ABOVE: A close-up shot of Stylophora pistillata polyps. The brown tint comes from symbiotic dinoflagellates.

Coral reefs face myriad stressors, from pollution to climate change. Understanding how they respond to these threats on a molecular level is essential for predicting what will happen to them in the years to come and devising the best means of protecting them, says Tali Mass, a marine ecologist at the University of Haifa in Israel. Unfortunately, relatively scant knowledge about the different cell types in their bodies has hindered that kind of research.

To fill in those gaps, she and her colleagues published a complete cell atlas from the smooth cauliflower coral (Stylophora pistillata) in Cell on May 3. Among the 40 cell types described were two kinds of immune cells, the first cells specialized for immunity reported for any coral.

“This is something we’ve been needing to do...

Cell-by-cell breakdown

The team chose the smooth cauliflower coral because it’s well-suited to this kind of work. “It’s a very common species. It’s a robust species. It grows fast, so you can grow [it] in the lab,” Mass explains. Even though the animals are collected from the wild for studies, including for this latest one, their ability to do well in captivity has made the species “almost like the lab rat in the coral community,” and an excellent natural system for molecular work.  

A wild colony of smooth cauliflower coral (Stylophora pistillata)
Hagai Nativ 

To pull off the massive amount of sequencing needed to build the atlas, Mass and her colleagues had to revamp their tried-and-true RNA extraction protocols. Because the coral cells were easily stressed when they were separated from their carbonate skeleton and isolated for individual sequencing, the team members had to speed up their work. Ultimately, they cut the cell prep time from a 48-hour protocol to a 15-minute one by combining chemical and technical processes, Mass explains. The coral fragments had to be submerged in calcium-free filtered seawater with EDTA to reduce the presence of adhesion-promoting metals as much as possible while the coral tissue was gently scraped from the skeleton using a 10-microliter pipette tip, and the team ensured the cells’ viability throughout using Calcein/Draq5 staining. “It took us about a year just to develop that protocol,” she says.

The effort paid off, as the new procedure allowed them to sequence the transcriptomes of more than 37,000 individual cells from three different life stages of the coral: free swimming larvae, freshly settled and metamorphosed polyps, and mature adult colonies. The tens of thousands of transcripts from each cell were annotated by comparing them to published gene sequences, and then the cells were clustered based on gene expression patterns using MetaCell, resulting in the identification of 40 distinct coral cell types, including the first documentation of coral immune cells. 

Whether the animals actually had specialized immune cells was “a topic of debate,” notes Traylor-Knowles, though her work has long supported their existence. “For me personally,” she says, the finding of not one but two distinct kinds of immune cells “was just so vindicating,” and will greatly aid her investigations into the animals’ immunity. 

Microscope image of smooth cauliflower coral cells after separation
Shani levy

The process also identified key genes that may be useful as markers to visualize specific kinds of cells during histology or to separate them from other cells during flow cytometry, as would be required to generate a pure population of cells for detailed in vitro work. The newly discovered immune cells, for example, both express NFAT, a transcription factor originally discovered in activated T cells, as well as interferon regulatory factors and other immune genes, but they differ in the expression of other genes, including those involved in apoptotic pathways. 

“There is an urgent need to understand how corals are able to defend and cope [with] the recent rise of numerous diseases affecting worldwide coral reefs,” says Mauricio Rodriguez-Lanetty, who studies coral physiology at Florida International University. He agrees that the immune cells are a “very valuable finding,” and tells The Scientist that the ability to visualize and separate these immune cells will make it possible to study coral immunity in much greater detail, and could even open up the possibility of “genetic manipulations to improve the response of the cells.”

See “Restored Corals Spawn Hope for Reefs Worldwide

What makes the study especially thorough, Traylor-Knowles says, is that the team didn’t stop at transcriptomes. They also “grounded it with other techniques,” including in situ hybridization using the potential markers to highlight different cell types in actual coral tissues. They demonstrated that cells that express the epidermal gene Peroxidasin were indeed located on the animals’ outer surface, for example, and ones expressing a gene for gastrodermal collagen lined the animals’ gastric cavity.

Debashish Bhattacharya, an evolutionary genomicist at Rutgers University who studies symbioses in corals and other animals and was not involved in the study, says he’s excited to use the atlas to really dig into the animals’ so-called dark genes that are highly expressed in some cells but whose functions are currently unknown, as that might reveal novel insights into corals’ unique biology. 

For Rodriguez-Lanetty, the most thrilling part of the paper is the possibilities it opens up for studying symbiosis. Dinoflagellate algae live inside corals’ tissues and provide them with carbohydrates and oxygen and help remove waste, while the corals give the algae protection and some of the components they need for photosynthesis. 

See “Dinoflagellate Genome Structure Unlike Any Other Known

Close-up of a coral polyp using fluorescent microscopy. The dinoflagellates' pigments are glowing red, while some GFP-containing coral cells are glowing green.

Up until now, he says, it was impossible to separate the cells involved in symbiosis from other nearby cells in the coral’s tissues. Prior transcriptomic studies simply extracted RNA from ground-up chunks of coral, which meant there was a lot of noise in the datasets. “This study, for the first time, provides an approach that allows [one] to specifically interrogate the cells that are important in symbiosis, and be able to dissect and determine what are these genes and what [are] the cellular processes that take place in accommodating that symbiosis and regulating that symbiosis” he says. “It’s very transformative.”

The case of the disappearing stem cells

In their categorizing of different cell types, Mass’s group paid particular attention to signs of pluripotency. “A lot of people are trying to find out if corals really have stem cells,” she says, so they put extra effort into looking for them. But at least in the adult corals, their searches came up empty. None of the 26,880 adult cells they sequenced bore the well-categorized markers of stem cells, though some of the cells from larvae did. “I mean, we were happy to find them [in the larvae],” she says, but future research will need to explain why they appear to be lacking from adult corals.

Traylor-Knowles says she wonders if they truly are absent from adults, or if their absence was an artifact of sampling. “That was one area that it was like, why? . . . Why didn’t they find them? We know they’re there! So that’s still the mystery,” she says.

She points out that the study raises other questions. For instance, the team wasn’t able to match every cell to a described category of cell from other animals; some were ultimately classified as “unknown.” Because these cells don’t annotate well to other species, they could have functions unique to corals, she notes. The study “just really opens up a Pandora’s box . . . but in a good way.” Traylor-Knowles says she hopes that other researchers will follow the authors’ lead and generate similar atlases for other coral species. 

Bhattacharya agrees. “When people get out in nature and actually apply modern tools, they’ll find way more information that’s very, very exciting,” he says. And while studying both models and natural systems is clearly important, he says, “I’m just making the case that we should expend more energy on the wild stuff.” 

S. Levy et al., “A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity,” Cell, doi:10.1016/j.cell.2021.04.005, 2021. 

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Close-up shot of smooth cauliflower polyps

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