Monthly Archives: November 2010

Notes from the field: In The Lab

Andi with samples

This is a blog post by Andi Haas, a PhD student in our lab, following the other side of field research.

While the majority of the lab is on a field cruise, generating data for future scientific publications, others are still working in the lab, processing samples collected on the last field trip and preparing for the next. Working in the field may be the most exhausting part of being a marine scientist, but at the same time it’s the most exciting and rewarding part. Though a lot of the time, the hours spent in the lab preparing for these field trips, processing the samples, and publishing our findings exceed the hours spent in the field. Back here at SIO we are analyzing data from the last trip to Moorea, French Polynesia, where, amongst other experiments like SIP and RR, an in-situ coral algae transplant experiment ended in a 6 hour dive-sample-swim triathlon.

As much as I enjoyed being in the field with the joint group of SIO, SDSU and UCSB, it is also exiting to get the results from our work there, evaluate them and think of continuative or improved experiments. We are also are trying out new tools that allow us to follow cycles of matter in the reef ecosystem more accurately. Once they prove their value and practicability in the lab, these tools will also find their way to beautiful, remote coral reef locations to assist in future studies – can’t wait for that to happen!

Notes from the field: Line Islands

This is a blog post by Levi Lewis, a PhD student in our lab, that follows his diving experience at Kingman Reef in the Line Islands.

“Getting it at Kingman Reef”
By Levi Lewis

“Okay, I get it.”  Dr. Sandin (fish team) was wondering what I thought of my first dive on Kingman Reef, one of the most remote and pristine coral reef ecosystems in the world.  As a new member of the coral reef lab at Scripps Institution of Oceanography, this was an exciting opportunity for me to witness all that I’ve heard and read regarding intact reef ecosystems.

My first dive of the trip was in the Kingman lagoon.  I rolled off the port side of our inflatable, splashing into a foreign world few humans have ever seen.  As I surveyed the landscape dotted in massive yellow mushroom-like mounds of lobe corals, I spotted the natives arriving to greet me—three grey reef sharks.  They examined me as I would expect Native Americans to have examined European explorers upon their arrival to the New World.  We could not communicate, though it was clear they wanted to know a few things:  “Who are you? What are you? What are your intentions? What is that shiny thing you‘re pointing at us?”  My only response was to continue aiming the camera at them, partially in excitement to get my first sharks on film, also to put something hard between myself and their concealed weaponry.  It felt, in part, a standoff and, in part, a warm welcome.  Regardless, I was happy to see them.

After three days of diving, I could write about these reefs ad infinitum:  the schools of crimson fang-toothed bohar snappers and their piercing yellow eyes; species-rich coral spires stacked high towards the sea’s surface;  the chaotic vortex of metallic jacks that swallowed me alive; an open-water plankton bloom that  fueled countless salps, ctenophores and barrel-rolling mantas; the infinite schools of convict tangs that coated the reefs, grazing frantically on…hmm, there seemed to be a lack of fleshy algae on the reef.

We traveled 4,000 miles to get here for a reason:  it is the only way we could really get it; “it” being an understanding of how coral reef ecosystems should look and function in the absence of local human impacts.  Though I understood much of this in my head, seeing the reef helped me truly get it in my core.  Through our science and outreach, we hope society, too, will begin to get it.

Notes from the Field: Hawaii

This is a blog post from Emily Kelly, a PhD student in our lab, following her current research in Hawaii.


Emily & Levi with a green sea turtle. Photo by Don McLeish

I’ve just returned from three months of diving and running experiments in Maui (what a great job!) and as I sit in my San Diego office pouring over datasheets, I miss the daily tropical diving and stolen underwater moments with spinner dolphins, hawksbill turtles, and frogfish.  The silver lining of this sad tale of a graduate student daydreaming out her office window is that hours in the office reflect the large amount of data we collected from our Maui research projects.  It’s this data that will help us answer some of the questions we’re asking about the ecology of coral reefs on Maui and the interactions between corals, algae, fish, and urchins.

Levi Lewis conducts herbivore bite surveys at Kahekili Herbivore Fisheries Management Area. Photo by Emily Kelly

Most of our work is focused on one reef in West Maui- Kahekili Reef Park aka Airport Beach in Ka’anapali.  The Hawaii Division of Aquatic Resources has collected data over the past 15 years showing a decline in coral reef health around the island.  This typically means that coral has been dying or has been overgrown by algae, it’s constant competitor for real-estate on the reef.  Having witnessed and mapped this decline, in July 2009 the state of Hawaii made Kahekili a Herbivore Fisheries Management Area.  This means that fish and urchins that eat algae (the lawnmowers of the reef know as “herbivores”) cannot be fished at this site.  The goal of the management area is to increase the number of lawnmowers (herbivores) on the reef so that they’ll eat the overgrowing algae and therefore help the coral recover.  Coral reef scientists have talked a lot about how herbivores could help keep coral reefs healthy and how they might help coral reefs recover from decline.  But this is the first time that this type of protection has ever been implemented on a reef anywhere in the world.  Wow!  That makes Kahekili a really exciting place to work and play and it’s a great opportunity to study how herbivores are interacting with the reef.

Frogfish sitting on a finger coral (Porites compressa). Photo by Emily Kelly

One of the goals of our work on Maui right now is to create the “grazing budget” for the reef.  This means we want to know how fast fish and urchins are eating different types of algae and we also want to know how fast those same types of algae are growing.  If algae is growing faster than it’s being eaten, we know it might increase its coverage on the reef (read: bad for coral).  If fish are keeping up with the algae or even eating it faster than it’s growing, algae might decline and make space for coral (you’ve got it- good for coral!).  Since it can take a long time for coral recovery to occur, a grazing budget will give us clues about what to expect on the reef in the future.

We’ve just finished our second summer working at Kahekili and two other nearby sites.  With funding from the Hawaii Coral Reef Initiative, we’ll be able to continue this work at sites all around Maui to compare what’s happening on different reefs.  We’ll be back in Maui in February 2011- see you in the water!  or check the Smith Lab website for updates from the reef.

Battle Zones

by Katie Barott, member of the Microbe Team

The corals are winning here at Kingman Reef. Photograph by Jen Smith.

Life on the reef is a constant battle for survival. For corals, the struggle begins as soon as the coral larva attaches itself to something on the bottom and starts to establish some space for itself. No space on the bottom is unoccupied. Every location is colonized by some kind of organism, be it corals, algae, sponges, or clams.Corals are superb fighters. They fend off encroaching corals by stinging them with their tentacles and by ejecting their stomachs to digest them. These coral-coral battle zones are easy to spot; when two different corals meet, there’s often a cleared band between the two where they’ve killed each other off. The same tactics are put to use to fight off invading algae. On healthy reefs, corals can maintain their territory, often beating back and even killing various types of algae. On degraded reefs, the tables are turned. Here the algae are the superior competitors with their own arsenal of weapons including chemical poisons and introducing bacteria that make the coral sick. Sometimes they directly overgrow and smother the coral.

On this expedition, we’ve been quantifying the interactions between corals and algae, documenting how many types of algae the corals are battling and who is winning at each of the atolls. On some of the human-impacted reefs, there are so few corals and so much algae that our surveys take only ~10 minutes each instead of the usual 45. At the more pristine sites we’ve seen beautiful reefs dominated by so many corals that our hands cramp up before we can write down all of the different coral species and the numbers of algal interactions. Although the algae don’t dominate here, they are still present, lurking in the crevices and along the edges of the coral colonies. Even on a healthy reef the corals have to continually stand their ground against the algae, but on these reefs the corals are winning.

Check out the research in the Northern Line Island Expedition!

by Jen Smith, head researcher on the Benthic Team

Prior to setting out on this expedition, I really had no idea how the Benthic Team was going to accomplish the goal we had set: performing three separate experiments at each island given no more than four days each. It seemed impossible. Now, after our fourth island, we have settled into a very efficient groove, our procedures have been streamlined.

On day one at a new island, our first task is to set up the seaweed (algae) growth experiments known as the DAWGS and described earlier here. Our goal is to measure the rate of growth of some common species. Because we have such a limited amount of time at each island—three days really isn’t long enough—we need to get these experiments up and running as quickly as possible. Usually Jill and Gareth attach the small protective cages to the bottom while Nichole and I carefully secure our measured algae samples inside the cages with plastic clothespins. The cages are used to protect our samples from hungry herbivores. Then just prior to leaving an island we retrieve the cages with their samples and we measure the change in size of the algae.

Our most elaborate experimental setups utilize our custom designed benthic tents or cBATs. With each of these we can measure the photosynthesis and respiration that takes place within a 1 m × 1 m × 1 m volume sitting on the reef floor. To set up and install six tents takes six divers two 60 min dives each to complete…depending on conditions, of course. First we lower the hardware which includes: (1) six tents; (2) six 12 ft pieces of heavy steel chain weighing 25 lb each; (3) hammers and chisels; (4) steel stakes to attach tents to the bottom; (5) six Eureka Manta sensors that measure oxygen, temperature, salinity, and pH; (6) six marine grade Sartek batteries; (7) six underwater pumps; (8) lots of very large zip ties; and (9) miscellaneous tubing, plumbing, and other odds and ends.

Since we are working at 30 ft depth, this lowering of equipment is a bit of a task. It requires free divers carefully guiding all of it to the bottom, and by “free divers” I mean Gareth. Finally the SCUBA divers drop in and arrive on the bottom at what looks somewhat like the site of a yard sale. We begin assembling our tent building supplies and then fall into our positions. Nichole and I select the sites where we will attach the sensors so as to span the range from high to low coral cover at each island. Once the sensors are attached, Jill picks up a tent and secures it closed. Gareth, Mark and I fall into place with one of us on each of the three tent corners. As Jill carefully swims the tent down to the bottom, each of us grabs one of the corner cables, a steel stake, our mallet, and some zip ties.Tent assembly begins by securing each corner to the reef with a steel stake. Note: It can be inherently difficult to anchor a steel stake into the reef floor because often the reef is either (a) as hard as cement, or (b) as fragile as hard candy. When, after struggling a bit, we have the three corners secured, we grab one of the 12 ft pieces of chain and drape it around the tent resting on the skirt so as to make a seal between the tent and the reef bottom. We use extra reinforcement to ensure that there are no gaps or openings where the skirt meets the reef. If the conditions are particularly destructive, we need to check and recheck the tents every day to ensure that we have no losses.

Side Story: I was relieved when the expedition left the highly-exposed reefs at Kingman for Fanning Island that I remembered as being such a beautiful atoll with somewhat more relaxing conditions. We arrived at our tent site, carried out our circus act of lowering everything into the water, and then spent the next two dives expertly attaching tents to the reef floor. When we climbed back onto our Zodiacs, we exchanged high fives, impressed as we were with how well everything went despite the strong surge we encountered underwater. (Surge, the back and forth motion you experience underwater as a result of waves passing by, can be gentle or powerful.) The next morning we head out to the site to collect water samples from the tents, as usual. Gareth jumps in to assess the situation and yells, “All of the tents are gone!” Our first reaction was “no way! How could this be?”  After a closer look he realized they weren’t all gone, but definitely two of the six have disappeared completely, leaving no evidence as to where they might be. At least our expensive sensors remained, along with other heavy items like the chain. After making our next dive there and feeling the intense surge ripping us back and forth, we understood why the tents suffered some casualties. This type of research work is clearly not feasible under extreme diving conditions. Perhaps, we consider, this is why no one else has attempted to do what we are doing here on the reef slopes in the Pacific where wind and waves are the name of the game. We feel very fortunate to have gotten the data we have!

After the tents are secured to the bottom, the plumbing team—Nichole and Tracy—move in to do their work feeding tubing into the tents. This tubing is then connected to a battery-powered pump that circulates the water inside the tent and allows us to conveniently sample water from inside every day on demand. Once the pumps are installed and checked, we are nearly finished. We collect our first water sample by simply connecting a Niskin bottle to the tubing and turning the pump on to fill the Niskin, and off we go. These water samples will be later analyzed for an array of water chemistry parameters that will allow us to determine reef community metabolism.At the larger islands we have had four to five days to do our experiments, but for the smaller islands only three, which means tent assembly on day one, tent sampling on day two, and tent dismantling on day three. As you can imagine, the days go by very fast. It is all worth it when we bring the sensors back onboard, download the data, and see nearly continuous sampling of the reef bottom during each of our deployments.

As if this schedule weren’t enough, the benthic team is also doing shipboard experiments to determine how the physiology of the same species of coral and algae vary from island to island. Specifically, we are asking if the same species collected from the same depth in the same habitat show physiological differences that may be related to local human disturbances or to differing oceanographic conditions. We run two of these experiments per island. This work involves myself, Nichole, Gareth, and Jill all collecting organisms in the field, usually on day two. Then begins the fun. Nichole and I spend the better part of six hours in the sauna…literally. The ship has a sauna that we have converted into a physiology lab where we can control the light level. Here we expose the organisms to progressively higher levels of light and measure how much oxygen they produce. (Recall that the coral animals host algal symbionts, the zooxanthellae, that carry out photosynthesis.) This may sound easy, but we have to make these measurements in airtight chambers under precisely controlled conditions, such as at a constant temperature and with well-mixed water. We have a fairly elaborate aquarium system that we brought thousands of miles with us. Furthermore, the sauna is not for everyone. It’s a good thing Nichole and I are not prone to seasickness.

Each of the science teams on the cruise have their own mini-circus with various props and activities that all need to be coordinated and used safely and efficiently. Speaking as the leader of the benthic team, I can say that our circus is satisfyingly beginning to feel like organized chaos.

The Underappreciated Reef Algae

Halimeda opuntia

The Underappreciated Reef Algae

by Jennifer Smith, head researcher on the Benthic Team


The green alga Dictyosphaeria cavernosa, commonly known as green bubble algae. Photograph by Jen Smith.

Coral reefs are known for their spectacular diversity and striking beauty. When most people think of coral reefs they think of the colorful coral animals themselves—the organisms that build the reef structure and provide habitat, shelter, and food for a number of other reef inhabitants. But much diversity and beauty are also to be found in a lesser known and certainly less appreciated group of organisms: the algae. The algae are incredibly important to reef ecology and productivity, but the very word algae often makes people cringe. Why, they typically ask, would you care about “pond scum” or “slime”? The answer is that in the tropics the reef algae (aka marine plants or seaweeds) represent a large number of species—in many places the total number greatly exceeds the number of coral species. These marine autotrophs get their energy directly from the sun. They capture this as chemical energy which they rapidly convert into usable “food” for the rest of the reef food web, making them essential for a healthy reef ecosystem. And they are fascinatingly diverse.

We scientists usually classify reef algae in three functional groups: the turf algae, the crustose coralline algae, and the larger macroalgae. Each of these major groupings contains hundreds of species worldwide and each group is unique and important in its own way.


A patch of pink crustose coralline algae, or CCA. Photograph by Jen Smith.

  1. Turf algae represent an assemblage of small, delicate, filamentous species that are the primary food source for many reef grazers.
  2. Crustose coralline algae or CCA are heavily calcified species that, like the corals, contribute to the growth and development of the reef structure. When alive and thriving, they generally look like pink rock. Some species of CCA are also important for their role in the recruitment and settling of the larvae of corals and other invertebrates, a necessary step for on-going colonization of the bottom.
  3. Macroalgae are a group of large fleshy and/or calcified species that span a wide range of growth forms. These algae can get out of hand when the grazing fish have been fished out, and then they compete with the corals and feed too many microbes.

All three groups are usually present on just about any reef, but their relative abundances can be a good indicator of the health of the reef.


Halimeda opuntia at Palmyra Atoll. Photograph by Jen Smith.

The chain of low coral atolls and islands that make up the Line Islands have less algal diversity than reefs at high volcanic islands such as the Hawaiian archipelago. This might be due the remoteness of the Line Islands and/or the lack of essential nutrients that are supplied by the lava rock of the high islands. The most common algae on the reefs in the Line Islands include members of the genus Halimeda, a group of green, calcified algae that are important reef-builders.

This group, believe it or not, is responsible for making up to 90% of the sand in some tropical locations. They are “unicellular,” but each cell is large and contains many nuclei. When they reproduce sexually, one cell gives rise to many gametes but dies in the process, leaving behind small, calcified, white disks that eventually break down into very soft, bright white sand.

The algae present on healthy reefs such as Kingman and Palmyra are usually eaten by reef herbivores almost as fast as they grow. Imagine what would happen if you mowed your vigorously growing lawn every single day. You wouldn’t have much grass despite the fact that it was still growing fast. This is essentially the situation for many species of algae on healthy reefs, and as a result they are present in very low abundance or closely-cropped. Other species have developed unique strategies to avoid the hungry mouths roaming the reefs, strategies such as chemical and physical defenses.

Here on Fanning Island (Tabuaeran) every location we dive has something different to offer. This high level of spatial variability often indicates a location in a state of change, one with a checkered past, or one with a layering of impacts from different factors. In the protected lee of the island we find vibrant reefs with abundant corals, coralline algae, and Halimeda. The reefs in front of an old ship wreck are covered in a cyanobacterial mat that doesn’t seem to allow anything else to survive. Traveling further north we find reefs covered in soft corals and filamentous algae. In the lagoon, there are only coral skeletons and some macroalgae, but the reef structure indicates that this once was a thriving community. People have certainly had an impact on the reefs here on picturesque Fanning Island. But the high variability from area to area, some still with healthy reefs, suggests that all is not lost here—yet.


Submitted by Merry Youle on Sat, 11/13/2010 – 18:12


The Past, Present, and Future of the Reefs at Fanning Atoll

Luxuriant and extensive live coral cover on the Fanning (Tabuaeran) western fore-reef south of the pass.

To a Paleo-Benthic, today’s coral reefs are rich in clues about their past and offer hints as to their future. Atolls such as those that make up the Line Islands are built of the dead skeletons of corals, foraminifera, and calcifying algae. Beneath the deep layers of marine skeletal debris is the old, extinct volcano that gave rise to the island originally. As the volcanoes age and cool, they sink deeper. The islands keep up with this sinking by growing upwards thanks to the constant supply of new skeletons produced by living corals, foraminifera, and calcareous algae. If natural or human disturbances cause the die-off of these organisms, the supply of atoll-building materials will decrease. Coupled with sea-level rise, this could spell disaster for the marine, terrestrial, and human communities living on coral atolls like these. This is yet another reason healthy, living coral reef communities are so important.

Fanning (Tabuaeran) Atoll, a recent port of call, was an interesting study in contrasts. Its lagoon is huge (110 km2compared to only 34 km2 of land), and most of the lagoon water is exchanged through a single passage on the western (leeward) side of the atoll. This creates amazingly strong currents—up to 3 or 4 knots—and huge standing waves during the peak incoming and outgoing tides. This jet of water seems to act as a barrier between the reefs on the northern and southern sides of the pass. South of the pass, the coral cover was spectacular, covering around 80% of the substrate. Gigantic plates of Acropora and multicolor whorls of Montipora blanketed the bottom.

The coral graveyard on the Fanning (Tabuaeran) fore-reef at the site of the shipwreck north of the pass

In contrast, north of the pass much of the coral is dead. Our “death assemblage” surveys indicate that the coral community was at one time similar to that on the gorgeous southern side. Nevertheless, now the corals are dead and covered with dense mats of cyanobacteria. Moving further north towards a shipwreck that occurred approximately 40 years ago halfway up the northern leeward side, the percentage of dead corals increases to about 99.5%. Something about the shipwreck seems to be killing the corals—probably pathogenic microbes fueled by the rusting ship. (For more details, see the earlier blog posts about the shipwreck sites at Fanning and Kingman.) The really shocking part is the extent of the mortality caused by this shipwreck—the reef is dead and black more than a kilometer north and south of the wreck.
Our team was also able to investigate the coral community on the eastern side of the atoll. In 2005, paleo-benthic Jessica Carilli visited Fanning with another team of scientists and snorkeled at many sites around the atoll. At that time she noted that aside from the luxuriant coral south of the pass, most of the corals were dead. During our dive on the east side of the atoll on this expedition, we found live coral cover in the range of 40-50%. Most of the colonies were smaller than the corals in the southwest. Perhaps we are seeing recovery on the windward side of the island after a massive mortality event—maybe the 1998 bleaching event, or possibly a major storm. Either of these events could have spared the leeward reefs due to the local topography and oceanographic conditions. Storms tend to come from the east here, the windward side, so the leeward side generally escapes major damage. The prevailing currents also flow from east to west. The island’s mass disturbs this smooth flow, causing turbulence and upwelling of deep, cool water on the leeward side. During a major bleaching event, when the east side of the island is bathed in exceptionally warm water, the western reefs may be spared that heat stress due to this “island wake” upwelling.

Our team can test these hypotheses by determining the dates when coral colonies died on the eastern and western sides. If those on the eastern side did in fact die in a mass mortality event that spared those on the west, many of the dead colonies that we sampled on the eastern reef will show very similar “last alive” dates, whereas those on the western (leeward) reefs would have variable “last alive” dates reflecting the constant natural turnover. Furthermore, bleaching events leave a record in the form of anomalous growth bands in massive Porites corals. Thus, if the Porites corals on the western side escaped the bleaching event, those anomalous bands will be absent from the cores that we obtained from them.

And the answer is? Patience. The rules of the paleo-benthic game are: Drill, sample, and measure now. Get answers later.

A Most Useful Useless Reef

Gray reef shark at Kingman. Photograph by Jen Smith.
Bohar Snapper

A bohar snapper (Lutjanus bohar), with fangs, at Kingman. These fearless, curious clowns of the reef habitually nip us or our dive gear, and will pick up and chew anything we leave on the reef. Photograph by Jen Smith.

Charles Darwin saw a world that was dynamic, changing, evolving. On his voyages in the Pacific he was struck by the geology of the myriad islands and doughnut-shaped atolls there. He was the first to connect the dots and realize that they all represented snapshots taken at different stages in a geological progression. Each had been born as a high volcanic island that became encircled by coral reefs. Over time, the islands eroded and the sea floor sank (subsided, in geology speak), while the corals continued to build the reefs upward to stay in the sunlit zone. Eventually, the land disappeared beneath the waves, leaving only a reef as a clue to its past. Kingman Reef is one such relic. By the time humans arrived in the Line Islands, only about three acres of land remained, all of which is awash most of the time. Without land suitable for settlement or airstrip construction, and lacking guano deposits or other usefulness, Kingman has been left alone—actually avoided as it poses a hazard to shipping. Being useless, it has proven to be extraordinarily useful for coral reef researchers today.

Free of current local human impacts, and without Palmyra’s history of military occupation, Kingman provides a near-pristine reef for study. Near-pristine, because no reef is remote enough to completely escape the fallout from our activities. Kingman, like all the others, is subject to the global effects of rising atmospheric CO2, including increased ocean acidity. There is also the endless stream of plastic trash brought from distant lands by ocean currents and that now accumulates on the windward face of the reef.

Gray reef shark at Kingman. Photograph by Jen Smith.

Gray reef shark at Kingman. Photograph by Jen Smith.

Nevertheless, the reef at Kingman is nothing short of stunning for those accustomed to the degraded coral reefs of today. It, along with a handful of other near-pristine reefs in the Phoenix and Southern Line Islands, gives us a glimpse into the past. We know from the reports of the early explorers that the reef waters were thick with large animals: sharks, sea turtles, groupers, to name a few. Kingman is a reminder that most of us, coral reef scientists included, don’t know what a healthy coral reef looks like because we have never seen one. Our first visit to a coral reef becomes the “normal” against which we compare future reefs. With each generation, our baseline for comparison shifts toward a more degraded state. Kingman forces us to reset our baseline.

Because even near-pristine reefs are now so rare, Kingman has taken on great importance as a research site. Data collected here during the 2005 expedition provided new insights for our understanding of coral reef ecology, some of which will be discussed in future posts. Based on those observations, the reef at Kingman was made the gold standard used when calculating the CHI for coral reefs around the world. (To learn more about the CHI, the Coral Health Index, check out this earlier post.)

Late on Friday the Hanse Explorer brought the research teams the 67 km from Palmyra to Kingman, and yesterday the researchers started their work here. Time is short. There is much to be counted, measured, sampled, and simply observed. But for today—Halloween—for the researchers going overboard at Kingman, it is a treat.

On our first day on Kingman, we dove the western terrace. This the side of the atoll that is sinking. This is also the side where the predominant current runs onto the reef and creates an upwelling. The nutrient-rich upwelling in turn feeds the plankton, which attract everything else. Coral cover is incredible, probably over 60%. There are schools of iridescent ctenophores [comb jellies], and the mantas are all over the place, twisting and turning to feed on all the things floating in the water column. We saw at least ten in just one dive. My dive partner and I were literally surrounded by a wall of big eye jacks.

– Forest Rohwer, head researcher on the Microbe Team

Read more from the field at:

scripps oceanography uc san diego