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Abstract
Autonomous Reef Monitoring Structure (ARMS) are standardised devices for sampling biodiversity in complex marine benthic habitats such as coral reefs. When coupled with DNA sequencing, these devices greatly expand our ability to document marine biodiversity. Unfortunately, the existing workflow for processing macrofaunal samples (>2-mm) in the ARMS pipeline—which involves Sanger sequencing—is expensive, laborious, and thus prohibitive for ARMS researchers. Here, we propose a faster, more cost-effective alternative by demonstrating a successful application of the MinION-based barcoding approach on the >2mm-size fraction of ARMS samples. All data were available within 3.5–4 h, and sequencing costs relatively low at approximately US$3 per MinION barcode. We sequenced the 313-bp fragment of the cytochrome c oxidase subunit I (COI) for 725 samples on both MinION and Illumina platforms, and retrieved 507–584 overlapping barcodes. MinION barcodes were highly accurate (~99.9%) when compared with Illumina reference barcodes. Molecular operational taxonomic units inferred between MinION and Illumina barcodes were consistently stable, and match ratios demonstrated highly congruent clustering patterns (≥0.96). Our method would make ARMS more accessible to researchers, and greatly expedite the processing of macrofaunal samples; it can also be easily applied to other small-to-moderate DNA barcoding projects (<10,000 specimens) for rapid species identification and discovery.
Highlights
An estimated 80% of living species remain unknown to science, including up to 90% of the world’s marine species (Mora et al, 2011; Appeltans et al, 2012; Wilson, 2017)
As the primary aim of this paper was to showcase the feasibility of MinION-based barcoding in Autonomous Reef Monitoring Structure (ARMS) research, we focused our analysis on demonstrating the reliability of error-corrected
We here demonstrate a successful application of the MinIONbased barcoding pipeline to process >2-mm samples from ARMS units deployed on tropical coral reefs
Summary
An estimated 80% of living species remain unknown to science, including up to 90% of the world’s marine species (Mora et al, 2011; Appeltans et al, 2012; Wilson, 2017). In the context of accelerating global change, there is an urgent need to more rapidly discover and assess species diversity, given that rates of species losses are predicted to occur faster than we can document them (Costello and Wilson, 2011). Fostered by the need to expedite species discovery, marine researchers have proposed the use of the Autonomous Reef Monitoring Structure (ARMS), a standardized. MinION Sequencing for ARMS Research sampling tool that enables comprehensive documentation of marine biodiversity beyond standard indicator species (Plaisance et al, 2011a; Leray and Knowlton, 2015). All organisms on the units are DNAsequenced for species identification and quantification (Leray and Knowlton, 2015). ARMS have become a widely utilized method for assessing benthic diversity in many shallow marine systems (Plaisance et al, 2011a,b; Leray and Knowlton, 2015; Al-Rshaidat et al, 2016; Hurley et al, 2016; Pearman et al, 2016, 2018, 2019; Pennesi and Danovaro, 2017; Ransome et al, 2017; Carvalho et al, 2019; David et al, 2019; Hazeri et al, 2019)
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