Coral monitoring in northwest Australia with environmental DNA metabarcoding using a curated reference database for optimized detection

Abstract

The need for efficient and more accurate ways of monitoring threatened ecosystems is becoming increasingly urgent as climate change intensifies. Coral reefs are an example of an ecosystem in crisis, with widespread declines in coral cover and diversity documented over recent decades. Novel molecular approaches such as biomonitoring using environmental DNA (eDNA) from seawater samples show great potential to complement future coral reef monitoring programs, especially when used in combination with conventional methods. However, eDNA metabarcoding studies often rely on public databases (e.g., GenBank) for assigning taxonomy, which generally limits the number of sequences that can be taxonomically identified. The extent to which building reference tissue sequences improves taxonomic resolution has yet to be fully examined. Here, we combined traditional coral reef monitoring data with eDNA assessments derived from seawater collected at the highly diverse Rowley Shoals in Western Australia. Using two ITS2 assays developed to target basal metazoan DNA and a reference database spiked with 70 local coral specimens, we identified 37 genera and 40 species from 56 1 L seawater samples. We identified considerable overlap of taxa with visual survey data and showed that assignment of amplicon sequence variants was significantly improved when “spiking” the taxonomic classifier with curated sequences of locally collected species. Our findings showcase the potential of eDNA metabarcoding for monitoring the biodiversity of reef corals and highlight the importance of custom reference sequence databases for improving taxonomic resolution in metabarcoding studies.

Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding

“…In addition, surface and 2-3-m sample pairs clustered together (Figure 5), indicating that eDNA does not vary based on sampling depth at these locations. No differences were observed in an eDNA survey in western Australia between surface and bottom eDNA samples; thus, sampling from the surface is sufficient (Dugal et al, 2021). In addition, no significant differences in marine metazoan diversity patterns were detected from eDNA samples collected at different depths (Ip et al, 2021).…”

“…The greater conservation of our Scle-CO1-Fw and Rv primer sequences may be related to the higher percentage of sequencing reads that mapped to scleractinian CO1 genes (72%, Figure 4A) than percentages of DNA reads mapped to anthozoan 16S (61%) and CO1 markers (51%) (Nichols and Marko, 2019). Although it may be related to differences of benthic fauna, the percentages of scleractinians among PCR amplicons using primer pairs, CoralITS2 and CoralITS2_acro, for nuclear ITS-2 genes were around 50% (46.7 and 57.5%, respectively) (Alexander et al, 2020), and those primer pairs sometimes required more PCR cycles (45 cycles), depending on sampling sites (Dugal et al, 2021). Note that percentages of identical nucleotides for Scle-12S-Fw and Rv primers were 86 and 95%, respectively (Figure 1B), higher than those of other 12S universal primers, 75% for ANTMTSSU-F and 85% for ANTMTSSU-R (Chen and Yu, 2000; Figure 1C) and primers mentioned above for the CO1 gene, indicating high specificity of Scle-12S-Fw and Rv primers for scleractinian mt genes.…”

“…Recently, eDNA has been used to monitor marine biodiversity, especially among fishes (Miya et al, 2015;Yamamoto et al, 2017). Several studies have reported detection of eDNA from stony corals (Shinzato et al, 2018;Nichols and Marko, 2019;Alexander et al, 2020;Dugal et al, 2021), and eDNA is expected to become a powerful tool in coral monitoring.…”

Metabarcoding the marine environment: from single species to biogeographic patterns

“…Furthermore, BRUV and eDNA metabarcoding techniques detected distinct fish communities, with some species recovered only by a single method indicating that a combined approach is desired if the goal is to capture total community diversity in these intertidal habitats. West et al (2021) and Dugal et al (2021) focus on an important coral reef network in the Kimberley region of northwestern Australia. Specifically, they showed that eDNA metabarcoding of the ITS2 region resulted in high rates of detection at the species and genus level for the habitat building scleractinian corals (Dugal et al, 2021;West et al, 2021), as well as other benthic invertebrates such as sponges and tunicates (West et al, 2021).…”

“…West et al (2021) and Dugal et al (2021) focus on an important coral reef network in the Kimberley region of northwestern Australia. Specifically, they showed that eDNA metabarcoding of the ITS2 region resulted in high rates of detection at the species and genus level for the habitat building scleractinian corals (Dugal et al, 2021;West et al, 2021), as well as other benthic invertebrates such as sponges and tunicates (West et al, 2021).…”