# Understanding ecological functioning of ecological habitats, and building New Indicators based on Genetic Tools to assess their GES (Good Environmental Status).

Aurélien De Jode, Sophie Dubois, Zinovia Erga, Dorian Guillemain, Romain

David, Frédéric Zuberer, Jean-Pierre Feral, Anne Chenuil

► To cite this version:

Aurélien De Jode, Sophie Dubois, Zinovia Erga, Dorian Guillemain, Romain David, et al. Understanding ecological functioning of ecological habitats, and building New Indicators based on Genetic Tools to assess their GES (Good Environmental Status). OT-MED, Feb 2015, Marseille, France. 2015. [hal-03663687](https://hal.science/hal-03663687)

HAL Id: hal-03663687

https://hal.science/hal-03663687

Submitted on 10 May 2022

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<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
The coralligenous is a typical Mediterranean marine habitat, Paradoxically, unlike *Posidonia* meadows, it is poorly studied. Like the famous tropical coral reefs, it is a complex biogenic habitat, based on encrusting red algae (Ballesteros 2006).

## Introduction

More precisely, it is defined by the bioconcretions of corallines red algae that grows at dim light conditions. Corallines are the main builders, or enginners species of this ecosystems but their diversity and their ability to colonize new sites is poorly understood. The genus of calcareous red algae Lithophyllum is one of the most important builders in the area of Marseilles, but some marine invertebrates, such as *Myriapora truncata*, directly contribute to the framework of the habitats because they build their own calcareous skeleton (Hong 1980). However coralligenous habitats are built by various organisms and provide very different ecosystems services from recreational diving to shelter or nurseries for baby fishes and other species.

### Heterogeneous coralligenous habitats

<figure><img src="image_2.png" /><figcaption>Paramuricea clavata</figcaption></figure>

<figure><img src="image_3.png" /><figcaption>Eunicella singularis</figcaption></figure>

<figure><img src="image_4.png" /><figcaption>Eunicella cavolinii</figcaption></figure>

<figure><img src="image_5.png" /><figcaption>Peyssonnelia squamaria</figcaption></figure>

## Abstract

The aim of this project is to improve our understanding of its functioning and resilience capacity, and establish biodiversity and connectivity patterns among localities and ecological profiles, providing information for rationalizing the design of Marine Protected Area networks and monitoring methods.

To reach this goal, a multidisciplinary approach will be used, combining population genetics, community ecology, microbial ecology and physical oceanography.

This requests four tasks, partly using the same data, but different analysis methods.
1. Establishment of the taxonomic composition of the engineer corallinale algae.

2. Establishment of the species composition using metabarcoding (together with traditional taxonomy and photo quadrate validation for some samples)

3. Population structure and phylogeography of two selected taxa: a red alga *Lithophyllum spp.* and a bryozoan *Myriapora truncata*, on the CIGESMED sampling network.

4. Synthesis and Comparisons: Propose new GES (good environmental status) indicators for the coralligenous and biodiversity management rules.

## Data

### Genetic data obtained after DNA extraction of the samples from the field

<figure><img src="image_6.png" /></figure>

<figure><img src="image_7.png" /></figure>

Lith CAS 1.1 2
Lith CAS 1.3 3
Lith CAS 2.1 1
Lith CAS 2.1 2
Lith CAS 2.5 1
Lith CAS 2.5 2

CATTGCTTTCGTTGCTGCTCCTCCCGTTGATATCGA
TTGCTTTCGTTGCTGCTCCTCCCGTTGATATCGA
ATTGCTTTCGTTGCTGCTCCTCCCGTTGATATCGA
TTGCTTTCGTTGCTGCTCCTCCCGTTGATATCGA
TCATTGCTTTCGTTGCTGCTCCTCCCGTTGATATCGA
TTGCTTTCGTTGCTGCTCCTCCCGTTGATATCGA

### Environmental data directly recorded on the field during the sampling

<figure><img src="image_8.png" /></figure>

### Orientation

<figure><img src="image_9.png" /></figure>

### Slope

<figure><img src="image_10.png" /></figure>

### Wall rugosity

<figure><img src="image_11.png" /></figure>

### Photographic data

## Method

In this project different methods DNA extraction, PCR, metabarcoding and disciplines will be used : population genetics, phylogeography, community ecology and hydrological modeling.

<figure><img src="image_12.png" /></figure>

Sampling in the field :
scraping part of the habitat

<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>

DNA extraction

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

DNA amplification with
universal barcode

<figure><img src="image_17.png" /></figure>

<figure><img src="image_18.png" /></figure>

DNA sequencing

<figure><img src="image_19.png" /></figure>

<figure><img src="image_20.png" /></figure>

Bioinformatics analysis :
Identification of the species using
reference databases

## Results

### Preliminary studies of the two engineers species revealed genetic differentiation in the Bay of Marseille.

*Myriapora truncata*

<figure><img src="image_21.png" /></figure>

*Lithophyllum spp.*

<figure><img src="image_22.png" /></figure>

<figure><img src="image_23.png" /></figure>

<figure><img src="image_24.png" /></figure>

## Conclusions

Our first results suggests that the engineers species are actually composed of cryptic species that may have live in different ecological niches. It emphasizes our lack

of knowledge about this endemic Mediterranean ecosystem and stresses our requirement for a better understanding of its functioning in order to rationalize its

monitoring and protection.

## Acknowledgements

This work is a contribution to the Labex OT-Med (n° ANR-11-LABX-0061) funded by the French Government «Investissements d'Avenir» program of the French National Research Agency (ANR) through the A*MIDEX project (n° ANR-11-IDEX-0001-02).

*Other Contributors to the CIGESMED program : Açik Çinar S., Andral B., Arvanitidis C., Aurelle D., Aysel V., Bakir K., Bellan G., Bellan-Santini D., Bouchoucha M., Cahill A., Celik C., Chatzigeorgiou G., Chatzinikolaou E., Chenesseau S., Çinar M.E., Dağli E., Dailianis T., Dimitriadis C., D'Iribarne C., Doğan A., Dounas C., Egea E., Emery E., Evcen A., Faulwetter S., Gatti G., Gerovasileiou V., Güçver S.M., Issaris Y., Katağan T., Keklikoglou K., Kirkim F., Koçak F., Koutsoubas D., Marschal C., Önen M., Önen S., Öztürk B., Panayiotidis P., Panteri E., Pavloudi C., Pergent G., Pergent-Martini C., Poursanidis D., Ravel C., Reizopoulou S., Rocher C., Ruitton S., Sakher S., Salomidi M., Sarropoulou E., Sartoretto S., Selva M., Sini M., Sourbes L., Simboura N., Taşkin E., Thierry de Ville d'Avray L., Tschanz L., Vacelet J., Valavanis V., Vasileiadou A., Verlaque M.