Identifying the world’s rarest coral

Dr. Bry Wilson of the University of Oxford has always had a passion for natural science. “I was brought up on Cousteau's voyages by my father, who was a diver himself.” He was always fascinated by marine environments. ”I don't just mean idyllic white-sand beaches, but also the rugged frozen north and the surging seas of the southern oceans.” So it was no wonder Wilson pursued a career in marine biology.

In 2005, after reading about the spread of coral diseases, he impulsively packed his bags and flew to the other side of the world to research the impact of disease on the Great Barrier Reef. Since then, saving the corals has become his life’s work. “I've had the good fortune to work in reefs in the South Pacific, Southeast Asia, the Great Barrier Reef, and even off the Norwegian Continental Shelf,” he says.

Coral is not the most straightforward subject matter to study, though. They exist in “this incredibly beautiful symbiosis” with the organisms that live in and around it, says Wilson. “They have representatives from essentially every single kingdom nestled within a single coral colony - viruses, bacteria, archaea, fungi, protozoa and then on top of that, you've got the coral itself, which shares this extraordinarily intimate relationship with the intracellular algae that live within it. Fish and crustaceans such as crabs and shrimp that live within the colony bring their own little microbial parties to the coral holobiont. Corals are immersed in this incredible microbial soup. It’s an extraordinarily difficult system to work with.”

A metagenomic jigsaw puzzle

But the corals’ complexity is what compels him. “Trying to tease apart what’s going on in that crazy chaos is something that drew me in.” It’s essentially a metagenomic analysis “because in a system this complex, you're never pulling out just the genome of a single organism. It's a huge jigsaw puzzle that has to be solved when you're doing genomic assemblies.”

While all corals are at risk, some are more resilient than others. And Wilson wants to find out why. “By using molecular tools, we can examine the DNA of these particular organisms and these very complex communities.”

“We’re looking at certain immune genes to see whether they’ve got differences in their systems and whether that’s giving them better resilience to heating events.”

Wilson and his team use an old North Sea firefighting ship as their research vessel while in the field. “Our field season is limited to about a month a year when the trade winds subside to allow us to have a fairly comfortable seagoing voyage,” Wilson explains. To create a cool refuge for RNA and DNA sample processing in the sweltering humidity and heat of the tropics, they built a lab on the deck out of a shipping container. It holds an air conditioning unit, a small freezer stocked with ice packs, a fridge, a worktable and benches. It’s equipped with a centrifuge, various lab paraphernalia and molecular testing tools, including a variety of QIAGEN kits, including buccal swab kits, blood kits and plant and soil kits. Back on land, QIAGEN’s Genomic Services group also helped Dr. Wilson analyze some of these highly-challenging samples, including purification of nucleic acids, NGS library preparation, and both whole-genome and 16S rRNA sequencing

RNA from reef to raft

A major issue with extracting DNA from environmental samples is the downstream processing, he says. “It's the inhibitors, the contaminants that are part of nature, and the chaos of the samples that affect the things that we do downstream, in particular the polymerase chain reaction, or PCR. One of the things that QIAGEN has done an excellent job of doing is using reagents that actually release and sequester these things that prevent us from amplifying DNA. Corals, in particular, are a major source of concern because they're such a complex mishmash of different organisms.”

Wilson even does some sample processing underwater, right at the reef. “I chisel off a tiny bit of coral and put it into a Ziploc bag underwater, and then we ascend and get back to the boat as quickly as we can usually within 10 or 15 minutes.” Sometimes he processes a sample while bobbing in one of the rafts they use to access reefs the vessel can’t reach.

He uses a proprietary RNA stabilization reagent that essentially freezes molecular time. “Pipetting 100 microliters of a compound or chemical when you’re in an inflatable boat in a two-meter swell is a challenge,” he says. Still, it can be critical because microbial and endosymbiotic communities can change drastically over a period of hours due to changing temperatures or conditions.

Stopping coral bleaching

A classically derived metric for gauging coral health is color. The bone-white hue of a damaged or dead coral reef is caused by coral bleaching. Environmental stresses like heat or pollution cause the coral to expel their colorful microscopic algae. Corals can starve to death without them.

But molecular testing can reveal what’s going inside the coral genome before a bleaching event occurs, says Wilson.

“We can use molecular tools to look at genes and see how these are being switched on and off. We can see these stresses long before the symptoms are manifested by looking at particular stress genes or immune genes, or even in some cases, the proliferation of certain bacterial pathogens that are going to lead to a disease state.”

The hope is that “given enough warning, if we knew a coral was under particular stress, we might be able to manage or mitigate these factors. This is something that a lot of people are currently investigating at blighted coral reefs around the world.”