In situ nanopore sequencing to study coral holobionts

ABSTRACT: Molecular characterisation of the coral host and its associated microbial assemblages (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. 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 chose 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, onboard of the research vessel Tara during the Tara Pacific expedition. We used Oxford Nanopore Technologies (ONT) to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 hours. Several potential new associations between corals and multiple taxa from the genus Cladocopium (family Symbiodiniaceae) confirm the complexity of this genus in its association with many coral hosts. Reef scale network analysis of the bacterial community associated with the sampled corals reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable at a large scale for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to further make informed decisions in the context of the current challenges affecting coral reefs worldwide.

SUBMITTER: Quentin Carradec 

PROVIDER: S-BIAD5 | bioimages | 2020-01-01

REPOSITORIES: bioimages