Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia

Abstract

Aim Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has rarely been tested across large spatial scales or biogeographical barriers. Here, we scale up marine eDNA metabarcoding, test its ability to detect a major marine biogeographic break and evaluate its use as a regional biomonitoring tool in Australia. Location North‐western Australia (NWA). Methods We applied metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes to 284 surface seawater eDNA samples collected from 71 mid‐shelf, inshore, coastal and nearshore estuarine sites over 700 km of the NWA coastline. Results Metabarcoding detected a wide range of bony fish (404 taxa), elasmobranchs (44) and aquatic reptiles (5). We detected bioregional and depth differentiation within inshore bony fish communities. These findings support the presence of a marine biogeographic break, which is purported to occur in the vicinity of Cape Leveque, demarcating the border between the Kimberley and Canning bioregions. Inshore bony fish and elasmobranch communities, as well as coastal bony fish assemblages, were additionally found to differ between the South and North Kimberley regions suggesting previously unrecognized subregional differentiation amongst these taxa. The overall compositional data have been used to update distribution information for a number of endangered, elusive and data‐deficient taxa, including sawfish (family: Pristidae), northern river shark (Glyphis garricki) and wedgefish (genus: Rhynchobatus). Main conclusions eDNA metabarcoding demonstrated a high level of sensitivity that was able to discern fine‐scale patterns across the large‐scale, remote and oceanographically complex region of North‐western Australia. Importantly, this study highlights the potential of integrating broad‐scale eDNA metabarcoding alongside other baseline surveys and long‐term monitoring approaches, which are crucial for the sustainable management and conservation of marine biodiversity in this unique marine region.

Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot

“…However, the performance of eDNA metabarcoding in comparative studies has brought inconclusive results, particularly in terms of its detection scale and in the number of detected and undetected species; e.g., studies in coastal habitats have suggested scales going from dozen meters (Jeunen et al, 2019;Port et al, 2016) to a few kilometers (O'Donnell et al, 2017). Detection scale is a relevant aspect because it determines the type of process that can be studied, from local reef dynamics within different habitats (Lafferty et al, 2020;West et al, 2020) to broader diversity gradients (Closek et al, 2019) and potentially even larger biogeographic patterns (West et al, 2021). In marine metabarcoding studies local oceanographic features influence this detection scale (Hansen et al, 2018;Thomsen et al, 2012) and can lead to larger diversity estimates than those captured by established monitoring approaches (Calderón-Sanou et al, 2019), because of the transport of the molecules from distant sources.…”

Observing Life in the Sea Using Environmental DNA

“…Vertebrate primers are particularly susceptible to off-target microbial amplification that can overwhelm the signature of the targeted vertebrate groups. Removal of these microbial products before sequencing is required to enhance the quality of vertebrate assays (West et al, 2021). b) shows the relationship between phytoplankton biomass estimated from microscopic counts and eDNA reads for diatoms; both follow an expected pattern similar to chlorophyll, given that diatoms are the primary bloom formers under upwelling conditions (Chavez et al, 2017).…”

Recent advances in environmental DNA‐based biodiversity assessment and conservation

“…In north‐western Australia, West et al. (2021) applied metabarcoding of the mitochondrial 16S rRNA and CO1 genes to detect bony fish, elasmobranchs and aquatic reptiles from 71 mid‐shelf, inshore, coastal and nearshore estuarine sites. Their eDNA metabarcoding was a highly sensitive detection tool that was able to discern fine‐scale patterns of marine fishes across the large‐scale oceanic region.…”