I’ve made it to Lizard Island Research Station, and have finally begun the actual sampling work that brought me to Australia!

The last week has been rather incredible. To get to the island, my field partner and I flew in a 5-seat airplane that held only us and the pilot. I’d never been in such a small plane, and was actually a little nervous as we walked out onto the tarmac! I was expecting the flight to be bumpy, but it was actually really smooth – even the landing was more smooth than most I’ve experienced.

Hmm... Well, maybe it was worth getting up so early

Hmm… Well, maybe it was worth getting up so early

I most certainly did not have any theme songs going through my head during the flight. Especially not Indiana Jones or Jurassic Park.


Katia window

Landing at LizardSince I’ve been here, I’ve had the chance to settle in, meet people, and begin my coral-search. The station and the people in it are lovely, and the reefs are too!

So now that I’m here, I should probably explain my project a little better. I mentioned before that I was searching for the normal, or ‘good’, microbes in the corals. The problem is, different coral species have different ideas about what is good for them, and environmental conditions can change those ideas even within an individual coral colony. For example, corals that grow fast and live in bright sunlight might get plenty of sugars from their algal symbionts, and bacteria that collect or produce essential protein compounds might be important for the coral. But slightly deeper-water corals that don’t get as much sunlight for photosynthesis could have a different balance of requirements, and it may be more beneficial to associate with other kinds of bacteria. I don’t know, that just came off the top of my head – it’s just one hypothesis that might be interesting to test some time in the future!

It’s hard to test hypotheses like that right now, though, because there are confounding factors that complicate things. If we compared the bacteria in deep-water corals to those in shallow-water corals, we would probably see quite a few differences. But if the deep-water corals have other things in common (for instance, if they’re all related to one another, or grow in similar shapes), it is difficult to tell whether those differences are actually due to their unique environmental conditions, or if they’re byproducts of the other factors.

To help out with such hypothetical future studies, we plan to describe the coral microbiome in the context of the various species’ relationships to one another. If a certain group of corals has evolved to associate with bacteria that other corals don’t, we can take this into account when we ask other questions, like “Why does Species A get diseases more often in high-temperature water than Species B does?”

On a more basic level, we just want to describe something new. To my knowledge, nobody has ever before taken a peek at the microbes that associate with the coral Galaxea fascicularis. And who knows – maybe there’s some crazy bacterium in it that makes a new type of antibiotic and lives nowhere else! We’ll never know until we look. So we’re exploring the diversity of microbes in many coral species that have simply never been sampled.

My description of the project’s probably not entirely clear yet, but that’s at least a good enough introduction to it to segue into what I’ve been doing for the last week. I can’t sample from all the different groups of corals unless I know how to distinguish them from one another, so I’ve been working on my species ID. It’s not so easy. Here’s an example. Below, I have pictures (that I took this week) of 5 different coral species:



Bushy Acropora










These corals are pretty common and I’ve actually chosen them because they were relatively simple to name. They are all related to one another like this:

In this diagram, relationships between species are displayed like a family tree. Species that are more directly connected with lines are closer relatives, so three Acropora species are closer to one another than any of them are to Diploastrea, for example.

Evolutionary biologists use the term clade to describe groups of organisms that are more related to one another than to any other organism. In this diagram, the three Acropora species form a clade, as does the combination of Symphillia and Echinopora, as well as the combination of SymphilliaEchinoporaand Diploastrea. The combination of Acropora nobilis and Diploastrea heliopora does not form a clade, even though they appear side by side (the location of the names does not matter, only their connections via lines). Does that make the diagram clear? I was struggling to put it into words, so let me know.

Of these corals, we would expect that Symphillia and Diploastrea would have microbial communities more similar to one other than either do to any of the Acropora species, for example. But can you guess which corals get grouped together by just looking at them? My task is to make these assessments so that we get a nice, broad sampling of coral diversity. I’ll put the answers in my next post.



Australia. Famous for its backwards-spinning drains, boxing kangaroos, deadly everything, and lost or forgetful fish, the nation/continent has so much more to it. Although I’ve come here to study a particular aspect of a specific animal, I don’t intend to waste the opportunity to learn whatever else I can about the place. So, I’ve done a bit of exploring.

Seen here is the Sydney Harbour Bridge and a partial silhouette of the famous opera house during a sunset ferry ride. Images may or may not be automatically righted during inter-hemispherical electronic transport. (Click picture to manually adjust – user experience may vary)

The program that got me here is the East Asia and Pacific Summer Institutes (EAPSI). There are 25 of us Fellows in Australia at the moment, and many of us met each other a couple months ago while at an orientation in Washington, DC. We decided we got along pretty well, so a few of us planned a short pre-EAPSI trip to Sydney together for some sightseeing. What did we learn there? A sample:

Sydney has a 'fernery'. Australia has many ferns. My family and I love ferns, something that I only found out recently was not a universal human trait. Maybe someday I'll write a blog post about ferns. There might be a poem in it.

Sydney has a ‘fernery’. There are many Australian ferns in this fernery. My family and I love ferns; this is something that I only found out recently was not a universal human trait. Thanks for an awesome interest, family! Maybe someday I’ll write a blog post just about ferns. There could be a poem in it. (And thanks for the photo, Ashley!)

The famous Sydney Opera House has a very distinctive 'texture' that threw us all for a loop when we first saw it. It's a beautiful building, but how had we never noticed the tiling on its surface??

The famous Sydney Opera House has a very distinctive ‘texture’ that threw us all for a loop when we first saw it. It’s a beautiful building, but in all the photos we’ve seen of it, how had we never noticed the tiling on its surface??

Don't let our happy faces fool you; most Australian beer is not tasty. But they're working on it. Maybe I've just gotten picky living in Oregon's, the brewer's paradise...

Don’t let our happy faces fool you; most Australian beer is not tasty. But they’re working on it (I know I can vouch for a brew from the Paradox Beer Lab). Maybe I’ve just gotten picky living in Oregon, the brewer’s paradise. In this picture is a great group of people: applied mathematician David White, nuclear engineer Ashley Reichardt, coral paleoclimatologist Kenzie Schoemann, and moi, the coral microbiologist. Not pictured is the photographer, marine biogeochemist Kateri Salk (Thanks for the photo, Kateri!). Check out their sites if you want to be dazzled by a bunch of big words!

A couple more things: Australians call crosswalks ‘zebra crossings’, which initially confused me by conjuring images of striped equines roaming the city and stepping in front of cars. Also, we’re doing cappuccinos wrong in the States. A morning run through the beautiful neighborhood of Pyrmont led me to a small Italian café where I discovered heaven in a coffee mug. I can’t tell you exactly what the difference was, but someone needs to figure it out. Seriously.

Of course, as a group of researchers, we couldn’t help but get our nerd on a couple of times. Most of us work with the ocean, so we spent a good deal of time at the Sydney Sea Life Aquarium and smaller Manly Sea Life Sanctuary. Both were great, and had me itching to get out onto the reef itself! They also clued us in to one of Australia’s most controversial environmental issues: shark culling. That is, the program by which the Australian government kills threatened animals that are vital to the ecosystem in order to reduce people’s fear of going to the beach. I could gibber about this for a while, especially as this policy is part of a broader trend against environmentalism in Australia, but for now I’ll just state a couple of facts. Shark culling is bad for the environment, and bad for the economy. Further, it isn’t even effective at reducing shark attacks. Scientists from around the world have been saying this for years, but the issue is driven by emotion and politics, not research. The aquariums in Sydney are trying to do their part to let people know just how important sharks are – if you want to learn more, don’t just listen to a coral biologist; ask the experts. That link’ll direct you to Southern Fried Science, the blog of a shark lab member at my alma mater, the University of Miami. They know way more than I do!

While in the city, we also learned a bit about the city’s history (details in a later post), and I visited some colleagues at the University of Technology, Sydney. It was an excellent trip – one of my favorite so far. But it was only the beginning of my Australian adventure. My next stop was the capital city of Canberra. A rundown on that trip is on the docket for my next post!


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


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.