My trip to Australia is part of a larger project to identify the ‘good’ microbes associated with corals. It may seem odd at first to talk about ‘good’ bacteria and viruses. They get us sick and spoil our food, and we’re constantly trying to get rid of them with antibacterial hand soap. Since scientists first began describing them, we have largely focused on these ‘bad’ microbes, for perfectly valid reasons. It’s (relatively) easy to make an association between a disease and the odd but plentiful bacterium that’s teeming in a sick person. It’s also natural to study how it works in order to stop it. On the other hand, the bacteria that just seem to hang out in healthy people don’t seem very interesting. As a result, when we talk about microbes, we tend to forget about the vast majority of them, which don’t cause disease. And if they don’t harm us, then why does it even matter if we forget about them?

The answer is that many microbes dismissed as loiterers are in fact hard-working members of the community known as the holobiont. This term for the combination of host and all associated microbes recognizes that the physiology and evolution of all members of such a community are linked together in a highly complex and stable way. We’ve only recently begun to appreciate just how important the microbiome can be. In various plants and animals, they produce essential nutrients, help digest food, compete with pathogens, interact with the immune and nervous systems, and even cue developmental processes. Without microbes, we ‘macrobes‘ would have to be extremely different. In hindsight, this shouldn’t be too surprising. There is practically no surface on Earth that isn’t naturally covered in microbial life, and larger organisms evolved in this context. If a given ‘function’ required for animal life is already performed by microbes, there is no reason to re-evolve the mechanisms to do it yourself.

One bacterium that’s tired of the bad rap it’s gotten in the past: Helicobacter pylori. It’s present in the digestive tract of around half the people worldwide. Initially connected with stomach ulcers and consequently targeted for eradication, H. pylori is now suspected to confer benefits to us by priming our immune system and reducing autoimmune diseases such as asthma. It’s possible that the sterile environments of the developed world have led to increases in these diseases due to the loss of this and other microbes in our bodies. This doesn’t mean it isn’t also involved in the creation of ulcers. It just demonstrates that there are other factors involved, and the elimination of bacteria from our lives may have unforeseen harmful consequences. Think of it this way: you can’t get lung cancer if you don’t have lungs, but does that mean we should remove them? Image from Wikipedia.

How does this relate to corals? Well, changes in ambient water temperature, nutrient levels, or fish communities can lead to shifts in the functions being performed by the microbial community, and we think this may be part of the reason we’re seeing strange diseases popping up around the world. The best example that we already know of is the phenomenon known as coral bleaching. As I mentioned in a previous post, corals form a close partnership with single-celled algae called Symbiodinium. This partnership, or symbiosis (hence the algae’s name), has existed for so long that most corals simply cannot live without their algae. However, when sea temperatures rise, runoff pollutes the water, or the corals become otherwise stressed, the algae is often expelled from the coral tissue. Because Symbiodinium is actually the source of most of the coral’s colors, the coral tissue is left white, or bleached, following this expulsion. In this bleached state, the coral becomes even more stressed, and eventually dies if the symbiosis is not re-established.

Healthy coral

Healthy (if slightly sedimented) coral

Bleached coral

Bleached coral (same individual, three months earlier)

Coral bleaching is an interesting case of sickness caused by the lack of a microbe, and we believe there are other similar cases waiting to be discovered. The large cell and population size of Symbiodinium, plus its conspicuous coloration, makes its absence more noticeable in unhealthy reefs. But the microbes we’re looking for are much more subtle. For one thing, they’re hiding in a crowd. No environmental factor will change the fact that hundreds to thousands of bacterial species are associated with coral at any given moment. And although many of them are somewhat transient, that doesn’t mean they aren’t performing an important function. Often, bacteria that are almost completely unrelated can fill the same role in a community. If two bacteria can each provide the same nutrient or chase off the same pathogens, lacking only one of them won’t affect coral health. So we need to use some tricky analyses to tease this all apart. I’ll go into the details some other time for those brave readers!

The first stage of this research, though, begins with sample collections. And even though it’s tough, stressful work, I think I’m the man for the job!

Somebody's gotta do it

Somebody’s gotta do it


For the past couple weeks, I’ve been in Townsville, Australia, where I’m a guest of Dr. David Bourne at the Australian Institute of Marine Science (AIMS). Between AIMS and the nearby James Cook University (JCU), the area is one of the world’s premier centers for marine and coral reef science, and it’s chock-full of the fields’ leading researchers. I’m here to meet them while continuing my own studies, and I’m excited for the opportunity!


If you squint really hard, you might be able to see me waving from Townsville. Map made with Google Maps Engine Pro, with more map details here

Before I get into the details of my research and this trip in particular, a little background would be useful.

In my first post, I introduced the cnida, the sub-cellular harpoon mechanism that defines the animal group called Cnidaria. But cnidarians are interesting for a number of other reasons as well. For one thing, they’re beautiful, and extremely common in the ocean. From giant green anemones in the tidepools of the Pacific Northwest, to the beautiful corals and deadly Irukanji jellyfish in the waters of Australia, it’s hard to get in the water without noticing this diverse phylum of animals.

Giant green anemones (Anthopleura xanthogrammica) fill the tidepools of my beloved home state of Oregon

Giant green anemones (Anthopleura xanthogrammica) fill the tidepools of my beloved home state of Oregon

They are also ecosystem engineers. That is, species such as corals are the irreplaceable foundation that supports all the other species in their habitat. Without corals, there would be much less physical structure in the areas now occupied by reefs. Less structure leads to less diversity, and less diversity is both boring and bad for people, who rely on reefs for food, tourism, storm protection, drug discovery, and more. Further, without thousands of years of coral growth, many islands would have completely sunk under the sea.

Living corals have have produced all of the slopes, ledges, cracks, and crevices that create a diverse environment on this French Polynesian reef

In addition, cnidarians have a strange and unique biology. Among other things, many cnidarians form an essential partnership with single-celled algae called Symbiodinium. In this partnership, algae are kept inside the cells of the cnidarian, where they use photosynthesis to store light energy in sugars that are shared with their host. In return for sugars, the cnidarian shelters its algae and provides it with the building blocks of proteins.

As wonderful as cnidarians are, some of them are in trouble. The corals that create some of the most diverse and beautiful habitats in the world are being wiped out by disease, predation, rising sea temperatures, and human activity. Although we understand some of the causes of coral loss, there are still many that we don’t. After years of study, we have still not identified the pathogens responsible for many important coral diseases, and we still don’t know exactly why they appear to have become so devastating only recently. In this context, our lab asks many questions in the field of coral microbiology, such as:

  • Which microbes are responsible for disease outbreaks, and which are mostly harmless?
  • Do rising ocean temperatures make corals more sensitive to pathogens?
  • How are pathogens transmitted? Via sediment or water? Or through vectors such as algae, sponges, and corallivores, like parrotfish?
  • What happens to the coral microbiome if the reef ecosystem is transformed by overfishing or increased agricultural runoff? Can the community recover from any harmful changes?
  • How do various members of the microbiome interact with one another and with their hosts?
One of our current studies investigates how direct contact with algae influences  the coral mucus microbiome

One of our studies in the Florida Keys investigates how direct contact with algae influences the coral mucus microbiome

Many of our projects focus on pathogenic viruses and bacteria, but the microbiome is even more interesting to me from a different perspective. I want to search for the microbes that are good for their hosts. With that information, our descriptions of stressor-induced microbiome shifts become even more useful. Fieldwork to begin a more detailed description of the ‘normal’ coral microbiota is thus one of the primary purposes of my visit to Australia. For a few more details, check out this page and come back for more later. And don’t hesitate to ask questions!!

My current trip is funded by the East Asia and Pacific Summer Institutes (EAPSI) program; a collaborative effort between the United States’ National Science Foundation (NSF) and the Australian Academy of Science (AAS). Since I’ve arrived in the country, I’ve had some time to explore a bit, and was hosted for an orientation session by AAS in the capital city of Canberra. In a couple weeks, I’ll be traveling to Lizard Island Research Station, and I expect to get some great photos while there. For more details on the people I’ve met and the fun stuff I’ve seen and learned, come back soon.