A Day in the Life

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?!

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.

Where did you say you were?

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

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

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

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

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

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

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

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

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

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

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

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

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

Acropora, Pocillopora, Echinopora.

Oh, and then there’s this:

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

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