Dynamics of the Pacific Oyster Pathobiota during mortality episodes in Europe assessed by 16S rRNA gene profiling and a new target enrichment next‐generation sequencing strategy

Type Article
Date 2019-12
Language English
Author(s) Lasa Aide1, 2, Cesare Andrea3, Tassistro Giovanni1, Borello Alessio1, Gualdi Stefano4, Furones Dolors5, Carrasco Noelia5, Cheslett Deborah6, Brechon Amanda6, Paillard Christine7, Bidault Adeline7, Pernet FabriceORCID8, Canesi Laura1, Edomi Paolo9, Pallavicini Alberto9, Pruzzo Carla1, Vezzulli Luigi1
Affiliation(s) 1 : Department of Earth, Environmental and Life Sciences (DISTAV)University of Genoa Genoa ,Italy
2 : Department of Microbiology and ParasitologyUniversidade de Santiago de Compostela Santiago de Compostela ,Spain
3 : National Research Council –Water Research Institute (CNR‐IRSA), Largo Tonolli 50 28822 Verbania ,Italy
4 : Department of Plant and Microbial BiologyUniversity of Zürich, Switzerland
5 : IRTA,Sant Carles e la Ràpita Tarragona, Spain
6 : Fish Health UnitThe Marine Institute, Rinville Oranmore Galway, Ireland
7 : Laboratoire des sciences de l'Environnement Marin, Institut Universitaire Européen de la MUniversité de Bretagne Occidentale – UMR6539 CNRS/UBO/IRD/Ifremer Plouzané ,France
8 : Ifremer, Physiologie Fonctionnelle des Organismes MarinsUMR 6539 LEMAR (CNRS/Ifremer/IRD/UBO) Technopole Iroise CS 10070 29280 PLOUZANE, france
9 : Dept. of Life SciencesUniversity of Trieste, Italy
Source Environmental Microbiology (1462-2912) (Wiley), 2019-12 , Vol. 21 , N. 12 , P. 4548-4562
DOI 10.1111/1462-2920.14750
WOS© Times Cited 47
Note Special Issue on Pathogen and Antimicrobial Resistance Ecology

Infectious agents such as the bacteria Vibrio aestuarianus or Ostreid herpesvirus 1 (OsHV‐1) have been repeatedly associated with dramatic disease outbreaks of Crassostrea gigas beds in Europe. Beside roles played by these pathogens microbial infections in C. gigas may derive from the contribution of a larger number of microorganisms than previously thought, according to an emerging view supporting the polymicrobial nature of bivalve disease. In this study, the microbial communities associated with a large number of C. gigas samples collected during recurrent mortality episodes at different European sites were investigated by real‐time PCR and 16SrRNA gene‐based microbial profiling. A new target enrichment next‐generation sequencing protocol for selective capturing of 884 phylogenetic and virulence markers of the potential microbial pathogenic community in oyster tissue was developed allowing high taxonomic resolution analysis of the bivalve pathobiota. Comparative analysis of contrasting C. gigas samples conducted using these methods revealed that oyster experiencing mortality outbreaks displayed signs of microbiota disruption associated with the presence of previously undetected potential pathogenic microbial species mostly belonging to genus Vibrio and Arcobacter. The role of these species and their consortia should be targeted by future studies aiming to shed light on mechanisms underlying polymicrobial infections in C.gigas.

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Publisher's official version 41 2 MB Open access
Figure S1 Geographic areas and shellfish farms investigated in this study 1 156 KB Open access
Figure S2 Rarefaction curves computed for total OTUs abundance (Alpha diversity analysis) (Va = Vibrio aestuarianus infected oysters; OshV1 = Ostreid herpesvirus 1 infected oysters) 1 170 KB Open access
Figure S3 Results from target enrichment NGS analysis targeting C. gigas pathobiota on a mock community sample (positive control) composed of ... 1 119 KB Open access
Table S1 primers, adapter and barcode sequences used in this study 2 297 KB Open access
Table S2 Core microbiota, shared genera in the different conditions at 0.1% of relative abundance and presence in, at least, 90% of the samples 1 147 KB Open access
Appendix S1: Supporting Information 1 MB Open access
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Lasa Aide, Cesare Andrea, Tassistro Giovanni, Borello Alessio, Gualdi Stefano, Furones Dolors, Carrasco Noelia, Cheslett Deborah, Brechon Amanda, Paillard Christine, Bidault Adeline, Pernet Fabrice, Canesi Laura, Edomi Paolo, Pallavicini Alberto, Pruzzo Carla, Vezzulli Luigi (2019). Dynamics of the Pacific Oyster Pathobiota during mortality episodes in Europe assessed by 16S rRNA gene profiling and a new target enrichment next‐generation sequencing strategy. Environmental Microbiology, 21(12), 4548-4562. Publisher's official version : https://doi.org/10.1111/1462-2920.14750 , Open Access version : https://archimer.ifremer.fr/doc/00508/61952/