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

Quentin Carradec (1, 2) , Julie Poulain (3, 2) , Emilie Boissin (4, 5) , Benjamin Hume (6) , Christian Voolstra (6, 7) , Maren Ziegler (8) , Stefan Engelen (3) , Corinne Cruaud (3) , Serge Planes (2, 4, 5) , Patrick Wincker (3, 2)

1 UMR 8030 - Génomique métabolique
2 GOSEE - Global Oceans Systems Ecology & Evolution - Tara Oceans
3 JACOB - Institut de Biologie François JACOB
4 CRIOBE - Centre de recherches insulaires et observatoire de l'environnement
5 LabEX CORAIL - Laboratoire d'Excellence CORAIL
6 KAUST - King Abdullah University of Science and Technology [Saudi Arabia]
7 University of Konstanz
8 JLU - Justus-Liebig-Universität Gießen = Justus Liebig University

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.

Mots clés: Biodiversity; DNA sequencing; Environmental biotechnology; Marine biology; Biodiversity

Domaines: Bio-Informatique, Biologie Systémique [q-bio.QM]; Génomique, Transcriptomique et Protéomique [q-bio.GN]; Biodiversité et Ecologie

Quentin Carradec, Julie Poulain, Emilie Boissin, Benjamin Hume, Christian Voolstra, et al.. A framework for in situ molecular characterization of coral holobionts using nanopore sequencing. Scientific Reports, 2020, 10 (1), pp.15893. ⟨10.1038/s41598-020-72589-0⟩. ⟨hal-02964556⟩