Robots give scientists unprecedented access to study coral reef biodiversity

Mesophotic coral ecosystems have some of the highest diversity of stony corals (Scleractinia) in the world, making them particularly important for researchers. These ecosystems are also unique because they host more native species compared to shallow-water coral ecosystems. However, they are difficult to monitor because they are often located at deeper depths of 30 to 150 meters.

To accurately monitor these corals, scientists require both scuba diving and taxonomy skills, which can be challenging. Existing monitoring methods therefore impose limitations on conducting thorough surveys, and new methods are needed.

Scientists have found an innovative solution: environmental DNA (eDNA) analysis using underwater mini remotely operated vehicles or Mini-ROVs. By collecting and analyzing genetic material that corals naturally release into the water – environmental DNA or eDNA – multiple species present in these deeper-water environments can now be identified without direct observations. This makes it easier to study previously hard-to-access biodiversity hotspots.

Researchers at the Marine Genomics Unit at the Okinawa Institue of Science and Technology (OIST) and their collaborators at the University of the Ryukyus and NTT Communications, have established a robust system to monitor mesophotic coral ecosystems using a combination of underwater robots and eDNA barcoding. Their findings have been published in the journal Coral Reefs.

Four monitoring sites in Shigeo Reef near Motobu Peninsula in Okinawa, Japan, were surveyed. Two sites were approximately 35-45 m in depth (SR1 and SR2), and two deeper sites were approximately 54-59 m in depth (SR3 and SR4). A Mini-ROV collected water samples from each site. Seawater samples were collected approximately 0.5-1 m above the reef bottom and carefully preserved to protect any coral eDNA present.

A scleractinian coral eDNA survey at four mesophotic sites using an underwater mini-ROV. (a) Four monitoring locations (SR1-SR4) at the Shigeo Reef near Motobu Peninsula. The location of Okinawa Island, Japan, and the survey area are shown in the upper-left squares. (b) Information on sampling locations, latitude, longitude, approximate depth, and water volumes collected for each sampler (left and right).

Satoh et al., 2024

(a) FIFISH W6Plus mini-ROV with two seawater samplers, (b) Shigeo Reef site SR1 view from mini-ROV camera, (c) Shigeo Reef site SR2 with dominancy of Seriatopora hystrix, (d) Shigeo Reef site SR3, (e) Shigeo Reef site SR4 with dominancy of Alveopora cf. catalai.

Satoh et al., 2024

The scientists analyzed mitochondrial DNA to identify coral species. To improve accuracy, a custom database using complete mitochondrial genomes of corals was created. This database helped identify the eDNA sequences and allowed the researchers to accurately identify and analyze coral genera present in their samples.

The eDNA analysis and underwater robot observations revealed different coral communities at each study site. SR1 was rich with several coral types, particularly Acropora, Seriatopora, and Pachyseris, along with some Cycloseris and Galaxea. SR2 was dominated by Seriatopora corals with some Galaxea present. SR4 showed a diverse community led by Alveopora, accompanied by various other coral types. In contrast, SR3 had the sparsest coral coverage, featuring only a few Lobophyllids and Cycloseris, despite being close to the more diverse SR4 site. These varied distributions made these sites ideal for testing the effectiveness of the new DNA sampling method.

(a) Bar graph showing the distribution and approximate proportions of scleractinian corals at four monitoring sites (SR1-SR4) of mesophotic Shigeo Reef. Brown arrowheads indicate Seriatopora corals. (b) The proportion of DNA in each water sample that matched to different types of coral.

Satoh et al., 2024

Importantly, the results from the eDNA metabarcoding analysis confirmed previous observational data on coral species at all 4 sites. However, the technique is not without its limitations. In some cases, the eDNA analysis could not distinguish between closely related coral species, and the success rate of DNA sampling varied between locations. Despite these challenges, the study represents an important step forward in coral reef research. The ability to detect coral species through water samples and visually confirm their presence provides scientists with a valuable new tool for monitoring coral reef health and biodiversity in hard-to-reach locations.