When we were on the Abrolhos research cruise aboard the HBOI/CEPEMAR ship Seward Johnson recently, I posted a little clip of the outside of the sub. In that post I promised better quality and longer clips when I got back to land. So here, (in HD goodness if you want it) is long-time pilot Don Liberatore giving a neat history of the Johnson Sea Link 2 submersible. What I find most interesting is his comment about how he got into being a sub pilot in the first place: sitting on the dock in the 70’s he and some buddies saw the HBOI ship pull into port with the original JSL1 or Clelia (not sure which) on the deck and he thought “how cool is that?”. This comment is exactly what I meant in my recent post about the importance of Human Occupied Vehicles (HOVs), or submersibles, for inspiring people to careers in marine science.
The 500pixel column width here on the blog is a bit limiting; if you want to see it in HD, roll over to the YouTube channel and check it out
There’s a new website up that talks about deep sea corals, including one of the species the science team has been studying here in Brazil - Lophelia. Its even called Lophelia.org and was put together by some Scottish scientists who discovered Lophelia reefs off the coast of Scotland in 2003. It’s very comprehensive and well worth a visit, and it’s recently earned an endorsement of the doyen of nature documentaries, Sir David Attenborough. One of the weird things to think about when you click on over is that the same corals that form those reefs in Scotland are forming deep reefs here in Brazil. How is that possible? I mean, one is in the chilly North Atlantic, while the other is in the tripical south Atlantic. Well, if you think about it, once you go deep, it doesn’t matter where you are, it’s always gloomy dark and cold! For example, even though the surface temperature was in the high 20’s (low 80’s for the US readers) here in Brazil, the temperature down where the sub was going was 7-9 dgrees (around 45).
A Dendrophyllia alternata (originally mislabeled here as Lophelia) colony collected from the Abrolhos platform
The new website is a great resource for learning more about Lophelia and other deep coral reef species and just maybe it will help us all broaden our horizons to start considering coral reefs in a context broader than the insanely colourful shallow reefs that most easily comes to mind when you hear the phrase.
As we were steaming along yesterday, we encountered a mysterious yellowish slick along the surface. Sometimes it formed into filaments stretched out like cobwebs on the surface, but in other areas it was thick enough to make the water surface totally opaque. What could it be, so far off the coast? fish spawn? coral spawn? algae? oil, maybe? So we slowed the ship and took a bucket sample from over the side (thanks Maurice!). The culprit? Trichodesmium. This blue-green alga is common in the nutrient poor waters of the tropics, and occasionally forms huge blooms like this. How can it bloom when nutrients are so scarce? The answer is that it makes its own nutrients; Trichodesmium is a “nitrogen fixer”. This means it can take nitrogen from the air and incorporate it into its own molecules and tissues, a relatively rare feat (the best known example on land are legumes like peas and beans).
If Trichodesmium blooms like this, then the impact can ripple through the ecosystem because, once fixed, the nitrogen is available to the rest of the food chain. This can make Trichodesmium a key species.
All of that brings us to Dr. Paulo Sumida from the University of Sao Paulo. Paulo is on this expedition to study organic matter, like the products of all that Trichodesmium. He’s especially interested in what’s happening on and just above the bottom, where the sub is visiting. One of the biggest questions: is the organic matter in the sediment of the dark deep made by organisms on the bottom elsewhere and transported there, or is it made by plankton in the water column above (like Trichodesmium), and then rains down like nutrient snow? One of their other hypotheses is that the southern part of Abrolhos is more productive than the north. In other words, that more organic matter is produced there by greater numbers of organisms. To work out the answer to these questions, Paulo looks for clues about how much organic matter there is, what “quality” it is and who made it.
Dr. Paulo Sumida peers out of a porthole on the JSL sub
Measuring how much organic matter there is is relatively straightforward with an instrument called a CHN analyser (C = carbon, H = hydrogen, N = nitrogen, the key ingredients of organic matter). To measure quality, Paulo looks at how much of the photosynthetic pigment chlorophyll is present. If the organic matter is old, most of the chlorophyll will have broken down in a process scientists call diagenesis, leaving behind waste products called phaeopigments. The relative amounts of chlorophyll and phaeopigments can be used as a measure of the quality of organic matter. Perhaps the coolest part, however, is trying to work out who made the stuff. To do that, Paulo uses a rare tool at the University of Sao Paulo, called a GC-IR-MS (gas chromatograph isotope ratio mass spectrometer, say that ten times fast). This instrument can look for chemical signatures that tell you who made the organic matter. For example, phytoplankton might produce organic matter with certain carbon isotopes in it, while benthic algae might produce a certain sterol compounds that, when Paulo sees them, he can say “Aha! Now I know that this organic matter was made by this group or that group”. It’s a great bit of detective work.
Taken together, all this information tells Paulo and the other scientists about how nutrients move from water to sediment and back again (properly called “flux”) and therefore how tightly life on the bottom is connected (“coupled”) to life in the water column. It also speaks to how connected different parts of the bottom may be, especially if organic matter proves to be made somewhere else and then transported to the dark zones. So what’s the answer? Is it produced on the bottom or in the water column? By algae or by phytoplankton? Unfortunately, we don’t know yet, because this is just the sample collection phase; his research is just beginning. I hope in a future post I can tell you about the results of Paulo’s work.
Yesterday morning on a tour of the bridge of the Steward Johnson following the deployment of the submersible, we had the opportunity to chat with some of the sub crew and a pilot. During our chat they were sharing stories of other dives. One in particular was incredibly interesting to me because it continues the idea of worlds within worlds (the sneeze theory). Craig Caddigan was mentioning that he piloted the submersible to a location in the Gulf of Mexico that contained an “underwater lake.” The lake was a dense brine pool, made up of water with an incredibly high density due to salinity and found at over 2000 feet depth. Craig described landing the sub on the lack and bouncing along the surface and creating ripples. The brine area has its own waves and “beach”, in this case surrounded by a 10’ ring of mussels. The mussels use methane as their primary food source. The submersible was unable to descend into the brine lake because it was too dense, but they did take along some tools that could sample the contents.
A brine pool in the Gulf of Mexico
What is amazing to me is that this brine sea is contained within the ocean. Do the animals that live around this area know that they are living in a sea within a larger ocean? When I sit on the beach am I merely sitting on the edge of a pool within someone else’s greater ocean. Am I at risk of being someone else’s sample? These big thinking questions are what keep me going but the scientists aboard the Abrolhos are focused on the small things that make up the ocean. Right now they are collecting small coral samples, sediment, rock, fish and other items. During the cruise other members of the HBOI staff have been creating maps so that the scientists can use them for future trips or they can clearly note the location of sample and sediment collections. The CTD collected water at the same locations where the submersible was deployed, so that bacteria and viruses can be measured and identified in the water column. The hope is that each of these small pieces can create a larger overall understanding of the structure and biology of the Abrolhos reef.
Generally-speaking, holes in ships are A Bad Thing, but in the center of the R/V Seward Johnson there is a hole, a really big hole, that’s both deliberate and critically important. It’s called a moonpool and it’s used to deploy the device that allows the Com-Track (see previous post) to talk to the sub: the transducer. This acoustic tool (basically a combination speaker and microphone) could just be dangled over the side, but the hull of the ship would interfere with the signal, so they lower it through the moonpool well below the ship. It’s a lot like putting up an antenna, only upside down. As I stared down into the blue glow, Sully the Com-Track officer was using the transducer to speak to the sub pilot, 800ft further down into the depths below…
PS - If you’re wondering why the water doesn’t rush up through the moonpool it’s because the water in the moonpool is level with the surrounding sea level, so there’s no pressure to push it up into the hull.
The swells died away this morning and the science crew was thrilled to make it back in the water. As I type, lead scientist Rodrigo Moura is in the sphere and geologist Alex Bastos is in the back and they’re 800ft down on the south edge of the Abrolhos Platform. They’re exploring a steep sandy slope (like, 45 degrees steep) expecting sponges and fishes and collecting sediment samples for the geological context and to measure the quantity and origins of the organic matter, which is important to understand how much the ecosystem there relies on plankton above or on its own productivity at the bottom.
In the photo above, Jim “Sully” Sullivan sits at the Com-Track for the submersible, while Brazilian scientist Paulo Sumida (U. Sao Paulo) takes notes. Com-Track is a station on the bridge of the ship, where sub crew staff and scientists can track the position of the sub and communicate with the scientists onboard. Its not that straightforward, though, because there’s no cable to the JSL and radio and other EMF frequencies don’t travel through water. Instead, communication takes place embedded in acoustic signals, with limited voice coms and a system of “pings” to serve as acknowledgement/agreement. The whole shebang is tied into the GPS system for the ship, which is what made it possible for Bill Baxley to embed the sub track in his lovely 3D model. If all goes according to plan, I’ll send an update on what they find later today
Kristie Cobb Hacke and I were given a royal tour of the JSL submersible today, by longtime pilot Don Liberatore. Unfortunately the ships satellite internet won’t handle the 20+ minutes of 1080p goodness, so these two snippets will have to do. I’ll splice together the full vid when we get back to a wired internet connection. In the first video, Don describes the sample bucket system and in the second, I poke my head into the rear observation chamber
When you set out to drive somewhere, or to sail a boat, you put a lot of faith in maps. You trust that things are where the maps says they are and that there’s nothing where the map says there’s nothing. Can you imagine the chaos if the map didn’t sync up with reality? It’s relaitvely easy to make faithful maps for roads because, for the most part, they’re man made, and someone planned and engineered them, so they have good survey data. But for oceanic charts, its a bit different. Charts are made by sounding (measuring the depth to the bottom at a specific point) and then joining up all the points of the same depths into contour lines (isobaths). But because you can’t usually see the bottom over which you sail, you really have to trust that whomever made the chart did a decent job of it.
In this overlain image of two charts, you can see how one (the black lines) does not match the other (coloured lines)
Bill Baxley noticed that some of the charts for the area of the Abrolhos shelf where we are working don’t even match up with each other very well. That means someone is right and someone is wrong, so Bill - the Harbor Branch director of technical operations for this expedition - is using downtime in between sub dives to better map the bottom. At night, while the science crew grabs some much-needed shut-eye, Bill and the ship’s crew sail back and forth across the shelf break, taking super accurate readings of the depth using sonar equipment and precisely geolocating the soundings by GPS. From all these data, he has not only created a much more reliable map for use on future research trips to this area, he’s even able to use GIS software to render the bottom in three dimensions. In the movie below, Bill animated his map so that you can quite literally see the north shelf break of the Abrolhos platform rotating before your eyes. He’s even put two submersible tracks on there. The deeper of the two in red is the one where the bottle was seen, and on which this photo and video post was based. If this isn’t just about the coolest thing ever, I don’t know what is!
If oceanography had a classic bread-and-butter technique, CTD casts would have to be it. The C stands for conductivity (basically salinity), the T for temperature and the D for depth. The “cast” refers to the fact that you measure these three properties as the instruments descend to - and return from - the sea floor. CTD casts tell scientists about the structure of the water column beneath them. How can water have structure? Well, differences in temperature and salinity can lead to layers in the water and these can tell you about how the water is or isnt moving and also have implications for animal life living there. If you’ve ever swum in a lake where your body was warm but your legs were cold, then you’ve experienced a structured water column, or water layers. (Strong structure like that often happens in summer when surface waters are warmed by the sun, which makes them less dense, so that they are even more buoyant. When winter comes, the surface layer cools until it is denser than the underlying water, at which point the surface water sinks and the water column “turns over”)
In a world of side-scan sonar, ADCP and satellite sensing, CTD casts still play a really important role in understanding the water column, so they are still a core part of any oceanographer’s toolkit. Let’s take a look at one. This CTD/rosette sampler is part of an instrument package belonging to the Rosenstiel School of Marine Science at the University of Miami:
This rather expensive bit of kit stands about 6 feet high and consist of 24 sample bottles arranged in a ring, with the actual CTD instrument package underneath. Together, this equipment can make accurate measurements of not only salinity, temperature and depth, but also dissolved oxygen and chlorophyll concentration, AND it can take a 10L sample at any depth using the “rosette” of bottles. In the following video, U. Miami oceanographers deploy the CTD, then I discuss the acquisition of data with Cepemar oceanographer Carlos Fonseca, and finally graduate student Nelson Alves collects water samples from the sample bottles for a study on bacteria and virus diversity
So far here in Brazil we’ve seen a typical “surface mixed layer”, where the temperature and salinity is the same throughout the top 10-20m. Below that, temperature drops sharply 4-5 degrees C to a colder underlying layer; this transition is called a thermocline (thermo = temperature, cline = a gradient) and is a standard feature of that well-layered water column. Below that, temperature drops more gradually, but with some jagged steps that result from “salt fingers”. These are small-scale turbulence features that tell oceanographers (like Carlos in the video) about mixing processes taking place in the water column.
The CTD - long time friend of oceanographers the world over!
The University of Miami’s Peter Ortner calls the Royal Caribbean cruise ship Explorer of the Seas” the world’s most luxurious research vessel”. That’s because he and his colleagues affixed instrument packages and even built a small lab on the luxury liner. Why do this? Well, if you think about it, cruise ships and commercial ships are criss-crossing the oceans all the time. What an awesome opportunity to collect data!
Commercial shipping lanes of the world - the ultimate scientific transects?
One of the best sorts of data that Peter’s team collects is called ADCP, for Acoustic Doppler Current Profiling. Its a sonar method of sorts, but not for measuring the distance to the bottom. Instead, it can tell you the direction and strength of the current (i.e. its vector) at every depth under the ship. That’s because the speed that sound travels through the water is distorted by current the same way that the speed of sound through air is distorted by speed (you hear this as, for example, the change in pitch when an ambulance goes by).
ADCP current vectors (black arrows) recorded by a ship and mapped on temperature of the Gulf Stream. You can see how well they match up
By putting a bunch of ADCPs on a bunch of different ships that cruise regular paths, oceanographers can build up a very detailed picture of currents across ocean basins, on a scale that individual oceanographic vessels could never match. Along the way, they have discovered new features, especially eddies of various sorts in some unexpected places. An eddy is a circular current, sort of like a gentle cyclone in water; sometimes they form by themselves, but more often they spin off the edge of a current as it passes through another body of water; these are called frontal eddies. Eddies can go clockwise or anti-clockwise and they can have a warm core or a cold core or a ring-like structure, depending on how they form. Eddies are important because they profoundly affect the biology within them - either stimulating or dampening productivity. They can also be really important for weather and climate, because an eddy can take a lot of heat energy from a warm current like, say, the Gulf Stream, and move it somewhere else. Climate and weather prediction models work much better when eddies are properly accounted for.
What an eddy looks like by ADCP. The ship travels left to right across the top. Red pixels is where water is coming towards you out of the screen, while blue is it going away from you, into the screen
ADCP also gives you BIOLOGICAL data. Here, backscatter shows variations in the distribution of plankton as the ship crosses an eddy like the one in the previous figure
The idea of using commercial ships to collect oceanographic data has proven popular and now a UN committee is working on an implementation plan that would see many ships constantly gathering oceanographic data in all the oceans of the world. That program is called Oceanscope, and when it reaches maturity, Peter’s dream would have become and reality and he can kick back and watch the data roll in.
On the very first Johnson Sea Link dive during this cruise, the very second thing seen on the bottom was the bottle shown in the video below shot by Johnson Sea Link crew. This was observed at 600m (technically, it was at 1,850ft), in soft calcareous mud, over 45 nautical miles from land and 60 miles from the nearest town. On the next dive, the scientists observed a lot of old longline fishing gear wrapped around the reef structure. It seems, even in this remote location, which has never before been visited by humans, trash from human activities elsewhere has made its mark on the habitat. It is a prominent and disturbing reminder of our impact on even the unseen parts of the planet. I can only hope that this bottle becomes a home for some small thing, or that it becomes crusted over with coralline algae such that one day it is simply a bottle-shaped rhodolith
The medusa lander. Img courtesy Adrian FlynnIt’s nice to hear a familiar Aussie accent from time to time and so it was when Dr. Adrian Flynn joined the Abrolhos expedition. Adrian hails from Melbourne but was based for a long time at my alma, the University of Queensland, where he applied tools developed in a collaboration between Dr. Justin Marshall at UQ and Lee Frey at Harbor Branch, to study animals in the deep sea. Specifically, they designed and built Medusa, a “lander” that can be deployed off a ship or from a submersible to sit on the bottom and film animals in a much less intrusive way than would be possible with a manned vehicle. The keys to the success of Medusa are that it can be left on the bottom for a prolonged period, that it can be baited to attract animals, and that it illuminates the surrounding scene using wavelengths of light that most deep-sea animals cannot sea. This allows the custom cameras onboard to record animal behaviour without their knowing, which improves the chances that the behaviours recorded will be “typical” and not a response to the presence of the equipment.
The results have been fantastic, as you can see in the video below. In it, Medusa is shown being deployed in the Coral Sea near Osprey Reef. Stay for the 6-gill shark at the end - it gets all Nom! Nom! Nom! on the tuna head!
AD - Its clear to me that Kristie is a repressed zoologist! Her pure joy at the sight of dozens of tiny brittle stars attached to a sea fan is the kind of emotion that drove many of us into marine science in the first place. But don’t take my word for it…
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When I was a kid I used to spend hours thinking about how small we are in a really big world. I would often ponder “what is at the end of the universe?” I would amuse myself by thinking things like “it’s a brick wall” and then assume if you walked around or knocked it over there was always something on the other side. I would have this same thought again and again sometimes stopping to pause and wonder if it is something just like a big brick wall and there is no other side. When I was in high school these thoughts were shared by some of my friends as we circulated and chatted about Douglas Adams and his version of the universe and the restaurant at the end.
Another popular thought of mine was that earth was created by a giant sneeze. Sometime in middle school biology a teacher posed the thought that there could be whole universes in something as small as a pin-head. I had this great vision of the giant humans, one standing in front of another being seized by a sneeze. This uncontrollable sneeze produced projectile droplets that landed on the other person’s glasses. Although the term “yuck” is the first thing that comes to mind the second was always….”what if that just created a whole universe?” Would some small organism in that universe consider the edge of the droplet the end of the universe? Would they push on to see what was on the other side? Would they live and die a whole lifetime in the instant between the sneeze and the inevitable wiping of the lens?
From the collection boxes of the Sea Link II the scientists brought up a bio-box of goodies. Their samples included a beautiful gorgonian sea fan. As they unloaded, documented and photographed the various items, they pointed out many beautiful teeny-tiny brittle stars on the single fan sample. One of the researchers suggested that the sample piece contained more than 30 of the sea stars. Each of the sea stars was amazingly blended to hide themselves among the thin fan structure of the coral. Their fragile thin legs curled around the fan and, when coupled with their patterning, it created the perfect camouflage. The researchers were amazingly accommodating and allowed me to touch and handle one of the sea stars and a piece of the coral. As I carefully unwound an arm I had a stunning flashback to the brick wall and the sneeze. I wondered instantly if to these sea stars is the edge of their universe the single fan, the whole coral colony, the structure to which it is attached or some expanse of sea floor?
Camouflaged brittle star attached to a gorgonian
When you consider the ocean as a whole it is amazing to think about all the millions of places that are yet to be discovered. Not to mention the uncountable species yet to be recorded. There are new depths known only through scans just waiting to be explored by humans. This journey has allowed time for conversations about new technology being created and innovative ways to use existing technologies or commercial vessels for research applications. As each of these becomes available and is applied it will undoubtedly lead to new discoveries. As this continued, in our lifetimes alone, there are bound to be millions if not trillions of questions to be asked and hopefully answered. Although I doubt the answer to life the universe and everything is as simple as “42” and I certainly cannot claim to know if there is a brick wall waiting at the bottom of challenger deep just waiting to be knocked over. What I do know is that research and its concrete ability to pose and then answer questions is incredibly important to our full comprehension of both the universe and the deep.
AD - This relationship between the brittle star and the sea fan is a great example of how little we know about symbioses in the oceans. Clearly the two organisms are living in close association, but in what manner? Is it pure parasitism, whereby the brittle star benefits and the sea fan is damaged? Or is it commensalism, where the brittle star benefits and the sea fan is indifferent to its passenger? Is it maybe possible that there is some sort of mutual benefit that we are unaware of? As a parasitologist by training, how little we know about the these associations makes it hard for me to define my own field. So, while Kristie’s vision is a little broader than mine (scaling up from brittle stars to the edge of the known universe!), I mostly grapple with smaller questions of who makes out better in this little biological transaction, and how does the sum of those transactions across the diversity of animal groups serve to reinforce or undermine stability in the whole ecosystem.
Sunday, February 20, 2011 at 8:34PM 
