Merci Beaucoup!

Posted on September 8, 2015 by Ryan

Although we generally like to post all the fun details of our project, doing fieldwork internationally is hard. Mountains of paperwork and preparation go into our trips (much of it often stressful and last-minute), and when we arrive, we generally don’t know the local corals very well, don’t know the language as well as we think we do, and don’t know the area at all. We’re learning as we go about all the best ways to make our trips go smoothly.

But for now, as I sit in the Paris airport on my way home, I’d like to give a shout-out to all the people who have helped make this particular trip happen. One of the first contacts Jerome made on the island was with Le Club de Plongee Suwan Macha – an organization of SCUBA divers that works like a co-op, buying and maintaining resources that are shared by members at a very affordable price. This system worked great for us as a way to get many customized dives in and seems like an awesome set-up for scientific diving in general. We even borrowed a few tanks of air for some of our ‘labwork’, unrelated to diving. After we joined the club, the acting president, Pierre Grisoni, volunteered his time to drive the boat and refill tanks for us for all the dives we did on the West coast of the island. These dives were essential to our collections and formed the core of our trip! Merci beaucoup à Pierre and the rest of the club!

Thanks, Pierre and Suwan Macha!

Another important contact was Dr. Jean-Pascal Quod, president of Reef Check France and manager of Pareto Ecoconsult. Jean-Pascal and the diving club SUBEST were instrumental in our collections on the East side of the island, and showed us some really great reefs over there.

Perhaps the most important local entity was The Natural Marine Reserve of La Réunion (RNMR), which provided us with local collections permits and prepared our CITES export permits. Dealing with this paperwork is often the most difficult part of our work, and being able to work with the local management authority is essential to our project.

Many other people have been helpful on this particular trip. For starters, I bummed a ride to and from the Portland airport with my parents, which is excellent. I also left my car with them and got lots of other help from them before leaving. I believe Amelia’s mother also took her and Jerome to the airport, after quickly sewing together my BCD weight pocket for me. Ummm, awesome!! Then there’s Jerome’s mom, who on multiple occasions hosted us all for outstanding dinners while we were in Reunion. Everything’s easier in life with parents like these!

Les parents McMinds: merci for all you do

We also met many of Jerome’s friends and family while there, and a number of them provided us with delicious food, too. Thank you to all of you for showing us your island and making the trip great!

Since we first started planning the trip, there has been one person who made the right contacts, spoke the right language, and put in a lot of effort to get all the permitting and paperwork done on the French end of things: our postdoc Dr. Jerome Payet. In addition to pre-trip organization, he also acted as our guide, facilitator, translator, and co-director throughout the trip. I’ve worked with Jerome a lot in the last couple years, and he has been an integral part of the lab for a bit longer than me, but working on this particular project was generous of him. This trip came at a special time for Jerome, as well, since he is now moving on to work with a different lab at OSU. The work he put into it is thus very much appreciated. Thank you – we will miss you!!

Au revoir, Jerome

Intro to Sampling Strategy

Posted on August 20, 2015 by Ryan

The sampling is ramping up here in Reunion, and the checkboxes are filling up next to target corals. In the last three days, we have collected samples from 27 corals, representing 22 species from 16 genera, 11 families, and 2 classes. Since the actual physical taking of a sample involves just rubbing a syringe against it and breaking off a tiny chunk, our number may not actually seem very high. However, there are a few things that make the process take longer than theory would predict. As Amelia mentioned in the last post, one thing that’s slowing us down is the environment. We’ve discovered before that working in shallow water is not easy. In the lagoon here on Reunion, the water is often so shallow that we are trying to spot live corals in ankle-deep water, then having to find a way to lie down to examine them without crushing the reef or sitting on a poisonous stonefish. In other places, the water is about waist-deep, and the huge waves breaking on the crest continue into the back-reef, sloshing us around amongst the sharp corals and stinging fire-corals, and making it very difficult to stay steady enough for photos and sampling. Plus, it’s winter here, and the water is ‘cold’. 76 degrees Fahrenheit seems warm at first, but after ~4 hours of being submersed in it, the water still saps out all of our body heat. We’re getting cold, sunburned, and beat up!

But if that was the only problem, I’d say we’d just have to suck it up and get the work done! But another, bigger problem is that we have to find the corals. Not just any, but a relatively specific list of coral types. We’re only planning to take a small number of samples from each type while we’re here, and I’d prefer not to take them all from the same location at the same time. I mentioned before that confounding factors can make it difficult to determine which variable is responsible for a given trend. If all we found on Day 1 were Porites and Acropora, and we immediately took all of the trip’s samples for those species, we would have confounded our species variable with time and location. Later, if we took all of our Fungia samples on a single, different day, it would be hard to be confident that differences in the microbes between our Porites and Fungia samples were actually attributable to host specificity. An equally good alternative explanation would be that microbes on corals on Day 1 were different than microbes on corals on Day 5, no matter which species we sampled on each day. This is likely to be true for many microbes due to differences in disease prevalence, tidal height, current direction, light level, etc. To be confident that differences are due to coral species, we need to have a clear sampling plan. A solution is to find and sample replicates from many different coral species on the same day. Differences among these samples would be more confidently attributable to individual colonies and, through replication, to coral species. So we are doing our best to find locations that have high levels of diversity. High diversity reefs were easy to find at Lizard Island and KAUST and made our sampling there go great!

We are not having problems finding Porites (massive) and Acropora (branching)…

This Fungia, however, is the only one we’ve found, so far.

The first couple of days that we were here in Reunion, we spent a lot of time exploring the lagoon just down the street from our rental house. We chose the house hoping that the majority of our sampling could be just a short walk and swim away. However, we weren’t finding much in those reefs. Of the ~16 families of corals that we hoped to find here, only 2 were common, and we only found 5 there in total. So after a weekend of exploring the island for fun (escaping the critical eyes of the heavy crowds at the beach), we began our sampling in the lagoon of Trou d’Eau, a short drive south of us. The reefs there were, if anything, less abundant and diverse than the ones here. We got samples from 5 families. So the next day we went even further south, to Saint-Leu, to see if our luck would be better. Indeed, we found a reef that had much more cover and much more diversity than those up north. We collected samples from 8 families, 5 of which were new! Still, with a total of 10 families, we were still missing a few that have been very common and conspicuous in other wide-ranging Indo-Pacific reefs that I have sampled. So we decided yesterday to try a different environment and brave the shark-infested fore-reefs via scuba. The day was great – I absolutely love the feeling of being on a boat in the tropics, and the feeling of breathing clean, cool air through a regulator while suspended underwater. Plus, the sampling is way easier while diving under the waves, and doesn’t tend to get us all beat up. But the reef wasn’t very diverse. We found 5 families of corals – only 1 of them new.

Ahh, I love being on the water!

Thought this was a Montipora – closer inspection reveals it’s just another species of Porites!

Weekend getaway

Cold mists of the volcano

As the trip reaches its half-way point, we are ready to buckle down and get going on replicates of what we already have. We’ll keep our eyes out for the missing coral families, but would be relatively satisfied with the current repertoire if it’s all we wind up finding. Today, we head south again, this time diving on the fore-reef, where we hope to find a beautiful combination of easy sampling and diverse corals.

Finding the moon and meeting Tiki

Posted on August 19, 2015 by fosteram

We had spent the weekend with Jerome’s family and after an evening of food and laughter we were ready to explore the island. Réunion has many different microclimates with landscapes ranging from arid forests to tropical beaches. On our way to the Piton de la Fournaise volcano we reflected on how these different microclimates reminded us of a mixture of places across the globe. We even found the moon!

Mountain or moon?

Piton de la Fournaise is a shield volcano and is one of the world’s most active volcanoes. It is around 530,000 years old and 2,631m high. Piton de la Fournaise is one of two volcanoes, the other being Piton des Neiges, that make up Réunion. Up until a few weeks ago, it’s most recent eruption was in 1986. Due to its activity, the hikes circling its peak were closed, but we were still able to get an awesome view of it!

Piton de la Fournaise!

Of course, we couldn’t have done any of this without our awesome matching hats!

Jerome’s mom outfitted us with matching hats to protect us from the sun.

Now that the weekend is over it’s time to get down to business. Monday came bright and early with birds chirping and the smell of science in the air! Like all good scientists we had our ritual morning coffee and then rolled out into the field. Spending the majority of the day sampling we were able to see most of the lagoon in Saint-Gilles. In the lagoon alone we were able to find five different clades of coral, a plethora of sea cucumbers and zero sharks.

A snapshot of some of the corals we collected! (Montipora sp., Porites cylindrica and Porites lichen)

The main thing that I have to say about Monday is this: weight belts. Even though we were in a shallow lagoon our buoyant weight kept on pushing us up, making it difficult – but not impossible – to sample. From shore I’m sure we looked like two poorly coordinated synchronized swimmers with our feet flapping in the air as we tried to stay down.

Today, we hopped in the car and went to a different section of the island in hopes of finding a more biodiverse reef. We struck gold and were met by beautiful reefs in crystal clear water. But there was one catch: strong currents (everyone’s favorite). The currents quickly introduced Ryan and I to the fire corals in the surrounding area and by the end of the field day I’d say we all became good friends.

Fortunately, we had brought Tiki with us so we weren’t scathed too badly. Tiki is the good luck charm of the Vega-Thurber lab and has been on almost every field trip the lab has gone on. That being said, Tiki has traveled a lot and spent many days in the sea (his black hair turned blond is proof). I’ll allow Tiki to introduce himself:

https://www.flickr.com/photos/131967103@N02/20690925201/in/album-72157651381609701/

And so folks, that concludes the past few days in Réunion!

Bienvenue à la Réunion!

Posted on August 15, 2015 by fosteram

Hi guys! My name is Amelia Foster. I’m currently an undergrad in Becky’s lab though I graduate soon (woo!). By the end of this summer, in fact, I will have finished my majors in Microbiology and International Studies. I started volunteering in Becky’s lab as a sophomore in 2012. Under her mentorship I have learned important molecular biology techniques associated with coral reef ecology. Recently, I have been given the opportunity to learn fieldwork techniques with Ryan and Jerome in Réunion Island, France.

Our flight pattern from Oregon to Réunion

After 30+ hours of flying, an inordinate amount of babies crying and lots of bread and cheese we arrived in Réunion just as the sun was coming up over the water. Originally named Bourbon, Réunion is a French department located in the Indian Ocean just east of Madagascar. Volcanic eruptions beginning 5 million years ago formed the island that today houses around 850,000 people. The island was uninhabited until 1643 when the French sent twelve convicts there into exile. In the mid 17^th century the island was further colonized. The settlers recruited a large amount of slave labor, from Africa, Madagascar, India and Tamil until the year 1848, which marked the abolition of slavery. Now, Réunion has a multi-cultural identity with people from all over the world.

Since arriving on the island just a few short days ago we have become fully immersed (though I still can’t speak at all) in French and have begun setting up field studies. From the house to the market to the beach, my daily life has become a game of charades. Picking up a few words here and there I can currently string together a few sentences that are inapplicable to almost all situations:

Je ne sais pas et jáime l´pomme et l´chat.

Ryan is doing much better than I am and can almost carry a conversation in French. But Jerome, who is from Réunion, remains our savior in almost every situation.

Hanging out with Jerome’s family

Jerome has not only introduced us to his family and friends on the island but has told us of the terrifying homme-coq. The homme-coq has the body of a chicken and the legs of a man. It roams around the island, terrorizing the people and stealing children. So, we better watch out.

But even in the face of the perilous homme-coq -and not to mention the bull sharks– we have been able to begin the preliminary steps in setting up our fieldwork. Ryan has already given me a crash course in coral identification as we were scouring the lagoon near our house in Saint Gilles for different genera of corals. And the other night we helped Jerome collect water samples to later analyze for viral content.

La bobine beach, where we are currently sampling

Today, we are coordinating with local dive shops to acquire tanks and begin sampling a few of the corals we identified.

A Day in the Life

Posted on March 24, 2015 by Ryan

Errrrgggg. I could tell you all about the dull, monotonous, and mind-numbing labwork portion of my trip, or we could sit and watch this video together. Remember the good ol’ days of fieldwork!

That there video was produced by Oregon State University’s media department. I am very pleased with how it turned out. The university is using this for advertisement purposes; however, the guys behind it are using the experiences and footage for a lot more. Media is an exciting aspect of the GCMP. We are doing our best to open our project, data, and experiences to colleagues and the public, and part of our funding is allocated toward ‘outreach’. For us, the outreach aspect is important, so we are working with the university media guys to produce a number of these short videos, a few online and magazine articles, and, most excitingly, a feature-length film about the decline of coral reefs and the consequences for the people who depend on them. Here’s a trailer (with most of the footage again from Lizard Island):

I briefly mentioned the media guys David and Justin in a previous post, because they came with us on this trip to Saudi Arabia. Having them around was great! Nothing helps clarify the purposes of a project like discussing it with ‘outsiders’.

But seriously, this labwork… For every day diving, I’ve spent two in the lab. And a day in the lab has been ~9:00 AM – ~11:00 PM on average. I DO NOT REMEMBER THIS TAKING SO LONG IN AUSTRALIA!

The GCMP

Posted on March 17, 2015 by Ryan

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.

Where did you say you were?

Posted on March 16, 2015 by Ryan

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:

Here’s another answer:

Oh, and then there’s this:

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)

Posted on October 15, 2014 by Ryan

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.

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.

Diversity

Posted on July 29, 2014 by Ryan

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

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

Since 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:

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:

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 Symphillia, Echinopora, and 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.

Significance

Posted on July 8, 2014 by Ryan

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 (if slightly sedimented) 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

The Cnidae Gritty

Searching for details in the study of coral microbiology

Category Archives: Science