From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach

Abstract

Few tropical marine sites have been thoroughly characterised for their animal species, even though they constitute the largest proportion of multicellular diversity. A number of focused biodiversity sampling programmes have amassed immense collections to address this shortfall, but obstacles remain due to the lack of identification tools and large proportion of undescribed species globally. These problems can be partially addressed with DNA barcodes (“biocodes”), which have the potential to facilitate the estimation of species diversity and identify animals to named species via barcode databases. Here, we present the first results of what is intended to be a sustained, systematic study of the marine fauna of Singapore’s first marine park, reporting more than 365 animal species, determined based on DNA barcodes and/or morphology represented by 931 specimens (367 zooplankton, 564 macrofauna including 36 fish). Due to the lack of morphological and molecular identification tools, only a small proportion could be identified to species solely based on either morphology (24.5%) or barcodes (24.6%). Estimation of species numbers for some taxa was difficult because of the lack of sufficiently clear barcoding gaps. The specimens were imaged and added to “Biodiversity of Singapore” (http://singapore.biodiversity.online), which now contains images for > 13,000 species occurring in the country.

MinION-in-ARMS: Nanopore Sequencing To Expedite Barcoding Of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures

“…MOTUs) had the highest identification success to 345 species-level, followed by Arthropoda (5 MOTUs;Figure 2). A similar pattern of 346 identification success was noted previously byIp et al (2019).…”

“…This was possible through the careful application of the 415 appropriate mitochondrial genetic code in the error-correction step. Our amplification and 416 identification success rates were similar to a previous barcoding study by Ip et al (2019), 417 which employed a combination of Sanger and Illumina barcoding, further suggesting that 418 MinION barcodes are viable and that performance success is defined more by primer choice 419 rather than sequencing platform. 420…”

“…Ultimately, we opted for a MinION barcoding approach for the >2-mm size fraction 421 over bulk-sample metabarcoding (as with the other size fractions) in order to remain true to 422 the intended design of ARMS (Leray and Knowlton, 2015), which is to retain sequence-to-423 sample association. Such an approach will be helpful for the confirmation of previous species Ip et al, 2019). We emphasize that many of our samples remain unidentified due 433 to lack of robust online database matches rather than the ambiguities that persist in the 434 MinION barcodes after error-correction ( Figure 3); the latter of which has been demonstrated 435 to be of minor concern (Srivathsan et al, 2018, 2019; Ho et al, 2020).…”

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

“…A primer pair targeting exactly this same region, but using instead LoboR1 (Lobo et al 2013(Lobo et al , 2017 has been shown to produce similar or higher taxa recovery (e.g. Haenel et al 2017, Ip et al 2019, Chang et al 2020, but it has not been tested yet in NIS-focused studies.…”

Takeaways from Mobile DNA Barcoding with BentoLab and MinION

“…We first trialed the BentoLab processes ex situ using samples that were routinely obtained from various intertidal and subtidal surveys. These collections were part of an ongoing effort to document the marine fauna in Singapore as well as to grow the local biodiversity knowledge base and barcode databases [ 38 , 39 ]. We then brought the sequencing setup out to the field and performed the entire sample-to-sequence workflow out at sea to demonstrate its utility.…”