Plumbing the depths with environmental DNA (eDNA): Metabarcoding reveals biodiversity zonation at 45–60 m on mesophotic coral reefs

Abstract

Mesophotic coral ecosystems (MCEs) are tropical reefs found at depths of ~30–150 m, below the region most heavily impacted by heat stress and other disturbances. Hence, MCEs may serve as potential refugia for threatened shallow reefs, but they also harbour depth‐endemic fauna distinct from shallow reefs. Previous studies have characterized biodiversity patterns along depth gradients, but focussed primarily on conspicuous taxa (fishes, corals, etc.). Environmental DNA (eDNA) metabarcoding offers a more holistic approach to assess biodiversity patterns across the tree of life. Here, we use three metabarcoding assays targeting fishes (16S rRNA), eukaryotes (18S rDNA) and metazoans (COI) to assess biodiversity change from the surface to ~90 m depth across 15‐m intervals at three sites within the Hawaiian Archipelago. We observed significant community differences between most depth zones, with distinct zonation centred at 45–60 m for eukaryotes and metazoans, but not for fishes. This finding may be attributable to the higher mobility of reef fishes, although methodological limitations are likely a contributing factor. The possibility for MCEs to serve as refugia is not excluded for fishes, but invertebrate communities >45 m are distinct, indicating limited connectivity for the majority of reef fauna. This study provides a new approach for surveying biodiversity on MCEs, revealing patterns in a much broader context than the limited‐taxon studies that comprise the bulk of our present knowledge.

Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats

“…In contrast, Cheilodactylus was only recorded at shallow depths in TUVs (9.9–28.1 m) but appeared only in the 60 m deep‐water samples. This suggests that Cheilodactylus may have extended bathymetrical distributions beyond those reported by depth range databases or literature, as documented in other mesophotic fish assemblages through eDNA assessments (Hoban et al., 2023 ; Muff et al., 2023 ). Conversely, Pinguipes was observed in both shallow and deep reefs in TUVs (8.5–81.3 m) but only in 30 m shallow eDNA water samples.…”

“…This suggests that Cheilodactylus may have extended bathymetrical distributions beyond those reported by depth range databases or literature, as documented in other mesophotic fish assemblages through eDNA assessments (Hoban et al, 2023;Muff et al, 2023). eDNA approaches are complementary and that eDNA metabarcoding can detect more species than TUVs (Muff et al, 2023;Polanco Fernández et al, 2021).…”

“…In the only two mesophotic eDNA studies that we know of, Muff et al (2023) did find a decreasing significant depth gradient in fish diversity between 60 and 140 m deep in the Mediterranean Sea (temperate) and La Perouse (tropical island). Hoban et al (2023) on the other hand, observed marked community differences in a tropical island across depths for eukaryotes and metazoans, in particular around 45-60 m, but not for fishes. To what extent differences between our study in central Chile and these others represent differences between mesophotic reef ecologies or differences in fish fauna between oceans needs to be assessed.…”

“…Hoban et al. ( 2023 ) on the other hand, observed marked community differences in a tropical island across depths for eukaryotes and metazoans, in particular around 45–60 m, but not for fishes. To what extent differences between our study in central Chile and these others represent differences between mesophotic reef ecologies or differences in fish fauna between oceans needs to be assessed.…”

“…One evaluated fish diversity in one tropical and one temperate mesophotic reef highlights the large diversity of fish species identified at the two study sites and especially at mid‐depths (Muff et al., 2023 ). The other one used three metabarcodes to evaluate fish, eukaryote, and metazoan diversity in a tropical mesophotic reef (Hoban et al., 2023 ). The general extent of these patterns in productive upwelling temperate reefs and in other groups of marine organisms has not yet been assessed.…”