A framework for in situ molecular characterization of coral holobionts using nanopore sequencing.

Quentin Carradec, Julie Poulain, Emilie Boissin, Benjamin C C Hume, Christian R. Voolstra, Maren Ziegler, Stefan Engelen, Corinne Cruaud, Serge Planes, Patrick Wincker

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9 Scopus citations


Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 h. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.
Original languageEnglish (US)
JournalScientific reports
Issue number1
StatePublished - Sep 28 2020

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: This project has been funded through the Tara Pacific consortium, France Genomique grant number ANR-10-INBS-09, and the Genoscope/CEA. We are keen to thank the commitment of the people and the following institutions and sponsors who made this singular expedition possible: CNRS, CSM, PSL, KAUST, Genoscope/CEA, ANR-CORALGENE, agnès b., the Veolia Environment Foundation, Region Bretagne, Serge Ferrari, Billerudkorsnas, AmerisourceBergen Company, Lorient Agglomération, Oceans by Disney, the Prince Albert II de Monaco Foundation, L′Oreal, Biotherm, France Collectivites, Kankyo Station, Fonds Francais pour l′Environnement Mondial (FFEM), Etienne Bourgois, UNESCO-IOC, the Tara Foundation teams and crew. Tara Pacific would not exist without the continuous support of the participating institutes. This publication is number 5 of the Tara Pacific Consortium.


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