Underwater visual censuses (UVCs) are one of the most widely used methods of studying species-rich coral reef fish assemblages. However, a considerable portion of reef fish diversity is missed or underrepresented by these traditional survey techniques. Environmental DNA (eDNA) sampling is an emerging technology that can detect traces of animal DNA from environmental samples, such as water and sediment, potentially including taxa that are missed by UVCs. Here, we assess the complementarity of eDNA to UVCs in surveying coral reef fish communities, particularly for cryptic and cryptobenthic taxa. We further investigate the effect of environmental sample source (water and sediment) and depth (10m and 30m). We conducted UVCs and eDNA sampling in three islands of the Farasan Banks, southern Saudi Arabia. A metabarcoding protocol was applied to environmental samples using a broad-spectrum fish assay targeting 16S mitochondrial DNA. Our eDNA surveys revealed 94 fish species, across 86 genera, 38 families, and 14 orders. Of the species detected by eDNA, 48.9% were also recorded on transects and 60.6% on roving diver surveys. eDNA also detected 6 cryptic, 10 cryptobenthic, and 13 pelagic species. Of these, only one (Eviota guttata) was recorded by UVCs. eDNA species composition was found to be significantly influenced by collection site (islands), and sample source (more species detected from water samples than sediment samples), but not by collection depth (10 versus 30 m depth). Our study provides further evidence that eDNA is an effective tool for the biomonitoring of tropical coral reef fish communities. However, we also stress that improvements are needed in methodology and reference sequence coverage for eDNA to realize its full potential of capturing cryptic and cryptobenthic diversity.

Knowledge of biodiversity within an ecosystem is essential when trying to understand the function and importance of that ecosystem. A challenge when assessing biodiversity of reef habitats is cryptobenthic fishes, which encompass many groups that have close associations with the substrate. These fishes can be behaviorally cryptic, by seeking refuge within the reef matrix, or visually cryptic, using cryptic coloration to match the surrounding habitat. These factors make visual surveys inadequate for sampling these fishes. One such group of cryptobenthic fishes are the gobies, family Gobiidae, which currently represent over 1600 species, although new species are continually being discovered. Gobies are often small (less than 5 cm), and many species will be associated with a very specific microhabitat type. Due to the understudied nature of the Red Sea, little is known about habitat preferences of gobies within the region. In order to determine the differences in goby community structure within the central Red Sea, fishes were sampled at one reef using 1 m² enclosed rotenone stations from three distinct microhabitats: hard coral, rubble, and sand. Following collection, specimens were photographed and sequenced using COI, to aid in species identification. 232 individuals were collected representing 31 species of goby. Rubble microhabitats were found to host the majority of collected gobies (69%), followed by hard coral (20.6%), then sand (9.9%). Goby assemblages in the three microhabitats were significantly different from each other, and evidence of habitat-specialists was found. These results provide essential baseline information about the ecology of understudied cryptobenthic fishes that can be used in future large-scale studies in the Red Sea region.