The use of molecular tools to monitor plankton communities

The use of molecular tools (i.e. tools based on DNA analysis) will be compared with the conventional method of monitoring plankton, which uses a binocular loupe to analyze the taxonomic composition of samples gathered using a plankton net. This R&D study will enable us to assess what these new approaches add to the conventional method.

Definitions: plankton, phytoplankton and zooplankton

Plankton are aquatic organisms that live in the water column. They drift with the currents: compared with the water bodies they themselves can travel only small distances. Nevertheless, they can move, particularly vertically (many plankton species migrate between the seabed and the surface depending on the time of day).

The word “plankton” includes both phytoplankton (vegetable plankton) and zooplankton (animal plankton). When we talk of the plankton community (phytoplankton or zooplankton), we mean all the species co-existing in a particular place over a particular period.

Context: monitoring phytoplankton and zooplankton communities in relation to the future construction of the offshore wind farm of Dieppe Le Tréport

When determining the baseline for the offshore wind farm of Dieppe Le Tréport, the plankton communities will be the subject of a specific study. The study will show us if, during the farm’s construction and subsequent operation, there is a change in the plankton communities that might be linked to a change in the environmental conditions.

The conventional method used to study zooplankton is to take samples using a net, filter them and study them under a binocular loupe, to identify the individual species present with the greatest possible taxonomic accuracy. Phytoplankton are identified under a microscope. This technique can be used to describe the diversity of plankton communities. However, the method has limitations for identifying species present in the form of eggs or larvae (for instance, the larvae of benthic species that form part of the plankton); for detecting rare species; and for differentiating cryptic species (species that differ genetically, but that are similar morphologically).

Sample of zooplankton seen through a binocular loupe. 1- copepods; 2- water flea; 3- gastropod larva; 4- bivalve larva; 5- egg sac of winkle, containing two embryos; 6- bryozoan larva; 7- (acorn) barnacle larva. (Photo Marie Le Goff, Roscoff Marine Biology Station)
Organisme du phytoplancton : diatomée du genre Coscinodiscus. (Photo Fanny Leroy, Station Biologique de Roscoff)

Objectives of the molecular analyses trial

The Éolien en Mer SIG thus proposed to trial the use of molecular tools at the time the baseline for the offshore wind farm of Dieppe Le Tréport was determined.

Recent DNA sequencing technologies now make it possible to compile an inventory of the species present in a sample of plankton, or even in a sample of water (using metabarcoding). This approach is expanding rapidly at the moment. It is receiving growing interest from the scientific community and is starting to be included in the strategies used to observe and monitor biodiversity.

Setec In Vivo tracks the phyto- and zoo-plankton communities as part of the regulatory environmental monitoring for the offshore wind farm of Dieppe Le Tréport, and has been tasked by the SIG, together with the Roscoff Marine Biology Station, to trial the use of molecular tools as a supplement to the conventional method.

Diagram showing the different stages of the analysis of environmental DNA using metabarcoding (diagram: Thierry Comtet, Roscoff Marine Biology Station)

The first stage will be a literature review and discussions with specialists in the molecular tools in order to define the protocols for sampling, extracting DNA, amplifying and sequencing, and then for analyzing the sequences. The samples will be taken at the same time as those required for the conventional method. Lastly, the inventory and abundance of species identified using the conventional method will be compared with those obtained from the DNA analyses, to assess the additional contribution from the new method. This phase of the trial will also aim to define an optimized protocol for making routine molecular analyses during subsequent phases of the offshore wind farm.