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A *bit* of a tour of the Johnson Sea Link

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


Taking mapping to a whole new level

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!


Good old-fashioned home-grown oceanography!

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!


Putting the world's commercial ships to work

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.



LOLcat goes all Cousteau

This is what happens when you have a lot of steaming time between transects:


A sobering sight at 600 meters

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


Eyes in the deep

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!


Planning a dive

The dive planning board in the lounge on RV Seward Johnson


Shedding some light on lanternfish

Diaphus parri, a lanternfish from the Coral Sea. Img: Adrian Flynn

Adrian Flynn’s PhD is about myctophids, or lanternfishes.  These are not well known to most people, but they’re probably among the most abundant animals on the planet, because they live in the largest habitat there is: the deep mid-waters of all the oceans of the world, neither near the surface nor on the bottom, what scientists call the mesopelagic zone (meso = middle, pelagic = in the water column).  Lanternfish, as the name implies, produce their own light from organs arrayed on the skin of the head and body.  These organs, which generate light through the action of the enzyme luciferase, allow the fish to signal each other, to find food and to disguise their own outline against the gloom from above, when seen from below.  Its a neat trick, but not nearly unique in the deep pelagic zone.  Indeed, it seems that just about everything down there makes light in some form or another (if you want some google fodder for that, check out Edith Widder’s work, she’s got a great talk on too).  Lanternfishes can be hard to study because they’re hard to collect in tact; they’re sort of flabby and the skin comes off very easily. But not to be deterred, Adrian is undertaking an ambitious study of how different species of lanternfishes are distributed from the tropic of Capricorn to the waters of the Antarctic - their biogeography - and also how the numbers of any given species are affected by oceanographic factors like major currents and places where deep nutrient-rich water comes up to the surface (upwelling). 

A nice ventral view of D. parri, showing the light organs arrayed on the skin

So far his results are showing that the deep pelagic zone is not as homogenous as previously thought.  It seems that lanternfish distribute themselves into biogeographic zones somewhat according to latitude, but more so according the oceanographic features like major currents and landforms like islands.  He’s had a couple of real eye opening results too.  In one case, they observed - for the first time in Australia - a lanternfish spawning aggregation, off the coast of Cairns in far north Queensland.  That’s cool, but what was a real trip was that the laternfish in question (the Dana lanternfish) was a species known only from Tasmania, almost 2,000km away!  How did they get up there?  How will their young get back again?  On another expedition, they found lanternfish close to the surface at Macquarie Island, a remote rock in the Great Southern Ocean.  The island juts up into the prevailing currents, causing upwelling that brings nutrients and lanternfishes alike well within the foraging range of penguins and seals/sea lions that nest on the island.  It looks like lanternfish in this unique location are an important part of the diet of at least three penguin species as well as the pinnipeds (seals), and that’s a pretty novel discovery.


Seized by a sneeze - more from Kristie Cobb Hacke

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…


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.


Dia 2 Campanha Seward Johnson - A guest post from Gustavo Duarte

Gustavo Duarte is a PhD student with the Abrolhos expedition.  Here, he describes for Portuguese readers, Day 2 of the research cruise.  Gustavo has a blog at IPAq; you can read more there.


Ontem o que fizemos basicamente foi combinar toda a estratégia de coleta para hoje. O submersível estava agendado para descer as 8:00 da manhã com dois pesquisadores: Clovis Castro, meu orientador do Museu Nacional e Shirley Pomponi, do Harbor Branch, além do piloto e do co-piloto.

O mergulho foi um sucesso total. Foram trazidas várias espécies de mar profundo. O destaque foi uma belíssima estrala do mar, vários caranguejos bem diferentes, um lirio do mar e várias espécies de corais vivos.

A temperatura da água durante o mergulho foi de 6˚C aos 700 m subindo para 8˚C aos 450 m. Na verdade o submersível desce até a profundidade máxima do mergulho e vai junto ao fundo até a profundidade mínima e então sobe a superfície.

Os corais estão nos aquários que estão por sua vez dentro de uma câmara fria, a tal “environmental chamber”. Lá eu tenho água do mar corrente saindo de uma torneira. Montei os fragmentos num suporte usando superbonder gel e depois durepoxi. Se sobreviverem até amanhã vou alimentá-los com naupilios de artêmia e plancton coletado pelo navio.

Deu muito trabalho triar todo o material, veio muita coisa diferente. Mais a noite eu tento postar as fotos. Agora estamos fazendo coleta de água em várias profundidades para medir nutrientes, penetração da luz, níveis de clorofila, temperatura, tudo isso de acordo com a profundidade. Um pesquisador a bordo vai filtrar esta água e congelar o material a -80˚C para análise genética dos microorganismos presentes na coluna d’água. Para isso estão usando um CTD com uma rossette.

As 4 da tarde faremos um mergulho mais raso, que começará em 120 m e terminará em 70 m. Coletaremos amostras de corais com zooxantelas e eu medirei a resposta fotossintética destes organismos. Depois, usando uma serra copo, vou retirar uns plugs de cada coral e no laboratório do Rio iremos medir a clorofila das amostras, a microbiota associada bem como uma contagem de zooxantelas.

Com isso esperamos conhecer um pouco mais destes corais que conseguem fazer fotossíntese em regiões tão fundas.


Foot in the Jackfruit - a guest post from Kristie Cobb-Hacke

Where in the world are you when the expression “foot in the jackfruit” makes sense?  Brazil. Recognizing that this euphemism “Pé na Jaca” loses some of its finesse in English, it is nevertheless something that makes travel beautiful.

My goal during this adventure is to avoid “ na jaca.” Yesterday in our travels from Vitorio to Nova Viçosa throughout the drive we were able to see coffee plantations, sugar cane and eucalyptus farms. All of these farms were on formerly-forested areas, so interspersed we were able to spot the pink mangos, purple mangos and many other varieties of native plants. Although the jack fruit thrives in this environment, it is an invasive species. It is originally from India and archeologists have revealed it was first cultivated there 3,000 years ago. This tree has the largest tree-borne fruit and has spread quickly throughout areas of Brazil as birds and animals eat the seeds of fallen fruit and deposit them elsewhere. In recent years there have been some forestry management efforts to rid the national parks of saplings as these fruit are thought to have contributed to the decline of certain bird species. 

 During our drive we discussed the cultural challenges that come with conservation efforts. The mere idea of discussing the lack of conservation in an area may be a time where I could certainly have been through of as insensitive. I certainly don’t want to be considered as an invasive species to the crew and scientists on the Abrolhos expedition.  We discussed the change in the landscape and the growth in the farming industry, particularly eucalyptus.

This area of the world is considered a biodiversity hot spot by conservation international. This is an overview:

The Atlantic Forest or Mata Atlântica stretches along Brazil’s Atlantic coast, from the northern state of Rio Grande do Norte south to Rio Grande do Sul. It extends inland to eastern Paraguay and the province of Misiones in northeastern Argentina, and narrowly along the coast into Uruguay. Also included in this hotspot is the offshore archipelago of Fernando de Noronha and several other islands off the Brazilian coast.

Long isolated from other major rainforest blocks in South America, the Atlantic Forest has an extremely diverse and unique mix of vegetation and forest types. The two main ecoregions in the hotspot are the coastal Atlantic forest, the narrow strip of about 50-100 kilometers along the coast which covers about 20 percent of the region. The second main ecoregion, the interior Atlantic Forest, stretches across the foothills of the Serra do Mar into southern Brazil, Paraguay and Argentina. These forests extend as far as 500-600 kilometers inland and range as high as 2,000 meters above sea level. Altitude determines at least three vegetation types in the Atlantic Forest: the lowland forest of the coastal plain, montane forests, and the high-altitude grassland or campo rupestre. (

The Atlantic Forest of Brazil

But in a place like Brazil that is growing and actively developing their resources, it is important to understand the ranking of conservation among the needs and challenges of a country that is home to approximately 3% of the world’s population: over 190 million people ( the vast majority living in urban cities. In many cases large numbers of citizens face much less complicated but much more personally critical decisions like food, clothing, water, waste management and health come long before thoughts of the care of the surrounding environment.

So for our bright and inspired scientists on this expedition it is going to be critical for them to be clear with their efforts and decisive with their results so that they can avoid sticking their ‘foot in the jack fruit” and they can begin the process of educating their fellow Brazilians and affecting change to preserve their native and incredibly diverse environment. On its own nature can maintain a diverse and complex system of life including production, consumption and disposal of waste. These processes are all seamless in a well-balanced system. If at any point a part of the system is disrupted the natural web may become imbalanced and threaten the health and loss of species at a minimum and, at a maximum, could be catastrophic.

Unfortunately, sometimes it takes catastrophe to serve as a wake-up call. One of our travel companions, Nina Bilton, is from the state of Rio de Janeiro and she shared that the recent torrential rains and the subsequent mud-slides have drawn tremendous attention to the environment and have activated the concern of a nation. So in all of this devastation one bright light is that dedicated committed scientists, organizations and corporations can occasionally come together to start the process of understanding the environment. At the core awareness is the science behind understanding the natural environment around us all.

As I write I am witnessing, for the first time, a completion of a submersible dive. I am excited to hear about what our researchers are seeing and learning and I’m looking forward to seeing the results. The data they have collected today is just one small piece to understand and protect the integrated web of life in the Abrolhos area.

(Kristie Cobb-Hacke is a vice president at Georgia Aquarium)


Diving is like a box of chocolates...

…You never know what you’re going to get.  In this video, the Johnson Sea Link (JSL) is recovered after the first dive of the Abrolhos2011 Expedition.  Brazilian scientist Clovis Castro was aboard with HBOI scientist Shirley Pomponi. 

Afterwards, the science team went to work processing invertebrate samples including gorgonians, the hard coral Lophelia, and a range of brittle stars, crinoids, urchins and miscellansous crustaceans

The Brazilian science team evaluates their first samples. L-R Gustavo Duarte, Clovis Castro, lead scientist Rodrigo Moura and Ronaldo Francini-Filho


Reporter Glenda Koslowski with Brazilian scientists (L-R) Gustavo Duarte, Clovis Castro, Rodrigo Moura and Ronaldo Francini-Filho


PhD student Gustavo Duarte takes Lophelia fragments for cultivation

 Alex Bastos with a fine carbonate mud sediment core from 600m



Day 1 cruise track

Here’s our Day 1 cruise track, taking us from Nova Viçosa out to a way point and thence to the R/V Seward Johnson.  Right click the link and save, then  open in Google maps or Google earth