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As promised, more of the Johnson Sea Link

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


Who's nourishing the deep reef?

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.


The moonpool

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.


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!


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


Welcome aboard!


Getting down to the nitty gritty

How deep can we go?  How can we collect fish?  How much water can we sample at once?  These are just some of the questions that filled today’s planning session in Vitoria for the Abrolhos 2011 expedition.  They’re not straightforward questions to which some resident authority has a simple answer.  No, when you’re planning work between 300 and 3000 feet down, no questions are simple, and nor are the answers easy; rather, they are crafted through a careful group discussion of what’s a priority, what’s possible, what’s practical, and what we have time for.  In other words, its not all The Life Aquatic, its large parts careful planning and preparation.

The day started with presentations from representatives of Cepemar, Harbor Branch and the Rosenstiel School of Marine Science at U. Miami.  After that, Rodrigo Mouraled the planning session where we talked reef biology for hours, fueled (as all the best science chats are!) by shots of excellent Brazilian coffee.  Dr. Moura is a faculty member at Santa Cruz University and a consulting scientist with Conservation International, who have a substantial marine conservation program focused at Abrolhos.  He explained all the things that make Abrolhos unique, from the 40,000km2 platform on which they occur, to the unique fauna and dominance of shallower reefs by the endemic coral Mussismilia braziliensis, to the unusual mushroom formation of these reefs (chapeiroes), and finally to the history of human impacts and conservation efforts surrounding these unique ecosystems and the deeper and less-known seafloor habitats around them.  The Abrolhos Marine National Park was the first marine national park in Brazil, established in 1983, but like many reefs it faces its fair share of threats from pollution, global climate change and marine development.

 Suitably up to speed on the history and context for the expedition, the next speakers were the 8 principal investigators to give details of the motivations for their respective parts of the expedition, and to outline their specific sampling needs.  Alex Bastos, a geologist from the Federal University of Espirito Santo, talked about the geological history of the platform, how its central depression was likely once a shallow coastal lagoon during the last ice age, and how taking samples of sediment from the bottom will explain more about how the reef came to be and how much it contributes to calcium carbonate production in that part of the Atlantic. Paulo Sumida from the University of São Paulo explained how organic matter (carbon based material either secreted from living organisms or leftover by dead ones) is distributed unevenly across the platform, with more in the south and less in the north.  We learned from Mauricio Torronteguy’sgroup at Cepemar how water sampling and measurements of the properties of the water overlying the reef would be used to provide a better understanding of the biology taking place on the reef.  Microbiologist and geneticist Fabiano Thompson from the Federal University of Rio de Janeiro explained what has been learned about the importance of Vibriobacteria on the reef, both as potential agents of disease in corals and, surprisingly, as possible agents of photosynthesis; i.e. food production from sunlight.  Vibrios were not previously known to use light for food, so this is potentially big news.  His graduate student, Nelson Alves, will be sampling for water-borne viruses by looking for their DNA signature.  These aren’t viruses as we know them (causes of A rhodolith bedhuman disease), but a natural and dominant part of the very smallest members of the plankton, whose importance has only been realized in the last few years.  Gilberto Filho, who is a head botanist at the Botannic Gardens in Rio de Janeiro, talked about the importance of rhodolith beds, which are an unusual sort of habitat made up of softball-sized lumps of reddish rock that are produced by algae that are able to secrete calcium skeletons as they photosynthesise, much like corals do.  These lumps then become substrate for all manner of other things to live on, since they are hard and rigid, unlike the soft, shifting sediments on which they sit.  In this way, rhodoliths can increase the diversity of a patch of otherwise empty seabed.  Ronaldo Francini-Filho talked about what is known and not known about some of the bigger critters that make up the reef community, like fish and larger invertebrates.  The final presentations from National Museum scientist Clovis Castro and student Gustavo concerned deep-sea corals of the Abrolhos, including those that use light and have symbiotic algae in their tissues (zooxanthellate) and those that lack algae and feed by filtering plankton or absorbing organic material directly from seawater (azooxanthellate).  We’ll learn more about each of these projects in coming days, so if you have questions for the researchers, by all means post them in the comments below. 

The hardest part of planning a research trip came next: deciding how on earth we’re going to meet everyone’s needs within a limited timespan, using the assets of the ship and the brain trust of people aboard it.  This is where the beautiful ideality of a proposed sampling scheme meets the stark and sometimes gruesome reality of what you can, practically speaking, actually do.  All scientists, especially biologists, know and dread this bit; indeed, Mmmmm…mesophotic reefs…argleargle….a lot of the very best biologists are those that have mastered this challenging process and can come up with intelligent and efficient sampling schemes that provide maximum bang for the research buck and minimize down or wasted time.  The upside of this process is that as everyone thinks and talks, you start to see the days to come materializing before you, and a sense of very real excitement sets in.  Ahead lie mornings spent deploying the submersible, afternoons sorting samples of sediment, deep sea corals and sponges, and evenings spent measuring water column properties with a CTD/Rosette and ADCP (more on these later).  It’s enough to make any marine scientist practically drool with anticipation. 


Abrolhos, here we come!

Mussismilia braziliensis at the Abrolhos Reefs, BrazilThings have been a little quiet around here over the holiday break, but that’s about to change in a big way.  In just under a week’s time, I’ll be representing Georgia Aquarium in a new international consortium of scientists for an exciting expedition to explore the Abrolhos reef platform off the coast of Brazil from January 20-28.  The Abrolhos are completely unique reefs: they’re the largest and southernmost in the South Atlantic and biologically very different from perhaps more familiar Pacific or Caribbean Reefs.  You’d think they might show some similarity to Caribbean reefs, but not so, possibly because unfavourable currents and the influence of the Amazon pouring into the ocean between the two may serve as an important barrier to animal dispersal (more on that in future posts).  There’s tremendously high endemicity there, which is to say that many of the resident critters are found nowhere else in the world.  Of key importance is the main reef-forming coral Mussismilia braziliensis, a massive species that forms an unusual bommie-like reef structure called a mushroom reef; we’ll meet this species in more detail later too.

The main aim of the expedition is actually to go a bit deeper than the known parts of the Abrolhos, and look at the depths where light starts to get dim: the mesophotic zone.  These parts of many reef platforms are poorly known and nowhere moreso than at Abrolhos, where these areas are completely unexplored.  That’s because mesophotic reefs are beyond comfortable SCUBA diving range and therefore hard to get to.   To study them between 300 and 3,000ft in depth, we’ll be using the Johnson Sea Link, a submersible that operates from the R/V Seward Johnson, which is on a 5 year assignment from it’s home at Harbor Branch Oceanographic Insitute to CEPEMAR, a Brazilian environmental services company.

The Johnson Sea Link and R/V Seward Johnson

There’s much more to come in future blog posts here and in my tweet stream @para_sight or using the hashtag #Abrolhos2011.  We’ll discuss the Abrolhos reefs, mesophotic reefs, some geology and biology, as well as meeting the people and partners and exploring the logistic challenges of making a complex expedition like this happen.  So, I encourage you to follow along and also to share this information with colleagues and (especially) students of marine science so that they might also follow and share in the excitement of discovering new parts of the ocean floor, never seen before, in tropical Brazil.