Thursday, June 26, 2014

Thank you!

Thank you!
We all had mixed feelings getting on the plane yesterday to leave Dongsha. Fresh fruit (mangos!) and vegetables (anything actually green!) await us back in Taiwan, but we are leaving behind the friends we made on Dongsha over the past month. Excited to begin digging into all the fascinating data that we collected, a bit sad to leave the beautiful coral reefs on Dongsha. Clean showers ahead, leaving behind that strangely gratifying feeling of being covered in salt after a long day working in the ocean.

The plane ride home is also a time to reflect on the amazing success of our expedition. On a reef that is a magnet for tropical storms (including a direct hit form Tropical Storm Hagibis a couple weeks ago!), strong monsoon winds, covered with fishermen, and in most places out of site of any land, we not only deployed a series of very expensive instruments and set up a 4-story scaffolding tower, we actually recovered everything a month later. As Dr. Soong, the head of the research station on Dongsha told us as we boarded the plane, "I never would have believed it in a million years".

My buddy Aloha of the Marine National Park
Of course, our team on Dongsha is only part of the story of that success. We owe huge thanks to so many who helped along the way: Dr. Wong and his group at Academia Sinica, Dr. Soong from National Sun Yat-Sen University, the Dongsha Atoll Marine National Park, our boat captains who put up with all our requests to go everywhere around Dongsha, and all the other researchers on Dongsha who tagged along to help us find temperature loggers and set up our scaffolding tower. Thank you all!

- Tom DeCarlo
Joint Program in Oceanography
Woods Hole Oceanographic Institution

Sunday, June 22, 2014

Almost Done

Our recovered E1 Mooring
Platform (ADCP + MicroCAT).

What’s a field expedition without the instrument recovery, cleanup, and packing duties? During the past week, our group has been working meticulously to retrieve our sea-faring instruments and prepare them to be shipped back home. Kristen, Pat, and Tom made a heroic effort in diving down to the various mooring locations and searching for the often obscured and barnacle-laden instruments. To our luck, most of the equipment has been recovered. Some of our moorings were in locations susceptible to strong currents and wave action, and were likely moved and bumped around during the last few weeks. This made our dive team’s job of finding the moorings more difficult, but their diligence and experience prevailed.
All the nooks and crannies...
poor Tom!
Although our devices have only been in the ocean for what seems like a relatively short time span, we still found that upon recovery, our instruments were covered with a slimy layer of sea gunk: algae, barnacles, mollusks, and various autotrophic marine organisms that find shiny, white temperature and pressure loggers attractive. Cleaning off all of this deliciousness was simply a matter of scrubbing the devices with abrasive pads and water, though some of us had a much more daunting checklist of items to clean. Ultimately, everyone pitched in and the work basically took care of itself. Something we hardly take for granted is the foresight that the engineers who designed these instruments had when they were making these devices; plastic casings, titanium hardware, and stainless steel mountings offer fantastic corrosion-resistance.
Cleaning instruments: more fun
than it sounds like.
One of the more exciting moments of our trip came when we began uploading and viewing data from the instruments. Seeing firsthand the preliminary recordings of temperature, pressure, pH, oxygen, and currents, amongst other variables, that reflect the highly dynamic conditions, perhaps unique to Dongsha atoll and characteristic of a coral reef exposed to such large internal waves, made enduring a month of, well…interesting food worth it.
All of us are eager to begin a more rigorous analysis of our data to better understand and demonstrate how internal waves affect corals on Dongsha Atoll, however, we must first be good stewards of our equipment, and finish properly cleaning and packing them, so as to prolong their useful lives; after all, this stuff ain’t cheap!

-Aryan Safaie
Graduate Student,
Coastal Dynamics Lab, UCI

Wednesday, June 18, 2014

Back to normal

After a week stuck inside while Tropical Storm Hagibis passed directly over Dongsha, we finally got back to our usual routine of research out on the reef. And when we got back out there, we were relieved to see that the corals are back to normal too.
The same coral colony bleached white on May 26 (top)
and recovered from bleaching on June 17 (bottom).

Corals that were bone-white a week ago were again green, a sure-fire sign that the corals are back to hosting photosynthetic symbionts. It appears the bleaching event is over at last.

While this is certainly good news, it doesn't mean all is well. We saw some mortality, so for some corals relief came too late. And the next bleaching event may be even more destructive.

Samples that we collected throughout the bleaching event will help us understand the resiliency of Dongsha corals. Using our coral cores, we can check how frequently bleaching occurs. We will also track how coral energetics (fat reserves, for example) changed as the corals bleached and then recovered. Further, we will see if the coral symbionts after the bleaching event are different than before bleaching. Certain "clades" of symbionts are more heat-tolerant than others, so the corals may have swapped out symbionts to better handle the heat.

- Tom DeCarlo
Joint Program in Oceanography
Woods Hole Oceanographic Institution

Wednesday, June 11, 2014

Weather Days

A tough team waits out a squall on the tower to finish
preparing the RAS to go back in the water.
Enjoying a windy (and wet!) bike ride down
the Dongsha Airport Runway
Anyone who does much field work will tell you that for any field expedition it is important to plan some time for bad weather, or some “weather days”.   Well, we’re using some of our weather days now!  The last few days have brought higher winds, rough seas, and rain.  We are all eager to get back out on the water to download data, check on instruments, and survey the bleaching, but until the weather turns around we are stuck in the lab – which leaves some time for preliminary data analysis, catching up on email, and bike rides down the runway!
Fresh mango - a.k.a. "heaven"!
 During this time we were also fortunate to meet some other researchers from the National Sun Yat-sen University in Kaohsiung, Taiwan, visiting Dongsha Atoll.  We enjoyed learning from them about their work on the reef and were very grateful for the fresh mango and bananas they shared with us.  Fresh fruit is a rare treat on Dongsha! 

- Kristen Davis
Coastal Dynamics Lab
University of California, Irvine

Tuesday, June 10, 2014

Time capsules

Kanmin, of the Dongsha Atoll Marine National Park, helps
us collect a core of skeleton from a massive coral colony.
In this photo, Kanmin is using a pneumatic drill to drive a
drillbit into the skeleton. The black hose is connected
to a spare SCUBA tank that powers the drill.
Our measurements of net ecosystem calcification (NEC) and our observations of coral bleaching, though incredibly valuable, are brief snapshots of Dongsha Atoll. We can also learn a lot about the reef from a longer term perspective. How have calcification rates on Dongsha changed in the past, and why?

Ideally, we could repeat our expedition year after year to see how calcification on the reef changes under different climate conditions. But I do need to write a thesis, so we need a different approach. One alternative is to use the growth histories preserved within the skeletons of massive corals living on Dongsha.

CT scans of corals collected from Green
Island, southeast of Taiwan. The
alternating light and dark bands are
high and low density bands, respectively.
Each year, one pair of high and low 
density bands form, providing a timescale
to interpret past growth rates. Counting
back the bands, and measuring the distance
between them, tells us how growth rates
have changed over the past several decades.
How do corals tell us about the past? Corals are constantly building their skeletons, the colony grows larger year after year. Yet corals respond to their environment, building skeleton of different density during different seasons of the year. This seasonal rhythm of skeletal density creates an intrinsic timescale within the skeleton, analogous to tree rings. As the colony continues to grow outward, the growth history of past decades, and sometimes even centuries, is preserved within the interior of the colony.

To access this information, we use underwater pneumatic drills to collect cores of skeleton from living coral colonies. Don't worry, we patch up the holes with cement and underwater epoxy and the coral grows over our plug in about a year. Back in Woods Hole, we send our cores through a CT scanner, which gives us a 3D map of skeletal density. Using software developed in our lab, we use the annual density banding to reconstruct coral growth rates in the past.

This information tells us how coral calcification on Dongsha changed during especially warm or cool years, or whether calcification is increasing or decreasing with time. Corals even form anomalous bands when they recover from bleaching, so we can tell when these corals have bleached in the past. How unusual is the bleaching event that we are seeing right now? Our cores will help answer that question.

- Tom DeCarlo
Joint Program in Oceanography
Woods Hole Oceanographic Institution

Saturday, June 7, 2014


The Ocean Researcher 3 sampling around Dongsha. Look
carefully and you can see the rosette of "Niskin" bottles
used for sampling resting on the starboard gunwale. Look
even more closely and you can see a strip of green seawater
just below the horizon - that is the Dongsha reef.
Coral reefs are amazingly dynamic ecosystems. Everywhere in the ocean, organisms are constantly changing the chemistry of the seawater around them. Seasonal variability often dominates in the open ocean, where the composition of the upper 100 meters changes relatively slowly as plankton photosynthesize and respire. Changes are "slow" because there is a lot of water, and plankton are very small.

On a coral reef flat, the table is turned. Here, there is much less water (1-2 meters) and reefs are teeming with life. The timescale of change shrinks. Seawater chemistry can change dramatically over the course of a day. Tracking these changes tells us a lot about the reef, such as the rates of net calcification (construction of calcium carbonate minus dissolution) and net production (photosynthesis minus respiration).

The "robot" of our sampling team, the RAS collects
seawater samples on the shallow reef flat. The smaller
instrument next to the RAS is measuring the pH of the 
But tracking changes in seawater in such a dynamic system requires an intense sampling effort. On Dongsha, we deployed the RAS (see June 1 post) to automatically collect samples every 2 hours on the reef. In addition, the research vessel Ocean Researcher 3 (OR3) steamed from Taiwan to Dongsha to collect samples just offshore of the reef every few hours for several days. During the day, we bring two more boats to the reef: the larger Atoll-2 is stationed just inside of the lagoon while the smaller Atoll-1 travels over the shallow reef to sample between the RAS and OR3. It was at these times that our months of planning truly felt worthwhile. A whole transect of sampling teams (including 1 "robot") stretched across the reef, perfectly synchronized. And at the same time, the DTS and offshore mooring (posts on June 3 & 7) are characterizing the physical processes around the atoll. Together, the samples that we collect will paint a unique picture of the dynamic processes occurring on Dongsha Atoll.

- Tom DeCarlo
Joint Program in Oceanography
Woods Hole Oceanographic Institution

Heavy Duty

Kristen setting the AWAC & SeaFET
(pH sensor) in place. 
The immense spatial nature of internal waves, stretching thousands of feet across different density layers below the ocean's surface, leads to their important role in the mixing of ocean waters. Here at Dongsha in the South China Sea, observing the water column as it flows from the ocean, over the reef, and into the lagoon, requires a baseline measurement of temperature and currents offshore of the reef. A few days ago we successfully installed ‘E1’, our dense 16 meter mooring that holds 7 temperature loggers spaced evenly between a temperature and pressure sensor at the top, and a MicroCAT (temperature + pressure + oxygen sensor) at the bottom, in the deep offshore section of the reef. Each temperature logger is 2 m apart, allowing us to observe the thermal stratification of the water column before it enters the lagoon. 

4 large buckets filled with concrete helped
weigh down the 'E1' mooring. 
We were also fortunate enough to have Tom and Kristen scuba down a platform that holds the AWAC, an acoustic surface tracking instrument that profiles currents and wave direction, and a pH meter to a depth of ~20 m. We already installed a similar platform in the shallower lagoonal side of the reef, which contains an ADCP (acoustic Doppler current profiler) and another MicroCAT. This hard work marks a significant portion of our efforts to characterize flow across the reef, and will make for some interesting data!

-Aryan Safaie
Graduate Student
Coastal Dynamics Lab, UCI

Wednesday, June 4, 2014

Bleaching continues

Corals on Dongsha are still feeling the heat. Two weeks into the bleaching event, more corals have joined the ranks of the bleached.
A coral colony tagged on May 26 is not bleached.

The good news is that almost all of the corals are still hanging on. They are going it alone though, their symbiotic algae mostly gone. When we look closely as the surface of the bleached corals, the coral polyps are stretching their tentacles out into the water, grasping for food.

By June 1st, the same colony as above has lost most of its
color, appearing bleached. The green on top of the colony
is a layer of mucus. 
Without their photosynthesizing symbionts, the coral animal is left to feed itself. Even though most of the coral's energy is provided by the symbionts, corals are equipped to catch food themselves. Seawater is constantly flowing across the reef, and this seawater carries plankton. Corals cannot move, they live inside the large skeleton that they build, and that skeleton is cemented to the reef. Instead, corals reach their tentacles out into the water and snag food passing by. That most of the corals on Dongsha are still alive despite two weeks without their symbionts suggests these corals are catching some food.

Another possibility is that the corals are not getting enough food without their symbionts and are burning through their fat reserves. If this is the case, the clock is ticking for these corals until those fat reserves run dry. The question is whether these corals can continue to feed themselves, or live off their fat reserves, long enough to acquire new symbionts.

A mucus layer shedding off a bleached coral. Notice the
white color of the coral where the mucus has fallen away.
The thousands of tiny white bumps are the living coral
Here are some of the changes that we have observed over the past two weeks:

The coral colonies that are bleaching on Dongsha are spewing out mucus, which coats the colony. Producing lots of mucus is a general coral stress response, the mucus may be a way for the coral to shed its symbionts or harmful bacteria.

When we first observed bleaching on May 26, it was only massive, dome-shaped corals of the genus Porites. Now we are beginning to see the start of bleaching in different species of branching coral.

Bleaching is starting in several different species.
At least a few corals appear to have died from the bleaching event. The colonies are bone-white and no living coral polyps are visible. A thin layer of algae is beginning to cover the skeleton - available hard substrate is a hot commodity on reefs and algae waste little time in taking over. Hopefully the few cases of mortality that we have seen are not a sign of things to come.

Recent coral mortality. A thin layer of algae is covering the
former colony.
The cause of the bleaching event is now more clear. Data from temperature loggers deployed on Dongsha show very rapid warming, over 4°C in just two weeks. While the seasonal range of temperature on Dongsha is around 8°C, the temperature changes slowly and steadily throughout the year. It's most likely the rapid burst of warming that the corals could not handle.

We will continue to keep an eye on the bleaching happening on Dongsha, keep following our blog for more updates in the weeks to come.

- Tom DeCarlo
Joint Program in Oceanography
Woods Hole Oceanographic Institution

Temperature recorded by a logger on the Dongsha
reef flat. The sharp up and down spikes are daily
temperature changes. The 4-5°C warming trend 
beginning around May 9th likely caused the
bleaching event on Dongsha.

Partial bleaching of branching

Tuesday, June 3, 2014

Ready for the BIG ones!

Google Earth Image of Dongsha Atoll with approximate
location of DTS cable.
New and full phases of the moon bring "spring" tides - the largest amplitude tides.  Energetic tidal currents flowing over bumps in the ocean floor drive waves within the ocean, aka, "internal waves" (see Science section for a nice explanation).  Spring tides in the South China Sea produce some of the biggest internal waves that have been measured in the ocean… and they'll be heading toward the Dongsha atoll on June 12th (full moon)!
Fiberoptic cable deployed behind a small boat
on the reef flat.  The small dot on the horizon is
the scaffolding platform where the DTS
base station is located.

But, we're ready for them!

Yesterday, we completed the setup of the distributed temperature sensor (DTS), which includes 4 kilometers of fiberoptic cable laid from the lagoon, over the reef flat, and
down the fore reef slope to 50 m depth offshore - acting as an internal wave antenna (see blog post on May 27th for more detail on the DTS).  The DTS measures temperature and along with other instruments we have deployed on the reef, will allow us to better understand how much of the deep offshore water the internal waves bring onto the shallow reef and how it affects the corals that live there.

Aryan, Austin, and Kristen are very excited to have an
empty reel!  Note the yellow "lazy susan" that saved the day!
Deploying 4-km of cable on a reef is no small task.  It requires a lot of teamwork, good timing, and a little luck.  Our luck came in the form of good weather (small waves on the reef crest) and a useful reel mount that operates much like a "lazy susan" on the dining table that we borrowed from a nearby construction site!  We had planned some other methods for spooling out the cable, but the "lazy susan" turned out to be the best option.  Sometimes in field work, improvisation is key!

DTS cable over spur and groove formations
on the fore reef slope.
We still have a lot of work to do surveying the cable and ground-truthing our measurements with more traditional single-point ocean temperature sensors, but we're looking forward to capturing some internal waves in our DTS data!

- Kristen Davis
Coastal Dynamics Lab
University of California, Irvine

Kristen places a temperature sensor on the cable to
calibrate the DTS signal.

Sunday, June 1, 2014

Robotic reef

Our team hard at work assembling instruments on the 
scaffolding tower.

Coral reefs are growing day in, day out, constantly constructing the calcium carbonate skeletons that form the reef. The reef does not have working hours. Unfortunately, we do.  We can only take small boats onto the reef during daylight hours. That gives us only half of the story of what’s happening on the reef. Photosynthesis dominates in daylight, respiration at night – like the reef inhales all day and exhales in the night. To understand how the reef is growing and “breathing”, we need to sample changes in the seawater chemistry at all times of the day.

Katie inspects the RAS - excited that the RAS is in the
water and starting to collect samples.
One solution is to program “robots” to sample around the clock. On Dongsha, we have instruments deployed on the reef that are continuously measuring the temperature, salinity, pH, and current speed of seawater flowing onto the reef. To measure net ecosystem calcification (NEC), which tells us how quickly the reef is growing, we need to collect bottle samples of seawater after it has flowed across the reef. The calcifying organisms of the reef, including corals and coralline algae, use ions in the seawater to build their shells and skeletons. Using seawater samples, we can measure how quickly these ions are removed from seawater, which gives us a measurement of the reef-scale calcification rate – and how this calcification rate changes as “internal” waves crash onto the reef.

The largest, and most complicated, “robot” that we have deployed on Dongsha collects seawater samples for us at all hours of the day, called the “Remote Access Sampler” or “RAS”. But the RAS is 5 feet tall and weighs over 300 pounds, and we need to deploy it from a small boat at shallow depth (~2 meters at high tide) on the reef 25 kilometers from Dongsha Island. In other reef systems, we assemble the RAS on land and bring it on a boat to where we want to sample. On Dongsha, instead we built a scaffolding tower out on the reef, brought the RAS in pieces to the reef, assembled the RAS on the tower, and lowered it into the water.

Assembling the scaffolding tower and the RAS took several days, but that was time well spent. The Dongsha reef is being sampled around the clock, while we are sleeping or eating dinner on the island. This gives us time to collect additional samples, such as cores of skeleton from individual coral colonies (more on this soon).

 The time-lapse videos below show us lifting and lowering the RAS in the scaffolding tower.

- Tom DeCarlo
Joint Program in Oceanography
Woods Hole Oceanographic Institution

Wednesday, May 28, 2014

Needle in a haystack

Finding something smaller than a soda can in the ocean is a bit like finding a needle in a haystack. But in this case, finding the needle means recovering very valuable information.
We found a temperature logger deployed on the forereef!
The logger was attached to a buoy to make it easier to find.
In this picture, Tom has just recovered the old loggers and
is about to attach new loggers to the buoy. Photo by Yalan,
National Sun Yat-Sen University.

During our expedition to Dongsha last year, we deployed about two dozen temperature loggers around the atoll. Every fifteen minutes over the past year, these loggers have recorded the temperature of seawater. These temperature records are incredibly important for understanding how internal waves affect corals living on the atoll, as well as identifying warm events that may have caused coral bleaching (see post below on bleaching at Dongsha).

The tricky part is finding our loggers. Dongsha Atoll is about 500 square kilometers, and our loggers are not much bigger than a pen. To make matters worse, after a year in the ocean the loggers will be completely covered with marine life, which acts as camouflage. The key is taking accurate GPS coordinates when we deploy the loggers, and a little bit of luck.
A temperature logger deployed in June 2013 that we just 
recovered. After a year in the ocean, the logger is
completely covered with fleshy and coralline algae, and
even a coral!

So far we have found all the loggers that we left on the reef flat, which is the relatively calm and shallow part of the reef. We haven't had quite the same luck (yet) with loggers on the deeper, rougher forereef - we found 2 out of 8 on our first attempt. Actually, finding any forereef loggers is a huge success because the only way to find them is by SCUBA, and at 70 feet depth we only have 10-15 minutes to search before we need to return to the surface. And of course there is always the possibility that our moorings broke free during storms - one of the largest typhoons of the year passed nearby Dongsha. Though very pleased with the valuable information we have already recovered from the loggers, we are holding out hope that we will still find the rest!

- Tom DeCarlo
Joint Program in Oceanography
Woods Hole Oceanographic Institution.

Tuesday, May 27, 2014

New technology

Austin and Pat load the DTS cable onto Atoll-1

Today we deployed the first 1 km section of fiber optic cable on the Dongsha reef between the lagoon and our scaffolding tower. Though it presented some challenges, we all made it through in one piece (especially the cable). The next step is to deploy another 3 km of cable to stretch from the lagoon all the way towards the open ocean to the forereef. During the next weeks the 4 km of cable that lies on the reef will collect accurate temperatures within 0.01°C every meter at 30 second intervals. These measurements will allow us to track the cold water brought to the reef by internal waves (see the "Science" section). All of this is accomplished using a technology known as DTS.

Tom swims behind Atoll-1, carefully laying cable across 
the reef. The scaffolding tower that will hold the solar panel
and electronics is in the background.
What is DTS? Distributed temperature sensing was developed for industrial use in the oil industry, but is more commonly being applied to hydrological and environmental applications. Instead of relying on data collected from individual sensors, the DTS records a continuous profile of temperatures along the fiber optic cable. It achieves this by measuring the light reflected back on sensor through a phenomenon known as Raman scattering. The signal consists of two wavelengths, Stokes and antiStokes. Because the antiStokes particle is strongly dependent on temperature, the ratio of the two can be translated into temperature. What does this all mean? Temperature can be cheaply and effectively measured over vast distances in time, using the same type of cable that plugs into your phone or television.

Ultimately, the scaffolding will hold the DTS, a small meteorological station, and solar panels to power the whole system. Stay tuned for progress on that in the coming days!

- Austin Hall
Water Resource Engineering
Oregon State University

Monday, May 26, 2014

Ghost reef

Diving into the water, it is as if we are surrounded by ghosts. Massive coral colonies surround us, but they are all bone-white. These are not actually ghost corals, they are "bleached" corals.

Tom inspects a recently bleached coral on Dongsha.
Coral reefs are typically found in the deserts of the ocean - regions where there are few sources of nutrients to the surface waters where the corals live. The reefs that corals build are like oases in the desert, but corals can only do this with the help of symbionts. Even though corals themselves are animals, within their cells they host photosynthetic algae. Everyone wins - the symbiotic algae provide energy to the coral from the products of their photosynthesis, and the algae receive shelter within the coral and benefit from coral waste products.

However, the symbiosis can go awry. Under certain conditions, typically when exposed to unusually warm temperatures, the symbiotic algae begin to produce chemicals that are toxic to the coral host. In response, the coral kicks out the symbionts. This is "coral bleaching" - the vibrant colors of coral colonies are actually caused by the symbiotic algae; once the algae are gone, the colony appears white because we are actually seeing the calcium carbonate skeleton through the translucent coral tissue. This is bad news for corals: without their symbionts, corals often starve and the colony dies. But bleaching is not always a death sentence - corals can acquire more symbionts from the seawater around them, and sometimes the coral colony fully recovers.

Sadly, we saw on Dongsha yesterday that most of the massive coral colonies are bleaching right now. They are still hanging on - with a close look at the colony surface, we could see that the coral animal is still alive. The question is whether they can hang on long enough to acquire new symbionts. With more than four weeks of our expedition remaining, we will continue to monitor these corals, and try to figure out why they bleached in the first place. Stay tuned for more - and cross your fingers that the corals here on Dongsha can recover!

- Tom DeCarlo
Joint Program in Oceanography
Woods Hole Oceanographic Institution