Will someone please think about the marine mammals?!

Marine mammals get a lot of attention in pop science because of their charismatic nature, but since our lab is mainly focused on coral reefs, marine mammals can sometimes be overlooked!

Hi, my name is Stephanie, and I am the one member in the Vega Thurber lab that has decided to study the microbiology of marine mammals. So, I like to explore the marine mammal side of things. For instance, Ryan is now diving in the Red Sea at KAUST, sampling and assessing coral diversity while surrounded by (but ignoring) frolicking dolphins. Through Ryan’s dolphin watch reports, I became curious of what other marine mammals Ryan may ignore in the Red Sea.

It’s me Stephanie

Doing a little research, it is easy to discover that the Red Sea is home to many marine mammals, but I was mostly surprised that it was home to the dugong, which roams throughout the Indo-West Pacific Ocean. The dugong belongs to the same order as the manatee, but has been the only member in its family, Dugongidae, since the Steller’s sea cow was hunted to extinction in the 18th century. The dugong itself is not listed as an endangered species, but is considered vulnerable. Unlike corals, dugongs have a tendency to swim around, which makes population counts difficult. One new way to solve this problem is by utilizing unmanned aerial vehicles, but this technology is still work in progress.

Dugongs vs. Manatees. Encyclopædia Britannica Online. Retrieved 18 March, 2015, from http://global.britannica.com/EBchecked/media/57538/Features-of-dugongs-and-manatees-compared

In spite of our inability to count all living dugongs, scientist can still use fancy math models to predict the dangers these animals may encounter. The dugong like many marine mammals, including the most endangered marine mammal (the vaquita, a porpoise), is threatened by overfishing. Initially this sounded a bit counterintuitive to me since dugongs are mainly herbivores, but will snack on the occasional jellyfish or some delicious shellfish. Instead, overfishing affects dugongs because it leads to the destruction of seagrass beds, which is where dugongs like to swim and eat. Dugongs are not alone in the plight that is overfishing. Overfishing causes ecological, social, and economic problems. One way to help this problem is by purchasing sustainable seafood, which is made easier by using an app by Seafood Watch.

Since I am a microbiologist I would like to end this post with some microbiology. Strangely, there are few studies that investigate the microbiome of many marine mammals, but it turns out that there is a study on the dugong gut! I know very exciting! Gut microbiomes can be studied by examining fresh feces, thus in this study scientist collected feces from wild and captive dugongs and extracted the DNA. Using DGGE techniques, they concluded that captive and wild dugongs have different bacteria communities. With captive dugongs having fewer bacteria types, which can be considered unhealthy.

I hope you guys enjoyed this marine mammal post and expect some more in the future.


Turbinaria stellulata. Family Dendrophylliidae (“Clade II”)[1]

In my last post, I mentioned that I was continuing the project I started last summer at Lizard Island, Australia. That’s true, but in my haste to get a post out about my current trip, I neglected some important updates. First and foremost: thanks to an NSF grant through the Dimensions of Biodiversity program, our project is official, and we have a name! The Global Coral Microbiome Project, or GCMP. The team consists of members of the Vega Thurber Lab at Oregon State University and the Medina Lab at Penn State University. Along with more money and a bigger team, the goals of the project have expanded a bit. We’re still aiming to understand how different corals have evolved to structure their microbial communities, but, as the new name implies, we are now also looking at how these communities differ geographically in corals around the world. We know that corals that are related to each other can inhabit vastly different environments, so describing the microbes they associate with in only a subset of those environments wouldn’t get the whole picture. For example, corals that look like this:

Porites lobata, Pocillopora verrucosa, and Pocillopora …?

can be found in places as wide ranging as the cold, nutrient-rich, upwelling-fueled waters of the Eastern Pacific, the calm waters of the Society Islands in the South Pacific (where I took this photo), and the crystal clear, positively balmy waters of the Red Sea, from whence I am writing this post. Most taxonomists place individuals from either end of their range into the same species, but at some point that is an arbitrary decision. There are clear physiological differences within coral species that are correlated with geography. If you transplanted a colony of Pocillopora damicornis from Panama to Saudi Arabia, the elevated water temperatures would almost certainly cause it to bleach and die. Why? Dunno. Some researchers, such as the Meyer lab at OSU, are trying to figure that out by looking at genetic differences in the corals. Others suggest that corals can gradually acclimate to such extremes in temperature. We think those hypotheses are part of the story, but that the microbes that live with corals might tell another important part. After all, the interactions with microbes through disease and bleaching are the most common causes of coral death. If we compare the differences in microbes across a host species’ range of environments to the differences explainable by the coral’s evolutionary history, we might be able to explain why some corals are more tolerant of variation in the environment than others.

Reveal your secrets to me, oh corals!

As I procrastinate on my mountains of queued labwork, I am happily organizing and editing my photos from the field. We have photographed each sampled coral colony, hoping to use the collection as a backup for the metadata that we collected simultaneously. The photo at the top of the page depicts the last coral we sampled on this trip – one that had me pumping my fists underwater in excitement! It’s not a particularly rare species, but Jesse and I had a long wish list, a short span of time, and a limited number of reefs to explore. In order to describe the broad levels of variation in the coral microbiome, we are trying to sample at least two species from each coral family we come across, in each location. After we visit a number of reefs around the world, we hope to have enough replication within each family to describe how they differ from one another. As our tanks of air slowly got lower on gas, we still hadn’t found a symbiont-bearing representative of the Dendrophylliidae, though we knew it was around here somewhere! Just as I had given up on it, I spotted that yellow rock. And to be honest, the excitement I felt at that moment is the real reason that I do what I do.

The prize is won.

The prize is won.

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.



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.