IEA FISHµBIOM

IEA FISH(micro)BIOM

French-Vietnamese International Emerging Action in Marine Biodiversity

IEA FISHµBIOM
2019-2021
Contact:
Dr. Jean-Christophe Auguet
jean-christophe-auguet(at)cnrs.fr
Dr. Bui Van Ngoc
bui(at)ibt.ac.vn

IEA FISHµBIOM
News

Buying fishes and lobsters in a local fish farm from Nha Trang in order to analyze their intestinal pathobiome and resistome. From the left to the right (Dr Huy Ngyen Quang, Dr JC Auguet, Dr Buy Van Ngoc and Dr Hanh Nguyen Kim)

Credits: Thierry Bouvier

Dissection of a lobster intestinal tract at the Institute of Oceanography in Nha Trang

Credits: Thierry Bouvier

Collecting water and sediment samples in the bay of Nha Trang in order to characterize the environmental pathobiome and resistome.

Credits: Thierry Bouvier

Introduction

The IEA FISHµBIOM (International Emerging Action Biodiversity and role of FISH MICROBIOMes in coral reef socio-ecosystems) managed by Dr. Jean-Christophe Auguet (MARBEC, University of Montpellier, CNRS, IFREMER, IRD) in collaboration with the MIVEGEC research unit in Montpellier (Dr Anne-Laure Bañuls), the Institute of Biotechnology of Hanoï (IBT, Dr. Bui Van Ngoc), the University of Science and Technology of Hanoï (USTH, Dr. Huy Nguyen Quang) and the Institute of Oceanography of Nha Trang (IO, Dr. Hanh Kim Nguyen) will be effective from 2019 to 2021.

Missions and research themes

Fishes represent the principal link between coral reef biodiversity and associated human societies as source of food and income, but also through regulation of ecosystem processes. This resource for millions of people worldwide is however endangered by the ongoing decline of their habitat owing to increasing anthropogenic pressures. Microbiomes, through their influence on the heath, physiology and ecology of their hosts could help in the comprehension of fish adaptations to these changes.

The FISHµBIOM project represents an unparalleled effort to characterize the biodiversity of microbial communities associated to coral reef fishes. Understanding the mechanisms generating this biodiversity is critical for management of coral reefs, which are endangered hotspots of biodiversity and ecosystem services, as it is a key challenge towards the establishment of relevant conservation strategies. From a social point of view, coral reef ecosystems support ecological and cultural services, especially as protein source for people living close to these ecosystems. The outcome of the project will help to understand and predict how deterioration of the coral ecosystems may alter the nutritional quality of the fishes and ultimately the health of humans. Determining if reef fishes represent potential reservoirs and vectors of pathogens and drug resistance in coastal areas and developing new diagnostic tools are a relevant objective in terms of human and animal health because of the growing importance of zoonotic diseases.

Main OBJECTIVES OF THE PROJECT

The general objectives of the project are to assess the biodiversity of microbial communities in the intestinal tract of coral reef fishes and to estimate their influence on their host phenotype and the surrounding socio-ecosystem. More specifically, we will address the following complementary questions:

  • Which lineages of microbes, associated functions and interactions are present in the gut of coral fishes?
  • Do coral reef fishes represent reservoirs and vectors of potentially pathogenic human bacteria (PPHB) and antibiotic resistance genes (ARGs)?
  • How gut microbiome affect growth and condition of coral fishes and their contribution to ecosystem services through food provision and carbon cycling?

institutions and laboratories involved

France
• Marine Biodivesity, Exploitation and Conservation (MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, http://www.umr-marbec.fr)
• Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle (MIVEGEC, Université de Montpellier, CNRS, IRD, https://mivegec.ird.fr/fr/)

Vietnam
• Institute of Biotechnology of Hanoi (IBT, www.ibt.ac.vn/en/)
• Institute of oceanography of Nha Trang (IO, www.vnio.org.vn)
• University of Science and Technology of Hanoi (USTH, https://usth.edu.vn/)

Collecting water and sediment samples in the bay of Nha Trang in order to characterize the environmental pathobiome and resistome.

Credits: Thierry Bouvier

Collecting water and sediment samples in the bay of Nha Trang in order to characterize the environmental pathobiome and resistome.

Credits: Thierry Bouvier

IRN PALBIODIV-ASE

IRN PalBioDiv-ASE

IRN PalBioDiv-ASE

IRN PalBioDiv-ASE
2019- 2023
Contact:
Dr Valery ZEITOUN
pythecanthro(at)gmail.com

Dr Julien CLAUDE
julien.claude(at)umontpellier.fr

PalBioDiv ASE logo

IRN PALBIODIV-ASE
Website

IRN PALBIODIV-ASE
News

Introduction

The International Research Network Paleobiodiverity in South-east Asia is managed on the French side, by Dr. Valery ZEITOUN, CNRS research director at the Centre de Recherche en Paléontologie, Paris (UMR7207) with the administrative support of Angelina BASTOS. It has been launched in January 2015 and renewed in 2019.

Missions and research themes

The IRN-PalBioDivASE aims to set-up a collaborative research network on paleobiodiversity in South-east Asia between seven CNRS French laboratories, accompanied by their supporting universities and Museum, and twenty European, American and Asian Institutes. The scientific topics of the network focus on the paleobiogeographical history of South-east Asia, the Asian Inter-basin correlations and the origin and recent dynamics of modern biodiversity in South-east Asia. It targets reinforcement of our knowledge on the evolution of biodiversity in South-east Asia at different scales.

    NETWORK ACTIVITIES AND EXPECTED RESULTS

    To reach these targets, the following activities are envisaged:

    • The organization of workshops, seminars and training schools within the network partners, but also open to additional regional collaborators.
    • To promote the exchange of permanent researchers and professors as well as master, doctoral and post-doctoral students. In particular, the training of students in the field and in collections will be pursued with the support from our different teams.
    • Co-participation to international congresses & conferences where the multidisciplinary expertise of the Network will be recognised and showcased.
    • To act as driver for attracting international attention to the erosion of Biodiversity.
    • To act for the enhancement and safeguard of the paleontological heritage.

    To draw-up joint publications and implementation of joint projects between French and Foreign partners within the IRN-PalBioDivASE research targets.

    institutions and laboratories involved

    France
    • Centre de Recherche en Paléontologie, Paris (UMR7207).
    Dr Valéry ZEITOUN, Dr Ronan ALLAIN, Dr Marie-Béatrice FOREL, Prof. Nour-Eddine JALIL, Dr Michel LAURIN, Dr Grégoire METAIS, Dr Jean-Sébastien STEYER, Colas BOUILLET, Yohan DESPRES, Renaud VACANT 

    • Institut des Sciences de l’Evolution de Montpellier, Université de Montpellier (UMR5554).
      Dr Julien CLAUDE, Dr Serge MORAND, Dr Emmanuel PARADIS , Prof. Pierre-Olivier ANTOINE
    • Laboratoire d’Ecologie des Hydrosystèmes Naturels Anthropisés, Université Claude Bernard (UMR5023).
      Prof. Gilles CUNY, Dr Marc PHILIPPE
    • Laboratoire de Géologie de Lyon : Terre, planète et environnement (UMR5276).
      Dr Jeremy MARTIN, Dr Romain AMIOT
    • Laboratoire de Géologie de l’Ecole Normal Supérieure (UMR8538).
      Dr Eric BUFFETAUT
    • Histoire Naturelle de l’Homme Préhistorique, Museum national d’Histoire naturelle (UMR7194).
      Dr Thomas INGICCO
    • Institut de Systématique, Biodiversité, Paris (UMR7205).
      Dr Romain GARROUSTE

    Thailand
    • Palaeontological and Education Centre, Mahasarakham University.
    Prof. Mongkol UDCHACHON (Director), Dr Pasakorn BUNCHALEE, Prof. Clive BURRETT, Prof. Varavudh SUTEETHORN, Dr Suravech SUTEETHORN, Dr Haiyan TONG, Dr Siria PONGSANGTHONG, Dr Bouziane KHALLOUFI

    • Department of Biology, Faculty of Science, Mahasarakham University.
      Dr Uthumporn DEESRI, Dr Komsorn LAUPRASERT
    • Northern Institut of Petrified Wood and Mineral Ressources, Nakhon Ratchasima Rajabhat University.
      Dr Wilailuck NAKSRI
    • Department of Biology, Chulalongkorn University.
      Dr Noppadon KITANA, Dr Thongchai NGAMPRASERTWONG
    • Department of Biology, Burapha University, Chon Buri.
      Dr Chantima PIYAPONG
    • Sirindhorn Museum, Department of Mineral Resources
      Dr. Phornphen Chantasit, Tida LIARD
    • Department of Archaeology, Silpakorn University.
      Dr Prasit AUETRAKULVIT

    Philippines
    • Achaeological Studies Program, University of the Philippines.
    Dr Kathryn MANOLO, Dr Marian REYES, Dr Michael HERRERA

    Malaysia

    • Department of Geology, University of Malaysia.
      Dr Masatoshi SONE

    Cambodia

    • Department of Prehistory, Ministry of Culture and Heritage of the Kingdom of Cambodia.
      Dr Heng SOPHADY 

    China
    • Natural History Museum of Guangxi Zhuang.
    Prof. Jinyou MO, Dr Duo XIONG, Dr Qiongyao FU

    Laos

    • Savannakhet Dinosaur Museum.
      Dr Lattanabanlang CHUNLAMUNTRY
    • Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane.
      Dr Thonglith LUANGKOTH

    Vietnam

    • Geological Museum, Hanoi.
      Dr Quý TRƯƠNG QUAN
    • Department of Geology and Minerals of Vietnam (DGMV), Hanoi.
      Dr Luong THE VIET
    • Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi.
      Dr Minh D. LE

    Switzerland
    • Department of Geology and Paleontology, Genève Museum.
    Dr Lionel CAVIN

    United-Kingdom

    • Cambridge Advanced Studies Program, University of Cambridge.
      Dr Simon SCHNEIDER

    Germany
    • Museum of Paleontology, University of Tübingen.
    Prof. Madelaine BÖHME, Dr Uwe KIRSCHER, Dr Jérome PRIETO, Dr Davit VASYLIAN

    USA

    • Department of Paleobiology, Smithsonian Institution.
      Dr Antoine BERCOVICI

    IEA FOOLFLY

    IEA FOOLFLY

    French-Thai International Emerging Action in "Convergent evolution of deceptive pollination syndrome in Ceropegia and Aristolochia"

    IEA FOOLFLY
    2020-2021

    Contact:
    Dr. Rumsaïs Blatrix
    rumsais.blatrix(at)cefe.cnrs.fr

    Dr. Aroonrat (Meekijjaroenroj) Kidyoo
    aroonratm(at)hotmail.com

    IEA FoolFly
    News

    Flower of Ceropegia tenuicaulis in Pha Taem National Park, Thailand, with the main pollinator, a fly of the family Milichiidae, ready to enter the pitcher-shaped corolla. The scent emitted by the flower deceives the fly by mimicking a food source. Photo credit: R. Blatrix.

    Introduction

    The IEA FOOLFLY (International Emerging Action “Convergent evolution of deceptive pollination syndrome in Ceropegia and Aristolochia“), managed by Dr. Rumsaïs Blatrix (Centre d’Ecologie Fonctionnelle et Evolutive, CNRS – Université de Montpellier – University Paul Valéry Montpellier 3 – EPHE – IRD) in collaboration with Chulalongkorn University (Dr. Aroonrat Kidyoo), Bangkok, Thailand, will be effective in 2020 and 2021.

    Missions and research themes

    Ceropegia and Aristolochia are two plant genera that are phylogenetically distant but seem to share the same deceptive pollination syndrome: recent results show that flowers mimic the scent of crushed insects in order to attract flies that feed on exudates of insects attacked by predators (kleptomyiophily). These two genera differ by the organisation of the pollen: free and abundant in Aristolochia and clumped in a reduced number of pollinia in Ceropegia. In this project we propose a comparative analysis of the pollination biology of Ceropegia in Thailand and Aristolochia in France to describe evolutionary convergence of a highly specialized pollination syndrome and address the consequences of contrasting selective pressures on pollen transfer.

    MAIN projects of research

    This project has two goals: 1. estimate to what extent Ceropegia and Aristolochia rely on kleptomyiophily as a pollination strategy; 2. test the hypothesis that sympatric Ceropegia species have distinct sets of pollinators because of a particularly high value of each pollen load, which is not necessarily the case for sympatric Aristolochia. To estimate the extent of kleptomyiophily in Aristolochia and Ceropegia, we will apply a four-step approach to various species in both genera. The first step consists in determining the diversity of pollinators (flies, mostly in the families Chloropidae, Milichiidae and Ceratopogonidae). The second step consists in identifying the chemical composition of floral volatiles using dynamic headspace technique and gas chromatography coupled with mass spectrometry. The third step is to infer, from the nature of the volatile organic compounds emitted, the type of resource the flowers mimic (i.e. the “model”). The fourth step consists in testing the efficiency of the putative model in attracting pollinators of the focal plant species by comparing flies attracted to the real model, to the synthetic scent of the model and to the synthetic blend of floral scent. To test the hypothesis that pollination is more specific in sympatric Ceropegia species than sympatric Aristolochia species, we will identify pollinators in sympatric populations of various species in each genus.

    institutions and laboratories involved

    France:
    • Dr. Rumsaïs Blatrix (Centre d’Ecologie Fonctionnelle et Evolutive, CNRS – Université de Montpellier – University Paul Valéry Montpellier 3 – EPHE – IRD).

    Thailand:

    • Dr. Aroonrat Kidyoo (Department of Botany, Chulalongkorn University).

     

    Ceropegia species in Thailand, like this one in Sai Thong National Park, show a very high level of endemism. Thus, they are of particular interest for conservation issues. Photo credit: R. Blatrix.

    Floral scents are extracted in the field using an apparatus specially designed for the purpose. Photo credit: R. Blatrix.

    Aristolochia pistolochia, in France. Ceropegia and Aristolochia belong to distinct plant families, but deceptive pollination using small flies has converged in several species. Photo credit: R. Blatrix.

    IEA SHARKSEA

    IEA SHARKSEA

    French-Malaysian International Emerging Action in Freshwater shark evolution, climatic change and biostratigraphy in the Cretaceous of Southeast Asia

    IEA SHARKSEA
    2019-2021
    Contact:
    Prof. Gilles Cuny
    Gilles.cuny(at)univ-lyon1.fr

    Dr. Masatoshi Sone
    masatoshi.sone(at)gmail.com

    IEA SHARKSEA
    News

    Dr. Masatoshi Sone on the field in Malaysia in 2017
    © Gilles Cuny

    Tooth of the hybodont Heteroptychodus steinmanni in the Lower Cretaceous of Thailand
    © Gilles Cuny

    Tooth of the Hybodont Hybodus photographed in scanning electron microscopy from the Terminal Jurassic of Thailand
    © Mahasarakham University

    IEA SHARKSEA
    Videos

    Introduction

    Hybodont sharks represent one of the most successful chondrichthyan lineages of all time. They appeared as early as the Late Devonian and they disappeared at the end of the Cretaceous. On the other hand, the modern-day sharks, or selachimorphs, started to diversify in the Early Jurassic and by the end of the Jurassic, they dominated marine environments. Although the real impact of selachimorph diversification on hybodont evolution is still unclear, there is a neat diversification of hybodonts in freshwater environments during the Early Cretacous, whereas selachimorph sharks remained very rare into such an environment until the disappearance of the hybodonts. This would suggest that hybodonts took refuge in fresh waters during the Cretaceous to escape competition from neoselachian sharks in marine environments.

    Missions and research themes

    The recent discovery of a freshwater hybodont shark fauna from the Lower Cretaceous of Malaysia represents a valuable opportunity to better understand the diversification and spreading patterns of these sharks in Southeast Asia. An important faunal reorganization of these freshwater sharks has been observed between the Barremian and the Aptian and we aim at testing whether this could be linked to the climatic cooling event that geochemical studies have recently identified. A taxonomic revision will also allow enhancing the use of freshwater hybodont sharks as biostratigraphic markers in non-marine environments, as dating and correlation in such environments are notoriously difficult.

    MAIN projects of research

    1. Evolution of freshwater hybodont sharks and climatic changes

    Three different assemblages of freshwater hybodont sharks have been found in northeastern Thailand. The oldest one, the Phu Kradung assemblage, is from the late Jurassic (≈150 Million years ago). Then come the Sao Khua assemblage from the Barremian (≈125 Mya) and finally the Khok Kruat one, from the Aptian (≈115 Mya). More recently, similar assemblages have been found in China (similar to the Khok Kruat one) and Malaysia (similar to the Sao Khua one). Important faunal turn-over are observed between these different assemblages and one of the aims of this project is to determine whether these faunal turnovers are linked to climatic events. In addition, the level of adaptation of hybodont sharks to life in freshwater is still not fully understood. Analysis of stable isotope of fossil shark teeth will allow to identify their origin (fresh, brackish or marine), and therefore to determine whether these animals had a full life cycle in freshwater, and whether this impacted their survival through climatic changes

    1. Biostratigraphic potential of freshwater hybodont sharks in Southeast Asia

    Dating and correlation in non-marine environment are notoriously difficult due to the absence of many biostratigraphic markers, usually restricted to marine environment (i.e. ammonites and foraminifera). The dating and correlation of the Khorat Group in northeastern Thailand and adjacent areas relied mostly on palynological data, although, like in Malaysia, palynomorphs are not always present in the Thais red beds. Recently, the use of hybodont sharks allowed locating the position of the Jurassic/Cretaceous boundary in the Phu Kradung Formation and the potential of hybodont sharks for correlation outside of northeastern Thailand has been demonstrated in Kut Island and South China The Malaysian discoveries offer an opportunity to establish a working biostratigraphic scale based on these fossils in the terrestrial Mesozoic of Southeast Asia.

    A full taxonomic revision of these sharks is, however, necessary before a reliable biostratigraphic scale based on hybodont sharks can be established for the non-marine Cretaceous of Southeast Asia. The deciphering of their phylogenetic relationships along with the isotopic characterization of their living environment will also vastly improve our understanding of their colonization patterns of freshwater environments.

    institutions and laboratories involved

    France:
    • Pr. Gilles Cuny (CNRS UMR 5023, Laboratoire d’Ecologie des Hydrosystèmes naturels et anthropisés, Université Claude Bernard Lyon 1)

    • Dr. Romain Amiot (CNRS UMR 5276, Laboratoire de Géologie de Lyon, Terre, Planètes, Environnement)

    Malaysia

    • Dr. Masatoshi Sone (Department of Geology, University of Malaya) 

    • Ms. Yu He Teng (Department of Geology, University of Malaya)

    China

    • Dr. Jinyou Mo (Natural History Museum of Guangxi)

    Thailand

    • Dr. Varavudh Suteethorn (Palaeontological Research and Eductaion Centre, Mahasarakham University)

    IEA SULMACGEN

    IEA SULMACGEN

    French-Indonesian International Emerging Action in environment

    IEA SULMACGEN
    2020-2021
    Contact:
    Dr. Julie Duboscq
    julie.duboscq(at)mnhn.fr

    www.macaca-nigra.org

    Twitter: @MNPTangkoko

    Facebook page: @tangkokoconservationeducation

    Muséum national d’Histoire naturelle – Musée de l’Homme

    Macaca Nigra Project

    Balai Konservasi Sumber Daya Alam

    Institute Pertanian Bogor

    Introduction

    The IEA SULMACGEN (International Emerging Action SULawesi MAcaques GENetics), managed by Dr. Julie Duboscq (CNRS-MNHN-Université de Paris, UMR 7206 – équipe IPE) in collaboration with Macaca Nigra Project will be effective in 2020 and 2021. The Macaca Nigra Project has a triple mission: scientific research, education and conservation. 

    Sociality of Sulawesi macaques: revisiting the impact of kinship on social behaviours in wild crested macaques.

    Missions and research themes

    The objectives of this collaboration are to study of the crested macaques in their natural environment within the established Macaca Nigra Project and to develop a specific study on the feedback loops between social dynamics and genetic relatedness. Macaques share the same social organisation but different social styles. The crested macaques are unique because they are far more social than any other species and their sociality is very dynamic. A pending question about the evolution of such specificity is the impact of kinship on social relationships, at the heart of the costs and benefits of social life.

    Main projects of research

    Currently, kinship in wild animals rests on noninvasive samples and is assessed through a mixed use of genetic markers and observational pedigree which is unsatisfyingly slow and imprecise. The project thus proposes to develop an advanced protocol to obtain high resolution genetic data through capture-based enrichment genotyping and sequencing. This will generate genomic data of great further application potential. In this specific project, we hope to determine genetic relatedness between individuals more precisely then relate it to sociality in more depth, building up on our long-term research about kinship and social relationships.

    institutions and laboratories involved

    France:
    • Dr. Julie Duboscq is a researcher at CNRS and co-director of MNP. 
    • Dr. Hélène Quach is a research engineer at the Musée National d’Histoire Naturelle (MNHN)

    Indonesia:
    • Dr. Muhammad Agil, senior lecturer at Institute Pertanian Bogor (IPB), is involved in the directorship of the Macaca Nigra Project (MNP) since 2006;
    • Dr. Dyah Perwitasari Farajallah is a senior lecturer (IPB).

    Planned activities

    1/ Summer school / training workshop August 2020:
    Location: Genomic lab, IPB, Bogor, with potentially an excursion of 4 days in Tangkoko, North Sulawesi, at the field station of MNP
    Duration: 4 days in the lab, 4 days in the field. Participants: French and Indonesian researchers, technicians and students
    Tentative programme: non-invasive sample collection for genetic analyses, sample processing for genetic analyses, DNA extraction, DNA genotyping, DNA sequencing, DNA sequence analyses, kinship analyses, population genomics, sociality & genetics
    2/ Visit of collaborators and partners for discussions about collaborative research August 2020 & August 2021
    Location: Jakarta, Bogor, Manado and Tangkoko Duration: 2 weeks. Participants: Julie Duboscq, Hélène Quach, Muhammad Agil
    Tentative programme: meeting at the French Embassy with the Attaché de Coopération Scientifique et Technologique and people at the Institut Français Indonesia (IFI) and at the Institut de Recherche et Developpement (IRD), meeting with Prof. Iskandar from the International Office at IPB, meeting with
    people at the BKSDA Manado office (Balai Konservasi Sumber Daya Alam – Natural Resources Conservation Center).
    3/ Data collection, processing and analyses 2020 & 2021
    Location: field station, Tangkoko, and IPB, Bogor. Duration: TBD. Participants: Julie Duboscq, Hélène Quach, Dyah Perwitasari-Farajallah
    Tentative programme: TBD.

    “Forest with a view: infant backriding on mum while foraging for food”.
    Credits: Macaca Nigra Project

    “Social session: a small group of crested macaques is grooming and socialising. A female approached an infant with a play face as an invitation to play; the mother threatens her with a soft vocalisation; the two females then exchange lipsmacking for peace-making”.
    Credits: Macaca Nigra Project