Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers

• Published in: BMC Microbiology
• Main Authors: Clerissi, Camille, Guillou, Laure, Escoubas, Jean-Michel, Toulza, Eve
• Other Authors: Interactions Hôtes-Pathogènes-Environnements (IHPE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff Roscoff (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2020
• Subjects: Holobiont; Metabarcoding; Microbiome; Ostreoida; Crassostrea; [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology; [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology; [SDV.EE.IEO]Life Sciences [q-bio]/Ecology; environment/Symbiosis; Pacific; Crassostrea gigas; Pacific oyster
• Online Access: https://hal.archives-ouvertes.fr/hal-02914979; https://hal.archives-ouvertes.fr/hal-02914979/document; https://hal.archives-ouvertes.fr/hal-02914979/file/Clerissi-2020-BMCMicrobiol-Unveilling.pdf; https://doi.org/10.1186/s12866-020-01860-1

International audience Background: Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far.Results: To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities were sequenced using metabarcoding. Alveolata, Stramenopiles and Archaeplastida were the main protist phyla associated with oysters. In particular, Codonellopsis, Cyclotella, Gymnodinium, Polarella, Trichodina, and Woloszynskia were the dominant genera. The potential pathogen Alexandrium was also found in high abundances within some samples.Conclusions: Our study revealed the main protist taxa within oysters as well as the occurrence of potential oyster pathogens. These new primer sets are promising tools to better understand oyster homeostasis and disease development, such as the Pacific Oyster Mortality Syndrome (POMS) targeting juveniles.