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A framework for in situ molecular characterization of coral holobionts using nanopore sequencing
Hume, Benjamin CC
Voolstra, Christian R.
KAUST DepartmentRed Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia.
Marine Science Program
Red Sea Research Center (RSRC)
Biological and Environmental Sciences and Engineering (BESE) Division
Permanent link to this recordhttp://hdl.handle.net/10754/663643.1
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AbstractAbstractMolecular 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 hours. 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.
CitationCarradec, Q., Poulain, J., Boissin, E., Hume, B. C., Voolstra, C. R., Ziegler, M., … Wincker, P. (2020). A framework for in situ molecular characterization of coral holobionts using nanopore sequencing. doi:10.1101/2020.05.25.071951
SponsorsJP, QC and PW designed the study. QC wrote the paper with substantial input from JP, BH, EB, CV, MZ, SP and PW. EB collected coral samples. JP coordinated in situ experiments and nanopore sequencing assisted by QC. QC, BH, MZ and EB performed barcoding data analyses. JP, QC, CC and SE contributed to the development of protocols and tools for nanopore sequencing and analysis. All authors discussed the results and commented on the manuscript.
PublisherCold Spring Harbor Laboratory