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

  • Carradec, Quentin1, 2
  • Poulain, Julie1, 2
  • Boissin, Emilie3, 4
  • Hume, Benjamin C. C.5
  • Voolstra, Christian R.5, 6
  • Ziegler, Maren7
  • Engelen, Stefan8
  • Cruaud, Corinne8
  • Planes, Serge2, 3, 4
  • Wincker, Patrick1, 2
  • 1 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France , Evry (France)
  • 2 R2022/Tara Oceans GO-SEE, 3 rue Michel-Ange, Paris, 75016, France , Paris (France)
  • 3 PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France , Perpignan Cedex (France)
  • 4 Laboratoire d’Excellence “CORAIL”, 52 Avenue Paul Alduy, Perpignan Cedex, 66860, France , Perpignan Cedex (France)
  • 5 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia , Thuwal (Saudi Arabia)
  • 6 University of Konstanz, Konstanz, 78457, Germany , Konstanz (Germany)
  • 7 Justus Liebig University, Giessen, Germany , Giessen (Germany)
  • 8 Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France , Evry (France)
Published Article
Scientific Reports
Springer Nature
Publication Date
Sep 28, 2020
DOI: 10.1038/s41598-020-72589-0
Springer Nature


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.

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