Palau is famous for its spectacular and rich coral reefs. But these divers were planning to descend past those sun-lit marine communities and down into a lesser-known twilight zone known as the “mesophotic coral ecosystem.”

Mesophotic essentially means “middle” and “light,” which is where these ecosystems are—not quite in the bright daylight, not quite in the profound darkness, but somewhere in between. For simplicity’s sake, we’ll call these communities, which range from some 30 meters to 150 meters below the surface, the “deep reefs.”One of the divers on the boat with me was a zoologist and curator at the California Academy of Sciences named Luiz Rocha, who has spent decades studying these deep reefs and their secrets.

“Anything between 30 meters and 150 meters is really, really unknown,” he told me. Because these deep reefs are so unknown, researchers like Rocha are left with big questions. They want to get a baseline picture of what is going on in these ecosystems—even just who lives there!—so that they can better understand how they function. They’ve also tried to work out whether (or not) these deep reefs might provide a refuge for species living in shallower coral reefs.

I was in Palau for Vox’s Unexplainable podcast because, in an effort to gather more information about these mysterious places, Rocha left some scientific structures down in these twilight depths back in 2016. Those structures then spent almost a decade becoming encrusted with all kinds of marine life. And now, Rocha was back to retrieve them, hoping that he—along with many other scientists — would be able to open them up, like a box of scientific puzzle pieces, full of clues about this under-understood marine world.

One thing that’s often acknowledged in papers about mesophotic coral ecosystems is that scientists don’t know as much as they’d like to. A National Oceanic and Atmospheric Administration article about them from 2019 is full of “mays,” as in: They may “serve as essential fish habitat for economically and ecologically important species.

Researchers do know some things, of course. They know that these deep reefs can be found in many of the same regions as shallower coral reefs—so mainly the tropical and subtropical parts of the world, like Micronesia, the Caribbean, and even the Gulf of Mexico. They’ve found that there are many species that seem to be unique to these places, and recent research points to their potential susceptibility to climate change.

Researchers have also gotten a sense of some of the key differences between these deep reefs and their shallower coral neighbors. In shallow reefs, hard corals team up with photosynthesizing algae. The algae provide the corals with nutrients, and the corals secrete a calcium-carbonate matrix that helps create the architecture of the reef.

As you go deeper, though, the light begins to fade, and the opportunities for photosynthesis start to fade with it. The temperature also drops. So the animals living down in the deep reefs are ones that can survive in a dimmer, cooler world.

Scientists can dive into the deep reefs to try to learn more about these understudied places—as Rocha has—but exploring down at 100 meters requires more difficult, riskier technical diving than exploring at shallower depths. The deeper you dive, for example, the faster gases get pushed into your tissues, which imposes limits on these really deep dives.

“We have a very, very short time,” Rocha says, “And by short time, I mean five minutes. Six, seven minutes.”Scientists can take some pictures in that time, make some measurements, or collect a few samples, but then they have to move back upwards—a process that can take hours, since they must rise slowly to avoid decompression sickness.

It is, obviously, not particularly efficient to study an ecosystem in five- to seven-minute intervals. People have also used remote-operated vehicles and submersibles to explore the deep reefs, but those have their own issues, and cameras can’t always capture all the detail you might want, or photograph more secretive, cryptic animals. So huge gaps remain in scientific knowledge about these ecosystems.

“Whenever we go somewhere,” Rocha says, “the first thing we find is new species. It’s the most basic thing in science you can do.”But this effort goes beyond just cataloging new species of fish, sponges, or sea slugs.

Rocha wants to answer fundamental questions like: What is the main energy source for everything down here in the dim light? What does the food chain look like? How have things evolved to live at these depths? How similar are they to the shallow ecosystems, and how different? How are they affected by climate change—and what’s the most efficient way to protect them?

But Rocha says that “in some ways, we don’t even know what questions to ask. We really only know what the crucial questions are when we have a baseline understanding of the ecosystem. And for deep reefs, we don’t have that yet.”Rocha is not deterred by the enormous number of question marks that surround these deep reefs. For years now, he has been gathering bits of basic information about them, often via those very short dives. About a decade ago, though, Rocha got interested in another method for sampling the biodiversity of this sort of marine ecosystem—a technique involving “autonomous reef monitoring structures” or ARMS.

Basically, each ARMS is a stack of several PVC plates, separated at uniform intervals and attached to a base plate. They look like little gray, featureless hotels. You take them to a place that you want to study, bring them down, secure them, and then leave them alone for a while to let them collect … life.

“As soon as you drop any kind of clean structure on a reef,” Rocha says, “it starts getting colonized by larvae of everything around it—of sponges, gorgonians, corals. And then, because there’s a lot of hiding spots between the plates—so between the floors of the hotel—they start getting colonized by shrimp, by mollusks, by ascidians, by anything you can imagine in the ocean. And it becomes this stable, diverse mini reef, if you will, packed with a lot of biodiversity that would be very hard to collect all at once in any given reef.”A few years after that initial drop, you come back, collect the ARMS, and then study the mini reef that has grown on them. You can sample and touch and analyze things to your heart’s content.

It’s not only a very effective way to collect lots of creatures, all at once, but also a great way to do so in a standardized way. If you went down—or sent a robot down—to collect an encrusted rock from a reef, you could learn a lot about the life on it, but it would be hard to compare the life on that rock to life on other rocks from other reefs, or even the same reef, because each rock would have its own unique characteristics.

Not so for ARMS. “ Every one’s the same,” Chris Meyer, director of the Smithsonian Global ARMS program, told me. “It’s prefab housing, and then you just look to see who moves in.”

To Rocha, this seemed like a great way to get a really good, long look at the deep reefs instead of the brief glimpses he was getting from diving. It was also, he told me, fairly cheap to deploy them. So from 2016 to 2018, with some private funding, he and his colleagues left ARMS in some of the deep reefs around Palau—as well as in Guam, the Marshall Islands, and French Polynesia. They installed some around 50 meters, and some around 100, and then some around 10 meters, so he could compare the deep reefs to their shallower neighbors.

After that, he waited. In fact, he waited a little longer than he would have liked, because the retrieval of ARMS is more expensive than deploying them, so he had to work out more funding.

Eventually, private funders agreed to underwrite the retrieval of the ARMS that Rocha had left. Which is how he and his fellow divers finally found themselves on a boat in Palau again, ready to pull up these structures from the deep. The process was, as it turned out, equal parts magical excitement and well-oiled, Cheez-It–fueled disassembly line. After the plates were taken apart, Meyer took photographs of the plates—what he called a “time capsule of the place.”

Others in the lab picked carefully through trays of debris, hunting for tiny crabs and worms and mollusks, or scraped samples off the plates and deposited them in tubes. They collected sea squirts, said to be our closest invertebrate relatives. They collected sponges—flat ones that felt dry underwater, thick ones with bristles like tiny, unmoving caterpillars, one as thin as a flake of skin and shot through with silver filaments. They collected strange, soft corals known as octocorals, and they collected colonies of animals called bryozoans, which created what looked like swirling, two-dimensional honeycombs. “We’re looking for every unique thing, which we call a morphospecies,” a Smithsonian research biologist named Sarah Tweedt explained.

“And we’re trying to get some representative tissue samples from all of these things so that we can sequence the DNA—and match the DNA to the organism.”That is, of course, assuming there is already a known genetic match in our existing DNA libraries. On the first day that I spent with the team, a Cal Academy curator named Terry Goslinger identified several potential new species. He is an expert on colorful, delightful sea slugs known as nudibranchs, and so, because of his deep knowledge (and because nudibranchs’ bright hues and patterns make them somewhat easier to tell apart than some other underwater creatures), he was able to make some on-the-spot calls about whether or not certain species were likely to be new to science, pending genetic testing to confirm.

Many of the animals were trickier to pin down, though. The researchers did their best to identify the creatures they were finding, but even now, several months out, there’s still a lot of work to be done. Of the close to 3,000 specimens, only a small fraction were identified at a species level. The numbers are a little bit inexact because researchers are still processing the data, but when I checked in with a Cal Academy postdoc working on the project, Susanne Bähr, in July, she told me that only 3 percent of samples had been ID’d by species, and a little less than 20 had a genus designation.

Many, many more were only identified at higher, broader taxonomic levels. Genetic testing of the samples, paired with photographs and descriptions of the samples, will help people work out more specific species, and also help them identify whether certain species are new to science.

The most important parts of this work will involve more than just identifying species. In fact, the more time I spent with these researchers in the lab (including one evening spent with them as they worked past midnight), the more I got the sense that, while they seemed excited about seeing new species, they seemed equally excited to witness relationships between animals.

When I walked into the lab one day, for example, several people urged me to go over and look through a microscope at a creature known as a pompom crab—a tiny yellow crustacean holding purple anemones in its modified front claws. Tweedt was extremely jazzed when she found something referred to as a “skeleton shrimp,” which looked to me like the marine equivalent of a stick insect, blending in on something called a hydroid. She pulled me aside another time, around 1 in the morning, to show me “the frosting on the cake” of the day, which turned out to be some bright red sea snails and the bright red octocorals they seemed to live on As she put it in a later conversation, these relationships are, in many ways, the key takeaway from this ARMS project, and what distinguishes it from efforts to bring up a few individual samples at a time.

Studying them, or even just looking at the fuller picture ARMS provide, is what will let researchers tackle some of the outstanding questions about these ecosystems. Bähr, for example, is already working with the data from ARMS retrieved in Guam, trying to analyze how much overlap (or lack thereof) there is between species at different depths in the deep reefs.

Really, though, this is all just the beginning. In one of our conversations, Rocha compared the work they are doing now to ecology work done in the mid-20th century to understand how species’ vertical distribution changes as you go up a mountain. This drove home for me how far behind researchers working on the mesophotic deep reefs are compared to their colleagues working on, say, shallower coral reefs. I asked him what kept him working on such a difficult puzzle.

“It’s the reward at the end of it,” he said. “If it’s a hard puzzle, at the end of it, the reward is always bigger.”“But in our lifetimes, will we assemble the deep reef puzzle?”I asked.

“No, we will not assemble the puzzle, no,” Rocha said, “but we’ll generate some good pieces for the next generation to assemble.”