Ecosystem biomonitoring with eDNA: Metabarcding across the tree of life in a tropical marine environment

Author(s)

Michael Stat
Megan J. Huggett, Edith Cowan UniversityFollow
Rachele Bernasconi, Edith Cowan UniversityFollow
Joseph D. DiBattista
Tina E. Berry
Stephen J. Newman
Euan S. Harvey
Michael Bunce

Author Identifiers

Rachele Bernasconi: https://orcid.org/0000-0002-7973-8803

Publication Date

2018

Document Type

Dataset

Publisher

Dryad

School or Research Centre

School of Science / Centre for Marine Ecosystems Research

Description

Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using ‘tree of life’ (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing ‘universal’ PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.

Related Publications

Stat, M., Huggett, M. J., Bernasconi, R., DiBattista, J. D., Berry, T. E., Newman, S. J., Harvey E.S., & Bunce, M. (2017). Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment. Scientific Reports, 7(1). https://ro.ecu.edu.au/ecuworkspost2013/3586/

Original article available at:https://doi.org/10.10...8/s41598-017-12501-5

Language

eng

Codes

Usage Notes: 18S V1-V3, 18S V4, COI, Fish 16S, Crust 16S, Ceph 16S, Mam 16S, Sym 23S, trnL, Prokaryote 16S

File Format(s)

FASTA files

Creative Commons License

This work is licensed under a Creative Commons Public Domain Dedication 1.0 License.

Citation

Stat, M., Huggett, M. J., Bernasconi, R., DiBattista, J. D., Berry, T. E., Newman, S. J., Harvey, E. S., & Bunce, M. (2018). Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment. [Data set]. Dryad. https://doi.org/10.5061/dryad.qq11c