Frequent Flier

Posted on October 12, 2015 by Ryan

Well, I just hit 50,000 miles that I’ve flown for this project. Since March. And to think, I laughed when Becky ‘warned’ me that the job would require a lot of travel…

Oh, btw, I’m in Montserrat. The volcanic island in the Caribbean that inspired Jimmy Buffett’s timeless classic ‘Volcano’. YouTube it.

Hopped on another little plane and landed on another little island.

I’m helping the Waitt Institute out with some ecological surveys, and in return, I hope to be able to get some samples for my project. But I found out about this just 7 days ago and am only just settling in to my accommodations. Such fun!

Because why not

Photo management

Posted on September 12, 2015 by Ryan

First off, go play with this interactive map of our sampling locations on our project homepage, because I’ve been working on it for the last week and I’m very proud of it :).

Now, I have a confession to make.

Despite the singular focus of my prior blog posts, my work is not entirely composed of swimming around in the tropics. In fact, most months of the year, you can find me right here, bathing instead in the light of my computer screen.

I’ve been meaning to write more posts while stateside, but the subject matter is a bit more difficult to ‘spice up’. So I’ve put it off. Today, however, I think I’ve got an interesting topic that will begin a new theme of post regarding the most interesting and time-consuming part of my job: computer work.

Since we returned from Reunion a couple of weeks ago, I’ve spent a considerable amount of time preparing the photos and data from our trips so that they are organized, useful, and publicly accessible. So far, the team has collected over 3,000 photos of more than 550 coral samples. Keeping these organized can become very difficult as we progress, so I’ve been working with a variety of tools to make it easier. When we’re in the field, we take tons of photos of each individual coral, from closeups that show small morphological details, to wide-angle photos that we can use later to determine the surroundings of the coral. We also take photos of the reef, photos of each other, and photos of that awesome creature that I’ve never seen before and it’s so close and so colorful and sooo cool and look at it feeding, it’s waving its antennae around and catching things and it’s so awesome!!

Seriously, this mantis shrimp was freaking cool

At the end of the day, I have hundreds of photos. Some are pretty, some need post-processing work to become pretty, some are definitely not pretty but can be used as data, and some might be useable as data with some post-processing of their own. Each photo might have one or multiple samples in it, or could be a great example of a particular disease, or maybe just it just has one of us making a funny face. To be useful, I need a way to find these photos again, somewhere in the midst of the 47,000 other photos on my hard drive (seriously).

Ummm… data?

The primary tool I use to manage the mess is Adobe Lightroom. Lightroom enables me to process my photos in bulk and add keywords to the photos so I can easily search for them later. When I import all the photos from a particular dive, for instance, I have Lightroom automatically add the GPS coordinates for the dive and keywords for the site name, project, photographer, etc. Then I go through the photos and add keywords to each one that include sample identification codes and everything interesting in the picture, like fish, diseases, or divers. Now, there are two very neat aspects about Lightroom keywords that I take advantage of. The first is that you can establish keyword synonyms so that every time you tag a photo with one word, its synonyms will automatically also be attached. I can tag a photo with ‘lionfish’, and that’s all well and good. But later, I might be thinking all sciency and want to find all my photos with ‘Pterois radiata‘ in them. If I have previously told Lightroom that the scientific name and common name are synonyms, my search will find exactly what I need.

But what if I want to find all photos of fish that belong to Scorpaeniformes (the group that includes both lionfish and stonefish)? The second handy aspect of Lightroom keywords comes in here: they can be placed in a hierarchy. I’ve placed the keyword ‘Pterois radiata‘ within ‘Pterois‘, within ‘Scorpaeniformes’, so every time I tag a photo with the simple term ‘lionfish’, it’s also tagged with its higher-level taxonomic groupings. For our samples, I even put the sample ID keyword within its corresponding species. In fact, I’ve set up an entire taxonomic tree of organism names within my keywords, so every time I tag a simple sample ID, the photo is made searchable with terms corresponding to all the different levels of the tree of life. It’s awwwesommmmeee.

Manual keywords (5): E10.17.Cyp.sera.1.20150628, North Bay, Octopus, Photo by Joe Pollock, GCMP Sample
Resulting keywords (29): Animal, Anthozoan, Australia, Cephalopoda, Cnidaria, Cnidarian, Cyphastrea, Cyphastrea serailia, E10.17.Cyp.sera.1.20150628, GCMP, GCMP Sample, Hard coral, Hexacorallian, Indo-Pacific, LH_282, Lord Howe Island, Merulinidae, Metazoan, Mollusc, North Bay, Octopus, Pacific Ocean, Photo by Joe Pollock, Protostome, Robust, Scleractinian, Stony Coral, XVII, AU

The next stage of photo management for me is post-processing. I am nowhere close to an expert photographer or image editor, but I’m learning. It’s still amazing to me how much a photo can be improved with a couple quick adjustments of exposure and levels. Most of the time, photos seem to come ‘off the camera’ with a washed-out and low-contrast look. Underwater photos always have their colors messed up. When we take photos of samples, we generally put a standard color card and CoralWatch Coral Health Chart in the frame so that we can make the right adjustments later. Fixing the color and exposure doesn’t just make the photos prettier, it can help us to understand the corals. It’s tough to spot patches of disease or the presence of bleaching when the whole photo is various dark shades of green. The best thing about Lightroom (at least compared to Photoshop and a number of other image editing programs)* is the ability to make adjustments in bulk. Often, a particular series of photos were all taken in very similar conditions. Say, all the photos from a single dive, where we were at 30 ft with a particular amount of visibility and cloud cover. I can play around with just one of the photos, getting the adjustments just right, then simply copy those adjustments and paste them to the rest of the photos from the dive. Voila! Hundreds of photos edited.

Before adjustments

After adjustments

Aaaand before

Aaaannd after

Once I’ve got the photos edited and organized, I can do fun things with them, like export them to Flickr for your browsing pleasure, or embed them in the map you explored at the beginning of the post. But explaining that is for another day…

*A note about software. The next-best photo software I’ve used is Google’s free (free!) Picasa. Picasa will also allow you to batch-edit photos, and had facial recognition long before Lightroom. iPhoto also has these features. But as far as I know, the keywording in Picasa and iPhoto doesn’t support hierarchies or synonyms.

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!

Will someone please think about the marine mammals?!

Posted on March 18, 2015 by rosaless

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.

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!

The Cnidae Gritty

Searching for details in the study of coral microbiology