Royal Netherlands Institute for Sea Research

Benthic Metabarcoding

Advanced measuring of biodiversity 

Due to expanding economic exploitation of seas and political agreements to protect ecosystems and biodiversity, there is a constant need for biomonitoring of marine benthic ecosystems. Acquisition of data on marine fauna in the traditional way from morphological characters requires a significant sampling effort as well as competent taxonomic experts. In monitoring programs of threatened, vulnerable or protected areas where changes in biodiversity are seen as an important tool, the traditional approach of measuring biodiversity is slow, expensive and difficult to replicate as it is highly dependent of the skills of the researcher. Metabarcoding is now a commonly used term for the study of genetic material obtained from environmental samples (i.e. marine benthic samples) directly. The ability to process bulk environmental samples in a fully automated process can greatly change the impact factor of large scale biomonitoring programs. Our objective is to assess the feasibility of metabarcoding techniques to measure benthic biodiversity, both in qualitative and quantitative terms. With the metabarcoding methods, research questions will be tackled where the present traditional taxonomic identifications are infeasible. 

Applying the techniques

The following case studies are proposed for applying metabarcoding techniques at monitoring programs in the field. The first three case studies will link with ongoing projects at NIOZ in the Wadden Sea, North Sea and Atlantic Ocean and are merely qualitative. The last project will focus on the quantitative aspects of presence/absence data.

1)       Wadden Sea

Mechanical digging for the lugworm Arenicola marina is supposed to affect benthic communities, including lugworms. Lugworms are known as key species for the benthic community on mudflats as they bioturbate the sand. However, both the spatial and temporal impact is unknown at present. A high resolution research; i.e. covering both meio,- and macrofauna, to the short terms effects of mechanical digging on the benthic communities at the digging site and its nearby surroundings will be conducted. The effects of lugworm digging on the surrounding benthic community can possibly model the effects of species removal from such a community. Point of interest is the spatial distribution of benthic macro and meiofauna before and shortly (days/weeks) after digging. In cooperation with Arenicola BV benthic samples will be taken before and after digging. Species composition of the samples will be analysed both traditionally and with metabarcoding techniques. 

2)       North Sea

Within the Insite project (INfluence of man-made Structures In the Ecosystem) the possible effects of the epifauna on artificial structures on the surrounding benthic environment in the North Sea is studied. This epifauna acts as a biofilter, depleting primary organic matter in the water column and enriching it by producing faeces, nutrients, dissolved organics and larvae. It is hypothesized that environmental conditions and particle fluxes are altered in the wake of an artificial structure, which will cast a so-called “shadow”, which will also affect the soft sediment ecosystem near that structure, possibly creating a new stable state. Studying these effects might provide insight in the effects of artificial structures on the surrounding benthic environment compared to the natural variability. The impact on the soft sediment ecosystem will be quantified and analysed by taking benthic and water samples in and outside the wake of an oil-platform to compare the existing benthic communities and larvae supply.

3)       Deep Sea

Seafloor Massive Sulfide (SMS) deposits are commonly found at hydrothermal vent sites through precipitation of hydrothermal fluids which are often rich in metals. Because of these valuable metals and worldwide shortages, these areas have recently gained the special interest of deep sea mining (DSM) industry. Mining of these sulfide deposits creates a risk for the organisms inhabiting the hydrothermal vent sites but also for the plume-affected environment. Blacksmokers; i.e. vents typically emitting particles with high level of sulphides, at active SMS sites form a large continuous plume of potentially harmful material covering an extensive area. We are interested in the influence of the plume on the benthic fauna as it can possibly serve as a model for the harmful plume created with deep sea mining. Both sites upstream and downstream of the vent will be sampled for benthic fauna and will be compared to answer the following questions:

a)       Is the meiofauna composition and distribution influenced by the plume and is there a difference between surface and deeper (up to 10cm) living species?

b)       Is the macrofauna composition and distribution influenced by the plume and can we compare the results of metabarcoding approaches to traditional taxonomy?

c)       Is there an influx of larvae in the deposit area from surrounding communities; i.e. is there a recolonization potential after potential disturbances of deep sea mining?

4)       From qualitative to quantitative

Metabarcoding studies are typically restricted to presence/absence data only. Quantification of biomass is often misleading due to DNA extraction and PCR amplification biases; an estimation of number of individuals is even impossible. During this case study we want to explore the possibilities of using presence/absence data of a large scale monitoring project for the estimation of abundance and dispersion of species. It is hypothesised that a variation in the presence/absence of one species within a large dataset can give an estimation of its overall abundance. We will conduct simulations using data collected at the NIOZ by the SIBES (Synoptic Intertidal Benthic Survey) program. The program collected 4,500 samples each summer throughout the Wadden Sea for seven consecutive years and for all samples benthic species composition and biomass has been analysed.

Project information
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University of Groningen
1 Jan 2014 - 31 Dec 2018

Meet the team

Veer van der, Henk
Head of Scientific Department
Klunder, Lise
PhD student