Episode Summary

Dr. Elizabeth Dinsdale, Matthew Flinders Fellow in Marine Biology in the College of Science and Engineering at Flinders University in Adelaide, Australia, uses genomic techniques to investigate the biodiversity of microbial communities in distinct ecological niches, including coral reefs, kelp forest and shark epidermis. She discusses how shotgun metagenomics is being used to characterize the architecture of microbial communities living in the thin layer of underlying mucus on shark’s skin, and how understanding the function of these microbes is providing clues to important host-microbe interactions, including heavy metal tolerance.

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Ashley's Biggest Takeaways

Sharks belong to a subclass of cartilaginous fish called elasmobranchs and are unique in that their epidermises are covered in dermal denticles—overlapping tooth-like structures that reduce drag and turbulence, helping the shark to move quickly and quietly through the water. These dermal denticles are sharp (if you’re going to pet a shark, make sure you go from the head to the tail to avoid getting cut!), and depending on the species of shark, may be more or less spread out across the epidermis.

Where do microbes enter the story? Dermal denticles overlay a thin layer of mucus, which provides a distinctive environment for microbial life. Collecting microbial samples from underneath a shark’s dermal denticles is quite difficult, and the technique varies by shark species (shark size, water depth and ability to bite all factor into the equation). Liz’s team uses a specially designed tool that the group affectionately calls a “supersucker,” to create and capture a slurry of microbes and water for analysis.

The team then uses shotgun metagenomics to identify and characterize the microbes in their collected samples. Sequencing has revealed biogeographical difference, as well as similarities in microbial architecture of whale sharks across the globe.

There are 2 populations of whale sharks—one in the Atlantic Ocean and the other in the Indian Pacific Ocean. Samples collected from both populations have revealed that each individual whale shark, from within each aggregation, shares many of the same microbes. In fact, unlike algae which may share 1 to 2 microbial species, whale sharks share about 80% of microbes across every individual. Since many of the sharks don’t cross aggregations, Liz’s team is investigating the possibility of coevolution between microbes and hosts.

Metagenomic sequencing also provides information about the function of the sequenced microbes. High presence of heavy metal-tolerant microbes has been found in the epidermis of all shark species that the team has analyzed. Sharks are known to carry high levels of heavy metals in their skin, muscle and even blood. However, muscle tissue samples contain lower concentrations than skin, indicating that there may be a density gradient in place, and raising questions about how microbes might be involved in this regulation. Is there a pathway by which the microbes metabolize and help to remove concentrations of heavy metals across the epidermis? Liz and her team are hoping to find out.

Featured Quotes:

“I chose sharks because they’re a very old lineage of vertebrate organisms. In fact, the oldest ones are still around today. They’re quite different from Teleost fish, which while they were evolved early on, had a radiation in more recent times."

“I’m wondering if the sharks actually have a longer-term relationship with their microbes than the Teleost fish and other vertebrates that we see today. And that might tell us something about the evolution of microbes and viral interactions with their hosts.”

“We’ve been able to collect samples from around 76 whale sharks from across the world in 5 different locations. They’re the most spectacular animal you’ve ever seen because they’re about 6-8 meters long. And we’ve gone out with collaborators in Cancún, Mexico; La Paz, Mexico;  Philippines; Tanzania and Ningaloo reef off Northern Australia, collecting the microbes on the skin of all of these sharks in all of these locations, which is really quite a big sample size.”

“We’re wondering whether the microbes on the epidermis change across the globe—whether they show biogeography—which they do. However, when we do a more robust analysis like a network analysis, we see that they have the same architecture, so the microbial community is structured in the same way, which is also quite interesting. So we’re wondering if that means that there’s a certain level of community or community structure that occurs on, or between, the dermal denticles.”

“Because we do shotgun metagenomics, we can actually identify what functions the microbes have. And the one really interesting standout that appears to occur is a high level of heavy metal associated genes. If you can compare the level of heavy metal associated genes on the sharks to the water column, it’s about 4x as much.”

“The other quite cool thing is when you do create these metagenomes, you do identify novel species. Many of our constructed genomes we can identify that they’re a gamma proteobacteria, full stop. They’re not matching any of the phylogeny any further, so that means we have some very novel microbes out there.”

“We’ve started looking at the viruses associated with the skin of the sharks, and most of them are phage as opposed to eukaryotic viruses, which is once again different from what people have seen on the skin of Teleos fish. Sharks are known as long-lived and health animals, so whether that is one of the mechanisms by which they’re not getting those high levels of viral infections is another outstanding question.”

Links for This Episode

History of Microbiology

Next generation sequencing (NGS), high-throughput sequencing methods that can process millions of individual DNA or cDNA fragments at the same time, became available and began to gain traction in the mid-2000s. In 2005, the 454 sequencing system became the first next generation sequencing platform to come to market, and Illumina acquired Solexa in 2007.

Metagenomic sequencing (mNGS) is a type of next generation sequencing that provides a hypothesis-free approach to detecting all nucleic acid in a given sample. Nothing specific is targeted, resulting in both host and microbial nucleic acid being sequenced. This gives researchers the ability to look at any portion of the genome sequenced, determine whether a microbe of interest is present in the sample, identify new or unexpected organisms and learn important information about the host.

The coral holobiont, is a dynamic group of algae, fungi, bacteria, archaea and viruses that form stable and species-specific associations with corals. In 2005, the group went to the Northern Line Islands, a group of Equatorial islands straddling the North and South Pacific Ocean that are all incorporated territories of the United States, and used metagenomics to investigate the microbes that were associated with a more pristine coral reef compared to a more degraded one. In addition to detection of 10 times more microbial cells in the water column of reefs on inhabited versus uninhabited islands, the group observed that the benthic communities on the most populated island had the highest prevalence of coral diseases. As Liz noted, shark numbers decreased in stressed coral populations where microbial communities increased in number and pathogenicity.

Prior to the research that Liz, Forest, Linda and Rob conducted between 2005-2009, disruptions in the holobiont were known to be associated with coral disease, but little was known about the specifics of how and why certain microbial species disassociate from their coral hosts in different ecological niches, a process called adaptive bleaching, and/or why they suddenly switch from mutualistic to pathogenic behavior. In order to learn more about these host-microbe interactions, the scientists exposed a species of marine stony coral, called Porites compressa, to a variety of known stressors, including increased temperature, elevated nutrients, dissolved organic carbon and lowered pH. They then isolated microbial communities and performed metagenomic sequencing (using a 454 Life Sciences system) and found that all types of stress increased microbial pathogenesis and the abundance of pathogen-associated genes, such as those involved in motility and virulence. Understanding how microbes are involved in the maintenance and degradation of coral reef ecosystems is a first step in preventing decline of one the most productive and biodiverse ecosystems on our planet.
If you are interested to learn more about the coral holobiont and want to read more content like this, check out our new issue of Microcosm, ASM’s flagship member magazine. The theme for our Spring 2022 issue is “Water Microbiology: Bringing Microbes to the Surface,” featuring exciting articles about waterborne pathogens, microbes and drinking water and how warming water temperatures are contributing to the spread of disease. Want to know more about “Symbiosis on the Reef,” and how research pertaining to corals and their symbionts has continued to advance? Are you curious about what retreating glaciers mean for microorganisms? Or how plastic pollution is contributing to antimicrobial resistance. We have all of this covered and more! Become an ASM member and start reading today!

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Mallory Choudoir