme estuary, the reference system monitored under the WFD.
- Four species are detected by both methods: herring, whiting, common goby and sea bass. The trawl shows 21 exclusive taxa, mostly benthic and demersal; eDNA shows 14, including mobile or freshwater species.
- Sampling efforts differ greatly: several years of trawl hauls on one side, a single campaign of water sampling on the other.
- The ranking of guilds is preserved between the two approaches; eDNA reveals a higher proportion of freshwater species.
Figure (opens in a new tab)
Figure (opens in a new tab)The effect of turbidity
Turbidity affects detection: detected richness tends to decrease as turbidity increases (R² = 0.32; p = 0.026).
The ways forward
- Campaigns over the four seasons in the Somme estuary, to measure the temporal representativeness of the method.
- Continuous turbidity monitoring during filtration.
- Longer fragments and long-read sequencing (Nanopore) to improve taxonomic resolution.
Figure (opens in a new tab)
Figure (opens in a new tab)The source documents
- Artois-Picardie Water Agency article (opens in a new tab)
- Final report: presentation of the results (opens in a new tab)
- Restitution meeting presentation (opens in a new tab)
Figures: final report and restitution presentation by the Qualyse, LDgenX and Prelevmar consortium for the Artois-Picardie Water Agency (2026), in French.
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