Diving the Twilight Zone: How Scientists Risk Their Lives to Reveal Hidden Reef Biodiversity

The sun shimmers across the glassy surface of Blue Hole, a heart-shaped sinkhole, as two divers prepare to descend into its turquoise abyss. On the small boat, the clack of buckles, the snap of straps and the hiss of gas through tubes and tanks mark the last minutes above water. Luiz Rocha, a National Geographic Explorer and ichthyologist at the California Academy of Sciences, and Mauritius Bell, the Academy’s dive safety officer, are gearing up to drop roughly 330 feet into the mesophotic "twilight zone."

A new species of sea slug in the genus Marionia discovered during the Guam expedition.California Academy of Sciences

The Mission

Their objective is to recover autonomous reef monitoring structures (ARMS) the team deployed years earlier on Blue Hole’s floor. ARMS are roughly one-cubic-foot stacks of plates that mimic seafloor complexity, offering vacant habitat that attracts corals, sponges, worms and other organisms over time. These devices let researchers sample depths that are too deep for most divers but too shallow for submersibles and many remotely operated vehicles, providing rare windows into largely unexplored ecosystems.

A recently discovered sea slug that looks like a snow-covered forest was among the marine creatures retrieved by the divers.California Academy of Sciences

The Risks of Rebreather Diving

To reach the target depth Rocha relies on a closed-circuit rebreather. Unlike open-circuit scuba, which vents exhaled gas as bubbles, a rebreather scrubs and recirculates that gas, allowing longer and deeper dives. The trade-off is higher complexity and danger: a malfunction can produce too little oxygen, too much oxygen or a buildup of carbon dioxide, any of which can incapacitate a diver. Rapid, uncontrolled ascents are also deadly because they can cause decompression sickness as nitrogen forms bubbles in blood and tissues.

This piece of the ARMS, adorned with sponges, anemones, and crustose coralline algae, came from the only shallow-water ARMS that the scientists recovered during the expedition. The rest appeared to have been swept away during a storm.California Academy of Sciences

Rebreather diving is estimated to be five to ten times riskier per dive than conventional scuba; some estimates associate roughly 20–25 deaths globally each year with rebreather accidents. For Rocha and his colleagues, the scientific payoff justifies the danger.

This ARMS plate, which has been taken over by tube worms, spent eight years at a depth of 150 feet.California Academy of Sciences

At Depth

"Entering the twilight zone feels like landing on the moon," Rocha says. At around 330 feet, sunlight is scarce, but life is abundant and often vibrantly colored. The rebreather delivers a helium‑dominant gas mix to avoid nitrogen narcosis and other gas-related pathologies, but the arrangement gives Rocha only minutes on the seafloor. A typical bottom time for these dives is short — roughly 10 to 15 minutes — followed by a slow, staged ascent that can last four to five hours to avoid decompression illness.

A polka-dotted larval octopus found refuge between the plates of the ARMS. Deep reefs are thought to serve as nursery habitat for a wide range of marine species, including those who live in the shallows.California Academy of Sciences

Recovering the ARMS and Surface Work

After detaching the ARMS and placing them in sealed, buoyant containers, Rocha and Bell begin the long ascent. A second dive team meets them partway up, taking the ARMS the rest of the way to the surface. On deck, crews transfer each structure into seawater-filled bins and swarm around to inspect the catch. What emerges from the plates looks like abstract marine art: orange sponges, winding white worm tubes, ruby-red tunicates, branching corals and tiny, startlingly colored fishes that have never seen direct sunlight.

Laboratory Analysis and Discoveries

The ARMS are rushed to the Guam Center for Biodiversity Research at the University of Guam. Technicians photograph each plate, remove large organisms, and scrape encrusting material for genetic sequencing. The expedition cataloged about 2,000 organisms; Rocha estimates at least 20 are new to science, and he expects DNA results to reveal many more previously undocumented species.

Notable finds include a new dottyback with oversized eyes and persimmon-orange color, a yellow‑spotted, tree‑like sea slug, a nearly transparent goby, and an unusual hermit crab that occupies a bivalve shell instead of a snail shell. Such discoveries underscore how much remains unknown about mesophotic reefs.

Why It Matters

Mesophotic reefs, generally between about 130 and 490 feet deep, are underexplored and underprotected. Because few scientists are trained and willing to dive in this zone without submersibles or ROVs, these habitats often receive little conservation attention. Rocha emphasizes outreach — scientific publications, underwater photography and community events — as essential for persuading the public and policymakers to protect these hidden ecosystems. The California Academy of Sciences has even exhibited several fish collected alive from the mesophotic zone to help bring these reefs into public view.

“People tend not to protect the deep reefs,” Rocha says. “They don’t know they exist or don’t know what’s living there.”

Back in a University of Guam classroom, students and scientists passed jars around, marveled at translucent shrimp, a yellow crab with disproportionate legs and sunset-hued sea slugs. For many of these organisms, the world had known nothing of their existence days earlier. Rocha sums up the expedition with characteristic understatement: “Just another day at the office.”