Where did you say you were?

Expedition log. March 2, 2015. King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

After a grueling 48+ hours of travel (including driving to and from airports, flight time, and layovers), we have arrived in Saudi Arabia. My feet hurt, my back hurts, my head hurts, and I am exhausted. In 2015, it should never take so long to get really anywhere. But we booked our flights only a week ago; our visas arrived only the day before we left. As a result of the last-minute nature of the plans, our itinerary had us stop in San Francisco, Chicago, Frankfurt, and finally Jeddah. There was enough time during the layover in San Francisco for the film guys David and Justin to meet with some family for dinner outside the airport, and enough time in Chicago for all of us to get a brief driving tour of the city. Having never been to Chicago, myself, I thoroughly enjoyed this time despite a fog of exhaustion and stale clothing. But at this point, I really only look forward to a good night’s sleep.

Expedition log. March 4, 2015. KAUST, Thuwal, Saudi Arabia.

We spent the last few days recovering from our travel, meeting members of our host lab, and getting acquainted with KAUST. What a fascinating place. An entire university town, built from scratch in the middle of the desert, in just a couple of years. The buildings are vast, monolithic, even monumental. I am living in student housing that reminds me more of a palace, with three floors, a full-sized bed, and an expansive balcony that allows me to enjoy the pleasant nighttime air. It’s more than impressive. And yet, there are odd signs of the quick planning and construction. Sidewalks that go nowhere, maps with no labels, shoddy adhesives leading to missing lettering on the signage. Yes, a strange place.

Expedition log. March 5, 2015. KAUST, Thuwal, Saudi Arabia.

We got our first dives in, today. What amazing reefs! The weather was a little rough, and we got a bit seasick during the extended attempts at anchoring, but once we hit the water, it all went away. The surge made collecting samples nearly impossible, so for the most part we settled with some exploratory dives, taking in the sights and getting up to speed on the local coral types. Incredibly, although we only expected to find somewhere between 4 and 8 coral groups (out of a total of 21+ worldwide), within three dives I had spotted 12, and expect to find at least one more. Those numbers rival what I found last year in Australia, and many genera overlap! This will be a very productive trip!

Expedition log. March 9, 2015. Somewhere between Saudi Arabia and Sudan. No land in sight.

We slept on the boat in port last night and steamed out to the Farasan Banks early in the morning. Tried to get a sampling dive in before breakfast… and I’ve decided that in the future I will not again work before eating. But after the first dive and a veritable feast prepared by the crew, subsequent trips under the surface proved productive. We visited four reefs today and got a good diversity of samples from two of them. We are off to a good start!

Expedition log. March 16, 2015. KAUST, Thuwal, Saudi Arabia.

After five days of diving, a long day exploring Jeddah, and a day getting ready for the other three guys to leave, I am exhausted! I spent yesterday getting caught up with computer work, and have started to organize our metadata and photos. Finally, I have some time to share some of the incredible sights we’ve been witnessing for the last couple weeks!

What a busy couple weeks it has been. I have never been so stressed during the planning for a trip – acquiring all the necessary permissions to travel, getting visas and flights and paperwork ready – it was crazy! I hope you never get a visa to travel only a day before your flights. And since Jesse, David, and Justin only had two weeks here to get things done, we’ve been packing the days full ever since. Whew!

If you’re wondering why I’m in Saudi Arabia, here’s the answer:

Jesse samples at Al Fahal.Here’s another answer:

Acropora, Pocillopora, Echinopora.

Oh, and then there’s this:

mind=blown.The Red Sea has some of the most incredible reefs in the world. Surrounded by desert, there is little to no run-off or pollution to muck up the waters. As a result, the visibility is amazing, the colors are mind-blowing, and the corals are as happy as they could possibly be. What’s more – they’re healthy despite the fact that the water temperatures here are way higher than the bleaching thresholds at reefs anywhere else in the world.

We’re continuing the project I started last year in Australia, looking into the different microbes that interact with corals around the world, and we decided we couldn’t generalize about all corals globally unless we included the corals from this unique environment. As you can tell by my logs, we were successful in our collections. Now, I have some labwork to do – DNA extractions, bacterial culturing, and coral species identification using microscopic skeletal features. I’m sure it’ll be a blast!



Hello again (and LIRS packing notes)

Ok, so I failed miserably at maintaining this blog while I was abroad. My bad. You know how it is – the internet goes down for 3-4 days, the pre-written posts you have ready to go are put on hold while you wait for the ability to attach photos, and before you know it, you’ve fallen off the wagon, your posting schedule is irretrievable, and the distractions and activity of fieldwork have consumed your time and attention.

Or at least that’s how it happened for me.

Fortunately for us, this is an opportunity for me to look back on my trip, savoring it all over again while we digitally explore the reef while heading into the Northern Hemisphere’s cold, dark winter months. Shiver!

So let’s pick up where we left off, with a post I wrote but did not publish on August 3, about halfway through my time on Lizard Island:

Packing notes for future Lizard Island trips:

Things not to bring:

  • Socks. You’re probably thinking ‘Oh, maybe a pair or two at least!’, but no. Bring no socks. Or shoes, for that matter. Haven’t worn either for two weeks now.*
  • Jeans. The nights may get a little chilly, but sand gets in the hems and tracks into places you don’t want it. Not worth the extra weight!
  • Hammer + chisel. I need these to sample my corals, but there are plenty of tools already at the station. Since these are really heavy and weight restrictions for the flights out here are strict, this was a big waste of packing space!
  • Bread, apparently. At least not so much as you’re thinking. Everyone orders too much bread, so there’s a ton of loafs in the ‘free food’ freezer, leftover from past groups.**

Things you might forget:

  • Chocolate. And Coke. And coffee. The food orders come on a barge only every two weeks, so if you leave these off your order, you’re done for. Nobody can go two weeks without coffee, Coke, and chocolate.
  • Condiments. Yes, people also often leave these in the free food area, but they can be quickly snatched up. Who wants a sausage without mustard? And if you can bring some good ol’ American BBQ sauce with you, you’ll be a hit at the Saturday night beach barbecues. The Aussies haven’t really figured this one out, it seems… Neither have they figured out ketchup. ‘Tomato sauce’?? Pah!
  • Your handy multi-tool. Yes, you have to be careful to always put it in the checked luggage, but boy, is a good Leatherman nice to have around.
  • A hat. Seriously, why didn’t you think to bring a hat? The sun, it burns!
  • Cables. I know, I know, you already checked and double checked to make sure you had your camera and phone chargers, your computer cables, and your adapters. But you still forgot one; I guarantee it. (Last time it was your dive computer cable, and you weren’t able to download your depth and air profiles. You were very sad.)
  • Oh, and science stuff – you’ll definitely need more gloves, pipette tips, and sterile plastic baggies (Whirl-Paks) than you’re thinking. That plan you had, where you only wanted 200 samples? Forget about it! YOU WANT MORE. You can never have too many samples!***
  • And of course, always bring a towel.****

Now, I know you’ve all been dying in anticipation for the coral ID answers from the previous post. So here we are:

A. Diploastrea heliopora. This coral has a very distinctive look to it, with ribbed volcano-shaped calyces that come together in a large mound.

A. Diploastrea heliopora. This coral has a very distinctive look to it, with ribbed volcano-shaped corallites that come together in a large mound.

Acropora loripes

B. Acropora loripes. This coral has short, bushy branches with relatively large, moderately spaced corallites on the sides and tips. This is in contrast to many of its congenerics, one of which can be seen in the background of this picture. That Acropora (formosa?) coral has long branches, with smaller, closer-spaced corallites on the sides and relatively larger corallites at the branch tip.

C. Echinopora mammiformis. This coral has large, shallow, distinctively ridged calyces on a colony that forms long branches or smooth plates (not shown).

C. Echinopora mammiformis. This coral has large, shallow, distinctively ridged corallites on a colony that forms long branches or smooth plates (not shown).

D. Acropora hyacinthus. Another acroporid coral, but with a very different colony morphology. These corals form huge plates from many tiny, organized branchlets that fuse over time.

D. Acropora hyacinthus (background). Another acroporid coral, but with a very different colony morphology. These corals form huge plates from many tiny, organized branchlets that fuse over time.

E. Acropora nobilis. Yet another acroporid coral, which forms long branches and has numerous fine lateral calyces.

E. Acropora nobilis. Yet another acroporid coral, which forms long branches and has numerous fine lateral corallites. Note that this species is similar, but not identical to, the blue coral in the background of the Acropora loripes picture.

F. Symphillia radians. This coral's polyps do not form individual calyces - they are fused together within each of the colony's winding valleys. This colony morphology is not uncommon, but the corals that form it are not all closely related to one another.

F. Symphillia radians. This coral’s polyps do not form individual corallites – they are fused together within each of the colony’s winding valleys. This colony morphology is not uncommon, but the corals that form it are not all closely related to one another.

As you can see, coral morphology is very diverse. But let’s look again at how these corals are related:

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.

Again, note that species that are connected with the shortest lines are the closest relatives. Would you have guessed that the branching Echinopora was more related to Symphillia and Diploastrea than to the branching Acropora?

As I spend more time on the island, I am becoming more confident in my ability to identify the corals I need for our project. I’m picking up the pace of my sampling and am really getting into the groove of island life. More updates to come!*****

*Note about shoes from the future Ryan: readjusting to the mainland was very difficult. I actually forgot to put socks and shoes on before walking onto the street from my hostel a couple of times!

**Later developments from my time on the island proved that having a ton of extra bread is not in fact a bad thing. When our barge lifeline decides two days before its scheduled arrival that, ‘Eh, we’re not coming this week!’, the denizens of LIRS begin hoarding. Lizards begin to look delicious, and fermentation experiments are attempted with coconuts.

***Future Ryan has noticed that actually, more samples=more headaches at home organizing, storing, and processing them!

****Remarkably, despite my love for Douglas Adams and general adherence to his guidelines for travel, this advice escaped me last year during my trip to Mo’orea. It’s not fun not having a towel.

*****Obviously this was a lie. Again, my bad.



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.

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

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.


A friend once told me that my puns were hilarious. Ignoring the sarcasm with which he said this, I decided that the world would be a better place if it shared in my comedy. The result is the title of this blog.

Since my jokes are actually really bad and I intend to be educational, I suppose I should explain my reasoning behind ‘The Cnidae Gritty’. From the Greek ‘knide’, meaning ‘nettle’, cnidae are spring-loaded harpoons that help jellyfish, corals, anemones, and other cnidarians capture prey and defend themselves. Some cnidae actually penetrate other cells (like when you get stung by a jellyfish), while others simply entangle or stick to their target. In short, they’re super cool.

Simple structure of a cnida. For a dramatic animation, watch this video (where they use the word nematocyst instead of cnida – same thing!): http://vimeo.com/37431528

The word is most commonly pronounced ‘nye-dee’, but if Colbert can drop the ‘t’ in ‘report’, then I think I’m entitled to rhyme cnidae with gritty.

My relationship with cnidae themselves is tangential. I am about to finish my first year as a PhD student studying the microbial associates of the coral animal. As I continue my research, I hope to update this blog often with the nitty gritty details of my work and anything else that I find interesting in the world of coral biology. Currently, I am getting ready for a 3.5-month trip to the Great Barrier Reef in Australia, where I’ve got some awesome fieldwork plans. I’ll post some more details in the next month before I go. In the meantime, you can check out my trip blog from last summer, when I went to Tahiti and Mo’orea to study viruses in the South Pacific. That’ll give you an idea of what makes this field so interesting, and I’ve got some cool reef pictures to boot. You can also check out our lab’s webpage for more details about our research and links to our papers, etc.

I’d love to be somewhat interactive with this blog, so if you have any questions, comments, corrections, or criticisms, please post them!


### Posts before and including this date were written for the blog ‘Expedition Moorea‘ and have been imported here for convenience. I wrote this post to connect the two blogs prior to my merging them. ###

The primary goal of science is to not just learn about things for ourselves, but to share what we’ve learned with other people. Sharing with the public is why I started this blog. I know I stopped posting before I had really gotten into the details of our research, but I hope this was at least a bit of a primer. Since I returned from French Polynesia, a lot has happened. Firstly, I started a second blog, which began with another field expedition (this time to Australia), but which I intend to keep going even while I’m not abroad. It’s called The Cnidae Gritty, and builds off the practice I got writing this one. Check it out.

Secondly, it is important as researchers that we publish detailed descriptions of our experiments and studies so that other scientists can verify our methods and conclusions. We have succeeded in doing this for the work we did in Mo’orea. If you want to see what the results of our research look like, check out our paper in the journal Frontiers in Microbiology.


This Irishman got a bit too much sun the other day. Still, what do you expect when you’re marooned on a tropical atoll?





We traveled to this atoll, Tetiaroa, to get a bit of outside perspective on the viruses in the region. Since Jerome is comparing viruses of different sub-habitats within Mo’orea, it will be interesting to see if those differences can be seen in similar systems nearby. It is possible that the large body of water between the islands creates a geographic barrier which prevents the transmission of viruses from one lagoon to another. But we don’t know yet!


All of French Polynesia is in red, and I’ve boxed the Society Islands, where we are


The Society Islands

To get to Tetiaroa, we took advantage of some new friends we recently made over at a nearby American research station. The station (Gump) is located just in the bay next door to ours, is run by UC Berkeley, and hosts researchers from lots of different American universities. We were planning our own trip to Tetiaroa through CRIOBE, but it turned out that one of the Gump researchers needed volunteers to collect specimens for his own island interconnectivity study. In exchange for helping, we got a free ride!

Part of the Gump team with Mo'orea in the background

Part of the Gump team with Mo’orea in the background


An aerial view of the atoll of Tetiaroa (thanks Wikipedia). After helping the Gump-ers, we took water samples at each of the points – a deep inner lagoon, shallow lagoon, reef crest, and fore reef. We also took a sample of water halfway between Tetiaroa and Mo’orea on our way back.

Tetiaroa is a pretty awesome little place. Like all atolls, it consists of a ring of flat, low-lying coral islets which surround an inner lagoon. And it has some interesting history. In recent times, it was privately owned by Marlon Brando, and he allowed researchers to visit regularly. In less recent times, it was a sacred retreat for Tahitian royalty, many of whose remains are buried on the islets. But wayyyy before that, Tetiaroa looked rather different. In fact, it might have looked something like Mo’orea or Tahiti at some point – a single, steep volcanic island surrounded by a shallow lagoon and reef. And before that, maybe something like the Hawaiian or Galápagos islands, which are bigger and have no shallow lagoons surrounding them. This is the natural evolution of many tropical volcanic islands: First, volcanic activity builds up a large mountain. The big island of Hawaii and the islands of Isabela and Fernandina of the Galápagos are still at this stage, actively erupting and growing. Coral reefs are initially less developed near these islands because the only water shallow enough for corals is constantly being replaced by new lava flows. Then, as volcanic activity slows, corals get a chance to build larger structures and form ‘fringing reefs’ immediately beyond the shore of the island. As time passes, two things generally occur to these islands: coral reefs continue to grow, and the island itself begins to sink and erode. Consequently, the original coral reef appears to move outwards from the shore of the island as corals build up on the outer slope. Eventually, the original fringing reef becomes a ‘barrier reef’, and a lagoon forms behind it. This is the stage at which we find Tahiti and Mo’orea. Millions of years later, when the original volcanic island itself sinks below the water, all that is left is the constantly growing coral ring, and we have an atoll like Tetiaroa. The islets around the ring are consequences of relatively recent sea level drop (i.e. thousands versus millions of years), which left the highest points of the reef exposed to air and allowed plants and such to take hold. Of course, as sea level is once again rising, these islets all face the threat of inundation once again.

Another interesting factoid: this theory of islands’ geological histories was first described by Charles Darwin. Although he is of course most well-known for his theories involving biological evolution, this contribution to geological theory was not trivial. In fact, it was initially rejected by many prominent geologists for some of the same reasons biologists rejected natural selection, including the massive amount of time required for these processes to occur. It is not much of a coincidence that Darwin formalized both theories based on the same voyage – once he primed himself to accept gradualism and incremental changes in geology, it was only natural to extend these concepts to biology.

Islands are fascinating! But that was a lot of text, so here are some pretty reef pix from Tetiaroa:


The landing area. Wave in…


… Wave out. We had to swim up to the ledge, which was about 4 feet above our heads when the waves flowed out, and wait for another wave to lift us up onto it. It was kind of neat to be plopped right down on the ledge as the water flows out around you, but then you had to quickly roll along the reef while holding all our sampling gear and taking fins off before the next wave came and dragged you back out!


The deep water beyond the fore reef ledge was shockingly blue


Lots of Pocillopora on the fore reef ledge


Some beautiful Acropora hyacinthus near the crest in the backreef


Porites lobata and Pocillopora verrucosa, chillaxin together like old pals


A crown of Porites lobata on a pedestal of… something my Caribbean-trained self thinks looks sorta kinda like an Agaricia of some sort?


Probably the most beautiful little patch of reef I’ve ever been able to take a picture of. Most of the coral is Porites lobata, but there are like four different color morphs in this picture. The reef crest was just stunning out there. And this sight is even more stunning when full of all the fish, which were just scared away before I could take the picture.


A couple of Blacktip Reef Sharks were circling while we were doing our work.


Giant clams were one of the Gump researchers’ target species


Acanthaster planci, the Crown-of-Thorns Starfish, is very evil looking. Aside from the fact that its spines are extremely painfully toxic, this starfish eats corals and is the direct cause of the devastation of entire reefs in the South Pacific. At this reef, we only saw about three, which is normal and healthy. However, certain conditions can cause outbreaks of thousands, which cause irreparable damage.

So that was our Tetiaroa trip! Thanks go out to the Gumpers for giving us a ride, teaching us about a lot of the local species and such, and for a good time.

Since the trip, we’ve finished up our transects on Mo’orea itself, and we’re ready to relax a little while we wait to wrap up our nutrient experiment in a little over a week. Phew! Fieldwork is exhausting!

Break Past the Anchor, Waves Come to Conquer

Combine sudden high winds, subpar anchor placement, and a tennis ball as a bilge plug, and what you’re left with is one goodbye to your sunglasses. RIP on the bottom of the bay, my polarized friends.

You served me well

You served me well

The tragic loss of my optical style occurred yesterday after we finished refreshing the nutrient diffusers for our experiment. During a short but fierce bout of wind and waves, our boat had dragged its anchor loose and had found its way into some very shallow rocks. While attempting to extract it from said rocks, we bumped the drain plug (/tennis ball) and the waves soon swamped our precious craft. In the ensuing mayhem (which occurred only ~50m from shore), we are happy to say that we lost nothing else! Lessons were learned about double-checking anchors, etc., even when close to shore and in a normally calm area.

I regrettably was not able to document our adventure with photographs, but here is a happy picture of our fearless leader

I regrettably was not able to document our adventure with photographs, but here is a happy picture of the fearless leader

But aside from boating lessons, we’ve been learning a bit more about the island’s geography while continuing our studies. Last I blogged, I mentioned that we would be heading to the outer reef. Well, that was indeed what we did the next day:

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At some point during our trip, I plan to collect some coral tissue and mucus samples from a variety of coral species. We are planning a project to describe the basic diversity of microbial associates of corals across a wide range of locations and coral types, and I want to do a trial run with samples I take here. Our dive on the outer reef helps me get an idea of the coral diversity on the island so that I can make an educated decision of how to do my sampling.

But the main purpose of the boat trip was to collect water from a number of points on a transect. It extended in a straight line from the shore to the outer reef. Jerome is going to look at how the diversity of viruses in the water changes depending on the distance from shore. We expect it to be quite interesting due to the distinctly changing environments which we encounter along the transect. For example, in the North, there is a distinct ‘fringing reef’ very close to shore, then a deeper channel area with a mostly sandy bottom. On the outer edge of the channel, the ‘barrier reef’ begins – the lagoon side of this reef is flat, shallow, and calm, and we refer to it as the ‘back reef’. The highest point in the barrier reef is the ‘reef crest’ – it is often completely exposed to the air and in some places forms small islets. On the other side of the reef crest is where we find the ‘fore reef’. This reef gets hammered by waves in the shallower parts, but quickly drops off to deeper water. This pattern occurs all around the island, although the zones are sometimes less distinct. The way these reefs form is fascinating – it was actually first described by Charles Darwin based on his observations aboard the Beagle. But I’m going to go over that in detail in a future blog post (after we travel to beautiful coral atoll this weekend!). 


Small waves break on the fringing reef in the foreground, while large waves break on the barrier reef in the background


A somewhat undefined sandy channel/backreef area between the two major reef structures on the West side of the island


Waves break just past the exposed reef crest. Backreef structures are just under the water in the foreground.

Over the last few days, we have taken samples from similar transects in the North, South, and West of the island. In the South and West, we took kayaks out to do our sampling.


And other than that, sampling and labwork are beginning to fall into a routine groove! We finish up our days with a little communal meal:

CRIOBE specialties – Mahi head and raw fish w/ soy sauce and vegetables