Seeking life in sedimented waters: Environmental DNA from diverse habitat types reveals ecologically significant species in a tropical marine environment

Abstract

Environmental DNA (eDNA) with metabarcoding or metagenomics will likely become a major biomonitoring tool in the 21st century, perhaps even more so in the face of increased coastal urbanization and its associated effects such as pollution, land reclamation, and seabed dredging. Together, these impacts and the consequent high turbidity pose severe challenges to traditional survey techniques that rely heavily on visual observations. We here demonstrate that eDNA can be used for biomonitoring in turbid waters, using Singapore as a case study. The cytochrome c oxidase subunit I (COI) locus was used to detect 525 metazoan molecular operational taxonomic units (MOTUs) based on eDNA obtained from 52 L of filtered seawater. Of these, 130 MOTUs (24.7%) were identifiable to species, including ecologically significant species that in some cases were invasive or rarely observed. Metazoan signals also enabled discrimination of discrete, but connected, environments from intertidal and subtidal zones. Taxa with known habitat preferences were found to have left trace eDNA at sites that matched putatively suitable habitats. Moreover, no coast-specific signals were detected in open water samples, which suggest that intermixing of water was limited. The study confirms that eDNA metabarcoding is a viable biomonitoring tool for coastal areas with highly sedimented waters.

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

“…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). Our results provide additional support for these findings.…”

Environmental DNA reveals a multi‐taxa biogeographic break across the Arabian Sea and Sea of Oman

“…Due to the sensitivity of the eDNA approach, there are some caveats to consider when interpreting data of this kind. The primary caveat is that the molecular assignments can only be as good as the DNA reference database on which they rely for species identification (Ip et al, 2021;Leray et al, 2019). In general, rare, regional endemic taxa are less well-represented than more common and widespread taxa, with marginal or insular seas often the least represented in DNA reference databases (Ip et al, 2021;Leray et al, 2019).…”

“…The primary caveat is that the molecular assignments can only be as good as the DNA reference database on which they rely for species identification (Ip et al, 2021;Leray et al, 2019). In general, rare, regional endemic taxa are less well-represented than more common and widespread taxa, with marginal or insular seas often the least represented in DNA reference databases (Ip et al, 2021;Leray et al, 2019). In our case, this deficiency in 16S reference sequences from Omani fishes available on GenBank may have led to some erroneous taxonomic assignments to closely related taxa that were better represented.…”

Prospects and challenges of environmental DNA (eDNA) metabarcoding in mangrove restoration in Southeast Asia

“…Environmental DNA metabarcoding allows for the early detection of elusive and invasive species at low densities, which is otherwise challenging to monitor using conventional techniques (Loeza-Quintana et al, 2021). Environmental DNA has been used to monitor the invasive Burmese python Python bivittatus in South Florida (Piaggio et al, 2014) and the Atlantic Charru mussel Mytella strigata in Singapore (Ip et al, 2021). Also, significant changes in indicator copepod species like Paracalanus indicus and Hexanauplia detected by eDNA metabarcoding can be used to monitor heat waves and their impacts on aquatic ecosystems (Berry et al, 2019).…”

“…Reliable monitoring of these organisms is crucial for data-driven conservation actions but remains a challenge owing to the lack of standardised methods, elusiveness of the species, and dependence on species experts (Thomsen et al, 2012). Environmental DNA has various proven applications in monitoring specific threatened taxa, including uncovering previously unrecorded elasmobranch species in Singapore's waters (Ip et al, 2021), mapping the distribution of endangered European eel (Weldon et al, 2020) and documenting rare and threatened sharks and rays across eastern Indonesia (Moore et al, 2021). This is accelerated by the development of universal primers that allows for metabarcoding and multi-taxa detection, e.g.…”