Monday, January 26, 2015

Reflecting on the past three weeks

While driving out to the transect on our last day of water sampling, I looked west and rain showered from an ominous cloud covering the sky. It seemed as though we would be spending the day drenched in a combination of fresh and saltwater. As we moved further from land and closer to the northwest barrier reef that surrounds the lagoon, the gray cloud began to dissipate, the ocean glassed over with silky blue perfection and I was reminded of how unpredictable the weather could be in Palau. The reflection of the sky on the ocean surface was so clear that the boundary between water and sky was indiscernible. This was not the first time during my trip that the beauty of Palau had rendered me speechless and I found myself reflecting on the past three weeks.
When Katie invited me to help with her research in Palau, I was ecstatic! Katie’s recent publication (Shamberger et al. 2014) was the first to report visually healthy and diverse coral communities in a naturally acidified system and had thus gained much interest, both in the media and scientific community. As oceanographers we ask ourselves, “How are these corals seemingly able to thrive at low pH and aragonite saturation levels and what does this mean for future corals in an ocean acidification (OA) world?” I was excited for the opportunity to assist in this timely and crucial research and over the next few weeks saw the amount of planning and work that goes into tackling such difficult questions. It took perseverance and dedication to spend long hours on the boat, often in harsh conditions, in order to collect the samples that would hopefully lead to answers about the health of these reefs.
In addition to conducting OA work, I had a chance to observe the interactions between Palauans and their environment. As a native Hawaiian, I am acutely aware of the intricate link between ecosystem and cultural health and the parallels between our cultures fascinated me. I observed many similarities between fishing methods, traditional uses for plants, and navigation techniques. Our coxswain, Gary, was a native to Palau and I was in awe of his intuition related to navigation and the weather. It was not unusual for Katie and I to be fiddling with the GPS, completely unaware that Gary had already placed us at our sampling site. I also depended on Gary for the daily weather forecast, as he was much more reliable than the forecast conditions provided by professional meteorological websites. All he seemed to do was take a quick look at the movement of the clouds and direction of the swell. On one particular day, a storm came through that covered the entire sky with clouds. For a minute Gary seemed disoriented, for he had clearly been using coral heads and landmarks from the distant islands to locate our instruments. Our GPS couldn’t detect a signal but thankfully Gary was able to position us once he had identified his rocks. This experience reminded me about the importance of integrating traditional and western science, for one compliments the other.
Near the end of our trip, I had a chance to visit Jellyfish Lake, a marine lake formed by the rise and fall of sea level over geologic history. The lake contains millions of jellyfish that have adapted to the new conditions and essentially lost the severity of their nematocysts (stinging cells). As we swam toward the middle of the lake, we were engulfed by a swarm of jellyfish so thick that we had to gently brush them aside. It was one of the most surreal moments of my life. At one point, Tom and I broke into hysterical fits of laughter. Not only had I realized the absurdity of floating amongst thousands of jellyfish, but in that moment a hopeful thought had crept into my mind; if these jellyfish could find a way to adapt and thrive to the current conditions of the lake, perhaps coral reefs of the world could find a way to maintain under the harsh conditions presented by global climate change. Biology is a miraculous wonder. One thing is for sure, with the dedication and knowledge of the Cohen lab, I have hope that the beautiful coral reefs of Palau will still be around for our future generations to enjoy. 

- Andrea Kealoha

Friday, January 16, 2015

Carbon Counting

I like to think of carbon as the currency of coral reefs. The bank account of (inorganic) carbon in seawater is adjusted by a number of different processes - respiration and CaCO3 dissolution make deposits, photosynthesis and CaCO3 precipitation make withdrawals. And the carbon in seawater is diversified, a little bit is in the form of CO2, most is bicarbonate (HCO3-), and some is carbonate (CO32-).

While conducting our experiments in Palau, we are accountants of sorts. We are keeping track of the carbon in seawater: adding up all the deposits and withdrawals and tallying all its different forms. How can we do this on a coral reef? Essentially, it boils down to (1) tracing changes in the carbon system parameters and (2) keeping track of time, or how long it takes for these changes to occur.

The RATS keeps track of the different forms of carbon in
seawater. Photo credit: Tom DeCarlo
Step 1: Tracking carbon. The heavy-lifting for this step is accomplished by our robots out on the reef. Every 90 minutes, the RATS (see January 13 post) measures the concentration of dissolved inorganic carbon (DIC) and pH. The DIC tells us how much carbon is in the seawater, and the pH tells us in which forms that carbon exists. While the RATS is positioned about half a kilometer onto the reef, every day we take a small boat just offshore to collect water samples that we can use to analyze the carbon system of the seawater that is flowing onto the reef.

One of our instrument arrays on the barrier reef. The
instrument on the right is one of our current profilers. Photo
credit: Tom DeCarlo

Step 2: Tracking seawater. From Step 1, we know what's in our carbon bank account offshore, and we know the total deposits and withdrawals made by the time the water reaches RATS. But what we really need is the rate of these changes, and to get that we need to know how long that seawater was on the reef while the carbon system was modified. We track the seawater using acoustic doppler current profilers, which measure how quickly, and in which direction, water is moving. Because we know the geometry of the reef (the depth and horizontal distance), we can calculate how much time elapsed between when a parcel of water flowed on the reef and that same water reached RATS.

Putting it all together, we can determine the rates of photosynthesis/respiration and calcification/dissolution on a certain stretch of the Palauan barrier reef. This is really key information. Our experiments are in the same location as where these measurements were made over a decade ago, so we can begin tracking long-term changes in these rates. We can also test whether these rates are influenced by the temperature or chemistry of water flowing onto the reef. And we can compare these rates to other reef systems around the world (for example, where we conducted similar experiments in Taiwan).

- Tom DeCarlo

Tuesday, January 13, 2015

The first of its kind

Today’s guest blogger is Josh Sokol, science-journalist-in-training at the MIT Graduate Program for Science Writing. Josh is traveling with the Cohen lab in Palau to report on their research.

It’s about two in the afternoon, raindrops from a sun shower are splashing into the cotton candy-turquoise water of a Palauan reef flat, and Bill Martin is visibly relieved. His instrument for measuring carbonate chemistry is safe, sound, and talkative on the sandy bottom eight feet below a gently rocking boat. The RATS has been deployed.

Bill packs the tools he will need to deploy RATS out on the
reef. In the background, RATS is ready for launch.
“RATS” is one of those forced acronyms; the kind scientists are fond of torturing into recognizable phonetic shape. It stands for the Robotic Analyzer (for) Total (CO2 system in) Seawater. Encased in a yellow-painted aluminum frame, two intake valves pull seawater through a set of tubes and chambers to determine water pH and the concentration of dissolved inorganic carbon. And the RATS does this autonomously, in place, for as long as you tell it to…all of which is a huge advancement over earlier devices that fill a limited number of bags with water, samples which then must get picked up periodically to be analyzed back in the lab.

Why total CO2 system? Because of the four quantities of carbon chemistry you can poke and prod seawater to measure – pH, alkalinity, the partial pressure of carbon dioxide, and the concentration of dissolved inorganic carbon – at least two are needed to understand the whole system. The RATS probes pH and dissolved inorganic carbon, the two measurable attributes that, when paired, yield the most precise estimate of what’s going on in terms of carbonate chemistry. With them you can calculate the aragonite saturation state, a key measure of how predisposed seawater is to letting animals like corals and clams pull calcium carbonate out of the ocean and into their hard skeletons. 

Lifting RATS off the boat and onto the scaffolding tower
before lowering it into the water.

RATS is useful, clearly. But the deployment of about 250 pounds of homemade water-resistant parts and electronics, initially developed by emeritus WHOI scientist Fred Sayles and shepherded for the last six years by Bill, was far from easy.

About an hour before the cool rain, before Bill Martin’s sigh of relief, the RATS had to be moved into position from the Palau International Coral Reef Center (PICRC). With the smell of gasoline fumes wafting from the waiting boat, technical lead Pat Lohmann, Cohen lab grad student (and Palau Expedition 2015 blog author) Tom DeCarlo, and PICRC staff use a stocky, squat red crane to lift the frame and deposit it on board.

After loading up dive equipment for Pat and Tom and a cooler that serves as a dry box for Bill’s computer and notebook, the small boat is crowded. Floor space is at a premium. The driver, Mars, takes the boat roaring out across the deeper, darker blue waters of the lagoon as the wind whips back. Up ahead, barely visible, are thin white tufts of fur: the waves breaking on the crest of the barrier reef itself, a vivid reminder of the service the reef does to Palau by sheltering the islands from the open ocean's energy.

Carefully transferring RATS from the dock to the small boat
that will transport it out to the reef.
As the boat approaches the reef flat, still behind the line of crashing waves, the water turns to iridescent blue-green when the depth drops dramatically. A rickety scaffolding tower of ugly, faded scrap metal, erected by Pat and Tom to lower instruments into the water, is visible first as a faint line on the horizon. Three platforms at different heights emerge into focus, looming out of the water like the bare girders of a tiny, absurd city skyline. Two birds sitting on it fly off as the boat draws near.

Using a pulley mounted on the tower, Tom, Pat, and Mars lift the RATS up and off the boat and lower it into the water. Tom free dives to grab the cable and hands it back into the boat, allowing Bill to talk to the instrument from the command line; to test it while hunched over his computer. Under the boat’s canopy it’s still too bright to see the screen, so Bill covers himself and the laptop with a jacket as if he’s an old-timey camera operator. Prompted from a checklist on laminated pages, Bill records pHs and temperatures as the RATS’ sensors equilibrate. After a sweaty half an hour, he’s taken a sample measurement and confirmed that the instrument works. Then Bill disconnects, his part done.
Pat and Tom walk RATS from the scaffolding tower to its
new home in an array of other instruments.

The command testing over and that light rain falling, Pat and Tom don SCUBA gear and splash into the water. Patches of coral are few and far in between on the sandy bottom, but small fish dart around clumps of algae. Pat and Tom harness the RATS, inflate a balloon to make it weightless, and walk the instrument over to set it down next to a row of other Cohen lab equipment – including the exact device the RATS (in theory) replaces, with its 48 bottles that fill with seawater one by one and then have to be retrieved.

The RATS touches down, the wide circles on its base sinking a little into the sand. A triggerfish, all dramatic curves and orange and black markings, loiters over a clump of nearby coral as Pat and Tom swim back over to the scaffolding, climb up, and clamber into the boat. RATS is home.

Sunday, January 11, 2015

Coral time-stamps

The clock started ticking on April 27, 2013. That's when Hannah and I put "time-stamps" on twenty coral colonies around Palau.
Staining a coral colony in Palau in April, 2013. 
Photo credit: Hannah Barkley

To a diver's eye, only the living surface of a coral colony is visible. But the living tissue is only a centimeter thick or less, just a thin veneer on top of the massive calcium carbonate skeleton below. In Palau, we are studying how quickly corals are able to build their skeletons, particularly in the relatively low pH regions of the Rock Islands. A typical technique to measure coral growth rates is derived from the annual high- and low-density bands that corals form in their skeletons. Like tree rings, we can count back the bands to determine the age and rate of skeletal extension. To be careful, though, we need a way to ground-truth the annual banding pattern, to make sure we are getting the right answer.

Perhaps the most direct method to measure coral growth rate is based on coral "staining". We cover a living coral colony with a plastic bag for two hours, and add a harmless red vegetable dye into the bag. This does no harm to the coral, and the red dye is actually incorporated into the skeleton. This serves as our "time-stamp" because we know the exact day that the dye was introduced.
Tom drilling a coral colony in Taiwan. Photo
credit: Anne Cohen

Two days ago, we collected short cores of skeleton from these colonies. The stain line is now well below the surface because the coral has built skeleton on top of it over the past 20 months. We know the stain line is April 27, 2013 and we know the top of the core is January 10, 2015. By measuring the distance from the the stain line to the top of the core, we can easily calculate the growth rate. This allows us to ground-truth our density banding estimates and to directly compare coral growth rates around Palau.

But we can learn even more from our staining experiment. The living coral tissue rests atop of thin, horizontal layer of skeleton, called a dissepiment. It's thought that the full moon serves as a cue to all the polyps of a colony to build a new dissepiment at the same time. This way, the dissepiments serve like rungs on a ladder, one formed each lunar month as the coral tissue climbs up and up. But the lunar timing of dissepiments has never been tested experimentally.
Two cores collected from stained coral colonies in Palau. The
pink lines are the stain lines, which were incorporated on
April 27, 2013. The thin green layer at the top is the coral
tissue layer. Each core is about 4 centimeters long. In this
case, one of these corals grew about twice as fast as the other.
Photo credit: Tom DeCarlo

We know that there were 21 full moons between our initial staining and our core collection. Does this match with the number of dissepiments? We will bring these cores back to our lab in Woods Hole, cut sections from the cores, and carefully count the dessipiments under a microscope. This will tell us whether or not dissepiment formation is consistent with timing of the lunar month.

- Tom DeCarlo

Thursday, January 8, 2015

A delicate balance

Severe bioerosion of a living coral colony in
Panama. In this example, the living coral 
(which is green) is infested by bioeroding
bivalves (the key-shaped holes in the 
skeleton). Photo credit: Hannah Barkley
Coral reefs exist in a delicate balance where rates of calcium carbonate production - primarily by corals and coralline algae - are nearly matched by rates of calcium carbonate removal.

An important component of this removal is bioerosion, the biologically mediated breakdown and dissolution of calcium carbonate. Our lab published a new paper, released just this week, which shows that rates of bioerosion of coral skeleton - by worms, sponges, and bivalves - are accelerated by ocean acidification and nutrients. As CO2 levels increase in the atmosphere, some of the CO2 enters the ocean, and through a series of well-known chemical reactions, seawater pH decreases (hence "ocean acidification"). Using cores drilled from living coral colonies across natural gradients of CO2 and nutrients in the Pacific Ocean, we found that bioerosion rates are greatest where pH is low and nutrients are high. In Palau, where there is a strong natural gradient in pH under persistently low nutrients, bioerosion rates clearly tracked the pH variability around the archipelago.

Computerized tomography (CT) scans of
cores of coral skeleton. The light gray to white
colors indicate the coral skeleton. Boreholes
are visible within these skeletons. Photo
credit: Tom DeCarlo
Our current expedition in Palau is an excellent complement to our bioerosion findings. By tracking changes in seawater chemistry (specifically, the alkalinity of seawater), we measure the integrated signal of calcification and dissolution of calcium carbonate as water flows across the reef. Corals and coralline algae build their skeletons using ions dissolved in seawater, a process which decreases alkalinity. On the other hand, dissolution of calcium carbonate reverses this process and alkalinity increases. The instruments that we are deploying in Palau will paint us a picture of the delicate balance between calcium carbonate production and removal, and how this balance tips one way or the other depending on the chemistry of the source water to the reef - for example, what is the sensitivity to seawater pH?

Our experiments begin here shortly! The 4-story scaffolding tower is built out on the reef, and some of our instruments are in the water collecting data. Today and tomorrow, we are deploying the rest of our instruments in time for our experiments to begin this weekend.

- Tom DeCarlo

Monday, January 5, 2015

The expedition to... find scaffolding

Benchtop of programmed
instruments, ready for 
Three days into our expedition, everything is right on track and spirits are high! But we aren't exactly on the tropical paradise trip that you might expect. Every morning, hordes of tourists flock to the local dive outfits and tour buses. Not us though; we have our own fun doing science.

Over the next few days, we will deploy instruments on the reef to measure temperature, salinity, pH, dissolved inorganic carbon, oxygen, water pressure, and velocity. That's a lot of instruments! And each instrument has a very specific role in the experiments that we have designed. That means that every instrument has to be carefully tested in the lab, and then programmed for deployment. Nevermind the hours hunkered inside behind a computer screen programming, once all the instruments are carefully assembled, and ready to go in the ocean, it's totally worth it.
The hunt for scaffolding

Programming completed for the day, Pat and I set out to find scaffolding. We are going to build a 4-story scaffolding tower out on the reef. Some of our instruments weigh over 300 pounds! The easiest way to get these off the boat and into the water, is to use a scaffolding tower like an elevator - with a hoist point at the top, we can lift the instruments off the boat, service them on the scaffolding, and lower them down into the ocean. Don't worry, we've done this before in Taiwan, and it worked beautifully.
WWII ruins

Tracking down just the right scaffolding for the job was a bit harder than we anticipated. We ended up searching around a whole lot of Palau. A few wild goose chases, wrong turns, and questionable directions, and we actually drove about 60 miles around these small islands. On the plus side, some of the wrong turns ended up being really interesting: we found some WWII ruins and a traditional dugout canoe.

Dugout canoe
At the end of the day, success! A pile of scaffolding, and a benchtop covered with programmed instruments. Katie, Andrea, and Bill arrive tonight, and we have a few more instruments to set up before we head out to the reef.
Pat and his scaffolding

- Tom DeCarlo

Sunday, January 4, 2015

Back to the field!

View from PICRC dock during a 
lunchtime break
We are back in Palau for our 2015 expedition! Tom and Pat just arrived in Palau, while Katie, Andrea, and Bill are arriving tomorrow night.

I think everyone is really excited about this trip because it is going to build very nicely upon the work that our lab has been doing in Palau for the past several years. With data that we will collect over the next six weeks here, we are piecing together how calcification rates on the reefs vary around the archipelago and how they change with time. This information helps us to understand how such rich and diverse coral communities can persist in naturally low-pH regions of Palau. Plus, we will make truly historic measurements with the first deployment of the Robotic Analyzer for Total CO2 System (RATS) on a coral reef.

Nevertheless, we have some chores to do before we can start the exciting science. Objective #1 was to unpack all of our equipment and organize our lab space at the Palau International Coral Reef Center (PICRC). We shipped 50 boxes of gear from our last expedition in Taiwan, plus another 30 boxes from Woods Hole for this trip. Needless to say, this made for a full day. But there was some adventure to start the day: in Palau, people drive on the right side of the road, but the steering wheel is also on the right side of the car. That made for an exciting time driving our rental car through town. I totally have it down now.

Over the next few days, we will program and deploy a series of instruments on the reef that will track physical and biogeochemical processes occurring on the reef. Stay tuned for more!

- Tom DeCarlo