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Engineering Coral Microbiomes with Dr. Julie Meyer By Rosie Kereston

It all started for Dr. Julie Meyer, assistant professor in the UF Department of Soil and Water Sciences, when she was asked to pick between collecting insects or plants for a middle school science project.

“We had to go outside and take notes on them, to find out what and where they were. I picked the plant collection and afterward decided: that’s it! I knew then that I would be a scientist.”

In high school, she considered going into medical research but the call to save the great outdoors was strong. After participating in a volunteer project on orchid populations, she began to turn her academic interests towards the promising field of genetics.

Dr. Meyer received her PhD in Marine Biosciences from the University of Delaware for her work on deep-sea microbes and hydrothermal vents.

“My deep-sea research was all very exploratory compared to what I do now,” she explained, noting it was difficult to physically see what she was studying. “It was great and exciting work, but I decided to move more towards the coast. I can actually manipulate [the organisms] I am studying in the lab, instead of just getting to see them once or twice a year from a submersible.”

She set her sights on coral reefs and seagrass beds, investigating “the structuring of their microbial communities and the impact of microbiomes on ecosystem functions.”

Healthy Orbicella faveolata colony in Belize. Photo courtesy of the Meyer Lab.

The Significance of Coral

Coral reefs form the backbone of the richest biodiversity found in the ocean, supporting millions of species and over half a billion people that rely on reefs for their livelihood. Diseases triggered by environmental imbalances, such as increasingly warmer waters or pollution, are quickly becoming major problems for coral all over the world. The Meyer Lab is working to combat these issues by researching and understanding the corals’ microbiomes and developing probiotic treatments for their diseases.

Corals are the result of millions of years of symbiotic existence between some of the ocean’s smallest animals and plants: invertebrates called polyps and a type of algae called zooxanthellae. While polyps use small tentacles to catch their microscopic food during the night, most of their energy is typically captured during the day by photosynthesizing algae that live safely within their tissues.

Polyps secrete a limestone skeleton to anchor their soft bodies to the seafloor and to one another, allowing the many polyps to act as a single organism. Over many hundreds of years, the remaining skeletons accumulate and create impressive limestone structures covered in polyp colonies. These complex biological structures rely on a uniquely balanced environment to maintain their well-being and are good indicators of the health of their environment.

Coral being observed in the Meyer Lab. The individual polyps can be clearly seen here as well as their limestone base.

Microbial Ecology & Bioinformatics in the Meyer Lab

Dr. Meyer’s research sits at the intersection of microbial ecology and bioinformatics. She strives to understand corals and their relationships with their microbiomes: the collective genomes of the many microbes that live on and within coral.

“We are taking what we know about the microbiomes of different keystone species, like corals and seagrasses, and then we look at the genomes of the bacteria that make them up,” Dr. Meyer stated. “We know that microbes are beneficial and do important things to maintain coral health, but now we want to know which strains of bacteria do what to support the coral’s health.”

Dr. Meyer is developing engineered solutions to coral diseases with this applied microbial ecology. In her lab, they sequence the genomes of bacteria, create gene libraries to identify different bacterial colonies, and isolate strains of bacteria that make up the microbiomes of corals. With this information, they can make a positive impact through a deeper understanding of the complex microbiome of coral.

The Meyer Lab collaborates with the Smithsonian Marine Station in Fort Pierce, Florida, and with the University of North Carolina Wilmington to develop these probiotics for the environment. Her lab has focused primarily on sequencing these various and potentially helpful probiotic strains, while her collaborators are testing the probiotics in the field.

With the recent addition of a new microfluidics system to the lab at UNC, Dr. Meyer is hopeful that results will now come sooner than they have in the past. She stated that, “it took sequencing and screening hundreds of potential probiotics to find a good one. If we can screen more and screen faster, our chances of a useful result will increase dramatically.”

Collecting microbiome samples from Meandrina meandrites in Little Cayman. Photo courtesy of the Meyer Lab.

Coral Diseases and their Treatments

A primary focus of the Meyer Lab is understanding stony coral tissue loss disease (SCTLD), a fast-spreading, dangerous infection that affects the entire Florida reef tract and is quickly dispersing into the Caribbean. It appears as white, dead areas on healthy coral and can kill it in weeks to months. This is considered by some to be the deadliest coral disease ever recorded, due to its high prevalence, progression, and the number of coral species impacted.

Montastraea cavernosa with stony coral tissue loss disease, Broward County, FL. Photo courtesy of the Meyer Lab.

It is suspected that the disease is traveling exceptionally fast due to its presence in ballast water, the seawater used in ships to maintain buoyancy. The environmental impacts of sea water being displaced are well known, including the introduction of invasive species and diseases into vulnerable areas.

The cause of this disease is still unknown, but Dr. Meyer is working to change that.

“We have been focused on identifying the pathogen that causes this disease. The scientific community is still debating if it is bacterial or viral, but we know it does respond to antibiotics. This suggests that it is a bacterium or that a secondary infection of bacteria is responsible for the corals’ symptoms.”

Dr. Meyer and her collaborator’s upcoming paper involves the description of the first identified probiotic strain and subsequent successful treatment to combat SCTLD. After successfully testing it on corals in the lab, she was faced with the unique task of applying this medicine to corals in the wild.

“That’s the tricky thing! We can just take a pill, but coral is more complex. Right now, scuba divers go down and apply the probiotic directly to the coral colony in a sort of paste. They can also cover the diseased coral with large, weighted bags inside which the probiotic is administered to the entire colony at once. We intend to use both of these methods simultaneously for our next trials, as it is most effective to have both types of treatment applications.”

Dr. Meyer explains that she is especially proud of her research on understanding black band disease, a similarly deadly illness that afflicts coral with a suffocating mat of harmful cyanobacteria.

Orbicella annularis with black band disease in Belize. Photo courtesy of the Meyer Lab.

It was discovered to not be a pathogen, but rather the result of an imbalanced environment negatively impacting the coral’s microbiome.

“We found that even corals that had no signs of the disease already had the bacteria in question present, just in very low numbers. These bacteria are normal and naturally occurring in coral, but under the right conditions they become destructive. When this delicate system becomes imbalanced due to environmental changes, the preexisting bacteria can take over and cause damage.”

Dr. Meyer is looking ahead to further applications of microbiome engineering to improve other marine ecosystem foundations, particularly seagrass.

“We have a lot of manatees starving because they don’t have enough seagrass to eat,” she explained, referencing suffocating algae blooms and other diseases that damage it. “Like coral, seagrass is the base for many ecosystems. If we can use probiotics to improve seagrass restoration in the same way we are currently working with coral, we can speed up their healing processes and encourage new growth.”

Future Medical Implications of Microbial Research

The tools and processes developed for the environment by the Meyer Lab could one day find use in medicinal applications.

Cyanobacterial mats, while generally dangerous for coral, often produce a lot of interesting materials. Dr. Meyer explained that as they photosynthesize and produce large amounts of energy, “some of that energy can go into the production of these weird products. We don’t know what the majority of these products do. They might even have the potential to be used as anti-tumor and anti-cancer drugs.”

By researching which genes within the bacteria produce which products, the health of the coral could be improved and the products produced by the related bacteria could lead to medical discoveries. A class of anti-tumor compounds called dolastatins has already been found to be a product of some cyanobacteria found in coral reef environments.

“We are working towards tying natural products to the genes that make them. If we know the sequences that make those important products, we can transfer that to biotechnology and make it ourselves, but better.”

Different strains of bacteria being cultured in the Meyer Lab.

Dr. Meyer hopes the general public can grow to appreciate how prolific and critically important bacteria are, not just for coral, but for our bodies and the world around us. Despite being an essential part of life, there is still so much about microbe function that is unknown.

“If we knew more about them, maybe they could help us more with the problems we are facing. We already actively use bacteria in many areas of our lives, like in food production and even wetlands and sewage treatment. We use them all the time without knowing much about them. I am uncovering some of the ways they do the things they do using genetics and multi-omic techniques.”

Dr. Meyer expressed that, “[her] love for this field ties into the thrill of being a scientist in general. When you sequence a new genome or uncover a new species, you are the first person that has ever seen it. There’s always such a sense of discovery!” ∎

Learn more about the Meyer Lab’s research and the people working to make these discoveries here.