Bruno Danis

Portman- ROV Sampling Gallery

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This gallery contains the pictures we extracted from the video transects that we operated in Portman (Spain, 2013). Each picture is a support for a Bay’ species cartography work.

Please Do not hesitate to contact me for any question/doubt about our identifications or to notice any specie you could identify on the pictures

From 17/10/2013 to the 24/10/2013 we captured some video transects of shallow benthic habitats encountered within or close to the bay of Portmàn (Murcia, Spain), which is subject to a strong pollution by metallic compounds due to an old mining activity. The following pictures, extracted from these video transects were used to fill species’ distribution files that sould be available for the whole scientific community through an online portail (Link). Thus this post aims to provide a visual support relative to this occurrence file, but is also open for suggestions about identifications that are not already tagged on the pictures and that would increase our data about species distribution. You might see some identifications relative to the class, family or genus. It is relative to individuals that we could not identify to the specie level ( we limit our identifications to the lowest taxonomic rank that we are undoubted about).

Anemonia viridis

Anemonia viridis – Echinoidea

Paracentrotus lividus – Echinoidea

Paracentrotus lividus

Echinoidea – Paracentrotus lividus – Padina povonica

Padina pavonica

Paracentrotus lividus – Echinoidea

Pinna nobilis

Posidonia oceanica

Echinaster sepositus

Ophidiaster ophidianus

Corallina sp – Echinoidea

Pinna nobilis – dictyota sp.

Echinoidea

Echinoidea

Echinoidea

Echinoidea

Paracentrotus lividus

Maxillopoda – Paracentrotus lividus

Asteroidea

Echinoidea

Anemonia viridis – Echinoidea

Echinoidea

Echinoidea

Echinoidea

Paracentrotus lividus

Codium bursa

Caulerpa racemosa – Echinaster sepositus

Spongia officilanis

Halimeda tuna – Echinaster sepositus

Arbacia lixula

Echinaster sepositus – Halimeda tuna – Padina pavonica

Paracentrotus lividus

Echinoidea

Paracentrotus lividus

Holothuria sanctori

Echinoidea

Corallinna sp. – Paracentrotus lividus

Eunicella sp.

Echinaster sepositus – Halimeda tuna – Padina pavonica

Paracentrotus lividus – Corallina sp.

Anemonia viridis

Echinoidea

Microbes, Diversity and Ecological Roles session at the SCAR OSC

Posted on January 24, 2014 by Bruno Danis

You can register now for the Microbes, Diversity and Ecological Roles session at the SCAR Open Science Conference , which will be held in Auckland, New Zealand from 23 rd August to 3rd September 2014

Most, if not all, Antarctic ecosystems are home to microbes that can span the range from sparse to dense and low to high diversity assemblages. These organisms o<en harbor specialized capabilities to withstand the environmental extremes that the high latitudes of the Antarctic pose. This session welcomes contribu/ons to our understanding and appreciation of Antarctic microbial systems, exploring diversity and ecological roles, contributions to biogeochemical cycles, and interactions between organisms (symbiotic, predatory or parasitic) and ultimately how microbes come together to influence Antarctic systems.

The increased recognition of microbes in all domains of life inhabiting Antarctic ecosystems – and in some cases not only surviving, but thriving in these systems (e.g. aquatic, icy, soil, rock, subglacial, marine benthic or pelagic) is gaining traction largely due to increased scientific exploration of diverse environments paralleled with technologic improvements in molecular sciences (e.g. next generation sequencing and bioinformatics analyses), application of geobiological tools, and remote sensing of both environments and organisms. This session has been developed by AntEco and the International Union of Biological Sciences.

The session is convened by:

Prof. Alison Murray, DRI, USA

Prof. Nils Chr. Stenseth, University of Oslo, Norway

Dr. Ian Hawes, University of Canterbury, New Zealand

Abstract submission deadline: 14 February 2014

Download the flyer here: SCAR-OS_MicrobesSessionFlyer

Biomar Lab hosting mARS workshop

Posted on December 9, 2013 by Bruno Danis

This week, we will be hosting a hands-on workshop to push the mARS project further, with Alison Murray (Desert Research Institute), Anton Van de Putte and Nabil Youdjou (biodiversity.aq project)

The Microbial Antarctic Resources System (mARS) is envisioned as an information system dedicated to facilitate the discovery, access and analysis of geo-referenced, molecular microbial diversity (meta)data generated by Antarctic researchers, in an Open fashion. The scope of diversity will encompass all freel-living and host-associated virus, Bacteria, Archaea, and singled-celled Eukarya.

mARS focuses on past, present and future works. It offers a community-driven platform for scientists to publish, document, analyse and share their (meta)data with the broad community for science, conservation and management purposes, in the spirit of the Antarctic Treaty.

mARS is composed of interoperable modules, iteratively building the microbial component of the biodiversity.aq network.
To the best extent possible, the wishes of the community regarding mARS functionalities will be reflected in the flexibility and scalability of the system. Feedback is expected from the users community in order to align their needs and the functionalities of mARS.

This week, we will try to get through Step 3 of the mARS system and prepare for Step 4 once we have enough data in mARS to make it worthwhile.

mARS steps include:

1. Data description and discovery

2: Habitat and Microbial Sequence Metadata Entry (MiMARKS Data Standard; Microbial_Sequence_Set_Template)

3: Georeferenced-molecular sequence database integration

4: Processing batch sequence data –Circum-Antarctic microbial diversity

You can find more on the mARS white paper page.

Mission Portman: a short report…

Posted on November 15, 2013 by Bruno Danis

Poster explaining the ongoing remediation programs in the Bay Portman

A small team from the BIOMAR Lab set a research mission to the Bay of Portman, Spain. The team was composed of Philippe Pernet (technician), three master students (Valérie Rossez, Andrea Garvetto and Maxime Coupremanne) under the supervision of Bruno Danis. The team reached the Bay on October 16th, 2013 for a 10-day stay.

The Bay of Portman was chosen for its exceptional environmental characteristics, from a contamination standpoint. A conference was recently held on the subject, involving our colleagues Drs Maria Jose Martinez and Carmen Perez, both from the Research Group of Soil Pollution in the University of Murcia.

A series of sampling and measurement were carried out in the framework of the master students respective projects:

Valérie Rossez worked on comparative acid-base physiology in two species of sea urchins (Paracentrotus lividus and Arbacia lixula), investigating the relationship between this physiological parameters and the uptake of contaminants but the sea urchins

Paracentrotus lividus (image from Encyclopedia of life, www.eol.org)

Arbacia lixula (picture from Encyclopedia of Life, www.eol.org)

Andrea Garvetto worked on microbial diversity, and took samples to investigate the link between the levels of contamination and microbial community structure in digestive pellets of two species of sea urchins (Paracentrotus lividus and Arbacia lixula), in various algae as well as in the seawater and sediments (various granulometries).

Maxime Coupremanne carried out a fine-scale mapping of the biodiversity and habitats of the Bay and its surroundings using underwater video transects using the lab’s ROV as well as videos shot by SCUBA divers.

Our ROV, Wally, in station S3, ready for deployment

Also, samples were taken for heavy metal levels analyses for each corresponding stations. The team was able to work in a total of 16 stations in the Bay, organised in a set of transects (from inside to outside the Bay as well as along the coast, following the main currents), and has come back to the Lab to process the samples. This pool of samples and video transects constitutes a unique benchmark to address potential future changes, for example in the mining activities of the Bay of Portman.

Sampling station in the Bay of Portman

On our way to Portman

Posted on October 14, 2013 by Bruno Danis

Tomorrow, we’re leaving for Portman, Spain for a sampling mission. We’ll be collecting samples for microbiology, ecotoxicology and habitat mapping. We’ll be using scuba diving and the Lab’s micro-ROV for this purpose. We hope to be able to screen the bay’s contamination status, and determine the impact on selected representatives from its ecosystems at various levels of biological organization. We’ll post more as we go! Special thanks to Guy and Fabienne, for allowing us to tryout the ROV in their swimming pool 🙂

Here’s a map of Portman:

The Bay is located close to Carthagena, in the south east Spain, and displays residual metal contamination caused by the dumping of mine tailings into the bay during the 20th century. High levels of concentrations of Hg, Cd, Pb, Cu, Zn, and As have been measured in different biotic and abiotic compartments of the bay.

New Website lifting off…

Posted on October 3, 2013 by Bruno Danis

We’re excited to announce that we’ve been working on a new website for our Laboratory. The new website can be found on both the ULB (biomar.ulb.ac.be) and general (www.marinebiology.be) addresses. It uses a CMS (WordPress) which allows us to progressively deploy a dynamic, modular and interoperable website. We will progressively be plugging in content (information, news, publications, but also raw data, model outputs and maps) and implementing more modules. Stay tuned, and don’t hesitate to get in touch with us for collaborations, networking or with suggestions.

Available only through your browser…

OpenROV étape 6: assemblage du boitier étanche

Posted on March 18, 2013 by Bruno Danis

Cette partie de l’assemblage se fait également sans difficulté particulière. Elle consiste à coller entre eux des disques concentriques de diamètres différents, ce qui permettra d’intercaler des o-ring qui assureront l’étanchéité. Les orifices latéraux servent d’un part de passe-cable (et seront étanchéifiés à l’aide d’une pâte époxy) et d’autre part d’évent, pour éviter une surpression à l’intérieur du cylindre.

Vue générale du boitier d’étanchéité. Photo: Bruno Danis

Les deux bouchons du boitier, formés de cercles de différents diamètres. Photo: Bruno Danis

Montage à blanc, tout s’ajuste parfaitement. Photo: Bruno Danis

Le boitier d’étanchéité, la webcam est placée. Photo: Bruno Danis

OpenROV by OpenROV is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

OpenROV étape 5: assemblage des blocs batterie

Posted on March 18, 2013 by Bruno Danis

Cette étape consiste à fabriquer deux tubes qui vont avoir pour fonction d’accueillir les 8 piles (LR01), qui vont alimenter le ROV (autonomie prévue, environ une heure dans une eau tempérée). Les blocs d’alimentation servent également de lest, et permettent au ROV de conserver son équilibre dans l’eau.
Nous avons fabriqué les blocs à partir de tubes PVC (32mm), bouchés de part et d’autre par des pieds de meubles détournés. La connectique consiste simplement en des contacteurs de piles récupérés d’un lecteur de CD (hors service), et du câble d’alimentation soudé à ces contacteurs (bouton et ressort), qui viendra se brancher au niveau du Cape. L’étanchéité est assurée par de l’époxy, qui est bourré au niveau des pieds en caoutchouc.

Les blocs d’alimentation terminés. Photo: Bruno Danis

Détail de l’un des bouchons et d’un contacteur, collé sur une rondelle d’acrylique. Photo: Bruno Danis

Les blocs sont fixés sur la coque du ROV, à l’aide de colsons adaptés. Photo: Bruno Danis

OpenROV by OpenROV is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

OpenROV étape 4: montage du châssis pour l’électronique (e-chassis)

Posted on March 18, 2013 by Bruno Danis

Cette étape consiste à assembler une autre partie de la structure du OpenROV: le e-chassis. Cet élément va accueillir les éléments électroniques embarqués du ROV, et venir se placer dans un cylindre étanche, qui sera placé à l’avant du ROV. L’e-chassis peut tourner dans ce cylindre, ce qui permet d’orienter la caméra embarquée et les rampes de LEDs.
Les éléments électroniques embarqués comprennent:

les variateurs de vitesse
l’ordinateur de bord (Beaglebone)
l’interface entre le Beaglebone et les autres éléments
un servo
une webcam HD
deux rampes de LED

Voici quelques photos de cet assemblage:

Pièces pour l’e-chassis, avant montage. Photo: Bruno Danis

Une partie de l’e-chassis est monté. Photo: Bruno Danis

Fixation de la webcam HD, à l’aide de colsons. Photo: Bruno Danis

Fixation des rampes de LEDs à l’aide de colle epoxy. Photo: Bruno Danis

L’e-chassis terminé, on voit l’encoche pour l’objectif de la caméra. Photo: Bruno Danis

OpenROV by OpenROV is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

OpenROV étape 3: montage du châssis pour la propulsion

Posted on March 15, 2013 by Bruno Danis

Le montage du châssis accueillant le système de propulsion (trois moteurs brushless, et hélices issues de turbines d’avion à réaction télécommandé) se faut sans difficulté particulière, en collant les éléments découpés au laser avec une très grande précision.