Tuesday, March 24, 2015

Simple Pleasures at Sea

I am going to begin this story in a cupboard because that was how it began for me.  Now, so far as cupboards go, this one is fairly spacious, and also somewhat of an anomaly, though it is not without the charms that should be expected of any good cupboard.  It is still rather compact, and the ceiling hangs just a bit lower than you think it rightfully should.  Of course, it is also as fully stuffed as it could possibly be while still fulfilling its function.  What separates this cupboard from most, however, is the menagerie of exercise equipment contained within its walls.
It was during my exploratory sweep of our ship, on the transit to where our many groups of scientists would begin taking samples, when I first stumbled upon this room.  It was dark and cramped, and I passed it over at first, thinking it to be nothing more than a storage space for unused equipment.  Only later, once I had explored every inch of the ship and found no further signs of the alleged exercise room, did I begin to seriously contemplate its purpose.  I returned to it once more, and upon closer inspection, discovered that it was indeed intended as a gym.  In the tiny gap between the stationary bike and the treadmill, hung a pull-up bar, and littered around the edges of the room were weights of varying intensity.  The floor had been covered in a thick black foam padding, certainly contributing the feeling that this room was just a bit shorter than all the others, and the ceiling above the treadmill had been cut away in a dome to accommodate the taller heads on the ship.  I also discovered down in the hold, quite a bit later, an elliptical and a mountain climber, tucked neatly into a corner like two stowaways. I opted not to use this equipment, however, due to the poor lighting and lack of circulating air. 

Colin Seifer enjoying the stationary bike in the exercise cupboard. Notice the scenic poster of mountains on the wall (right).
Though the workout cupboard did not seem like much at the start of our voyage, I quickly warmed up to it, and it in turn, warmed up for me, necessitating the addition of a fan.  Soon after, I abandoned my use of descriptive words like “cramped” and “tight” in favor of kinder adjectives like “cozy” and “quaint,” for though it has no extra space, there is enough.  Now, it serves as a haven of sorts for scientists looking to take a break from the daily triumphs and failures that come with sending electronics and other sampling devices to more than four-thousand meters below sea level.  Some view it as a way to relax and unwind their tightly spooled thoughts, while others use it for the rush of chemicals that keeps them happy day after day.  Others still, such as myself, use it as an excuse to indulge in every incredible flavor that comes wafting from our kitchen three times daily.

The Versa-Climber Challenge Chart, where participants post their distances and times and track their progress up Mount Everest with magnetic sea-creature placeholders.
It is also worthy of mention, though I am not a participant in this myself, that many keep track of how far they have run or biked, and compete with others for the longest distance, fastest time, or just against themselves, trying to cover the ground, so to speak, between our port of departure in San Deigo, CA and the site where we took our samples.  Next to this signboard sits another, holding the times and distances for the mountain climber downstairs.  This, I am in awe of, as the records held on this board are such that no human made of flesh and blood should be able to accomplish.

The poster of the infamous AB02 Fittness Challenge

Though our expedition is now nearly complete, I intend to savor the time I have left to the best of my ability.  Back on land, many will surely return to more commercialized gyms, while some will resume outdoor running, and a few will give up exercise entirely, deciding that the couch is a much more comfortable place to spend the evening.  Still, I am certain that I will not be alone when I look back to the workout cupboard aboard the R/V Thompson and think fondly of the memories and time that it represents.

Written by: Colin Seifer, University of Hawaii

Saturday, March 14, 2015

Little Giants of the Deep

Have you ever heard about benthic foraminifera? If not, let’s introduce you to these amazing creatures.

Benthic foraminifera, affectionately known as ‘forams’, are unicellular organisms (protozoans) living in marine sediments. These little monsters – about 100–500 µm in size – build around their cell body a shell also called a 'test' that can be composed of calcareous or organic material, or agglutinated with particles found by the foram in its environment (mineral grains, sponge spicules, radiolarians, etc...). You can find benthic forams from salt marshes, coral reefs and other coastal environments down to abyssal and hadal depths (including Challenger Deep, deepest site ever sampled, 10,890 m depth), and under well-oxygenated to hypoxic (low oxygen) and even anoxic (no oxygen) conditions. The current diversity of benthic forams has been estimated at 3,000–5,000 living species, but at least 40,000 have existed on this earth (who knows, they are so tough that we might find them in Martian sediments!) since they appeared 525 million years ago (Cambrian).

So, if we had to choose one single word to describe them, it would be ‘tough’.

Now, if you skipped the previous paragraph because you are a geologist, and so the words ‘benthic forams’ sound familiar to you, sorry, but forget everything you know about them. Well, no, not everything. In the abyssal Clarion–Clipperton Fracture Zone, about 4100 m water depth, benthic forams are still very tough guys. But they definitely do not look like the common, classical, 'normal' forms that we can find in the fossil record and shallower environments. We still get few ‘traditional’ species – hormosiniids, miliolids, rotaliids, textulariids, trochamminiids – but these are a minority. Actually, in our study area, some of the most abundant forms belong to Komokiacea, a superfamily that typically dominates benthic foraminiferal faunas in the abyssal deep sea. However, most of the species we find in our samples are uncommon, mainly agglutinated or organic-walled morphotypes, often tubular in shape, and mostly (~80%) totally new to science.

Some specimens of foraminiferans sorted on board from ABYSSLINE 02 samples (scale bar: 500 µm).

Aurélie Goineau ‘fighting’ with Inga Mohrbeck to get the best sediment cores from a megacorer after its recovery from ~4100 m water depth.

Aurélie and Bin Qi Gan processing the cores recovered from the megacorer in a cold van (2°C) in order to preserve foraminiferal DNA for on-board live sorting. Over the past 4 weeks, we have sorted almost 900 specimens that will be analyzed for genetic sequencing at the University of Geneva (Switzerland).

Aurélie and Bin Qi starting to process another core from the megacorer. The core is sliced until 5 cm depth and fixed with formaldehyde for post-cruise analysis of foraminiferal faunal density, diversity, and taxonomical composition in our lab based in Southampton (UK).

We also get specimens of xenophyophores, a group of giant foraminiferans (up to 20 cm!) confined to the deep sea. They are fairly abundant in our area, and are often found on the surface of boxcores sitting on polymetallic nodules (like this Psammina, left-hand photo), a nice hard substrate on which to get settled. But we sometimes can be very lucky and recover a megacorer with xenophyophores proudly standing at the surface of a 10 cm-wide core (on the right-hand photo, a specimen of Galatheammina).

But, by the way, how do you describe your data when 80% of the things you get in samples are unknown? Well, you just need a bit of imagination. And this is how you end up with species names like ‘Rough sausage’, ‘Cushion with arms’, ‘Rugby ball of spicules’, ‘Whale-like tube’, ‘Reophax duck face’, or ‘Flipper the Reophax’ (inspiration tends to be more prolific late in the shift).

In the UK1 claim area, benthic forams are so abundant and can get so many different shapes that a sort of ‘private joke’ arose over the past few weeks on board the R/V Thompson. If we find something nobody really knows what it is, the general opinion is "Well, that's probably a foram".

The happy ABYSSLINE ‘Foram team’: Andrew J. Gooday (middle) and Aurélie Goineau (left side) from the National Oceanography Centre, Southampton (UK), and Alexandra Weber (right side) from the University of Geneva (Switzerland).

Written by: Aurélie Goineau, National Oceanography Centre, Southampton (UK).

Monday, March 9, 2015

You'll never believe who we ran into!


It was just past midnight on the 7th of March 2015, and there was a huge audience gathering to witness the deployment of the Autonomous Underwater Vehicle (AUV) (for the first time for most of us). The Woods Hole Oceanographic Institution (WHOI) team was ready to put this intelligent robot into the deep ocean to collect important information from the seafloor, then a bright white light and a blinking red light caught the eyes of the scientists.

They contacted the bridge and were told that there is a Chinese vessel “Fu Yuan Yu” (远渔) in the vicinity. The Chinese vessel did not respond to the bridge’s repeated hailing. So, we, the Singaporeans, were activated to communicate with the Chinese in Mandarin.

“Hello, Fu Yuan Yu. We are an American research vessel. We are of no harm. We would like to deploy our research equipment and just want to know if you have any fishing gears in the waters, so that we do not damage your and our equipment. Please reply. Thank you.”

There was no response, despite multiple attempts to reach them.

We did an internet search on “Fu Yuan Yu” and found that the Fujian-based company Pingtan Marine Enterprise Ltd. has a fleet of 129 vessels with the same name (www.ptmarine.com/fishing-operations/our-vessels).  “Fu Yuan Yu” can be literally translated as “Fujian long-distance fishermen”.

According to various sources, several of their vessels have been caught for illegal fishing by countries such as Argentina (en.mercopress.com/2013/07/24/argentina-

We were later informed that the name of the vessel is “Fu Yuan Yu 022”.

It is a longliner http://www.wcpfc.int/node/18193and appears to fish frequently in the North Pacific Ocean where we conduct our surveys.


After assessing the risk of the AUV getting caught in their fishing gears, we decided to abort the operation and amended our survey programme for the entire day. Luckily, we have enough buffer time to complete the tasks in time.

That is the fun of deep sea research. You never know what people (or animals) you are going to meet in the vast oceans! A little of excitement before we end our shift!

Written by: Chee Kong Chim National University of Singapore

Saturday, March 7, 2015

Wildlife Encounters

It's a bird, it's a plane, it's a Flying Fish! Flying fish can be seen skirting the water alongside the ship nearly every evening.

Helena Wiklund captured the graceful leap of this flying fish

Under the glow of the work lights from the back deck, we often see squid darting after the small flying fish in the black ocean below. Today, some squid mysteriously appeared on deck. We have jokingly deemed them "flying squid" because they certainly propelled themselves quite far from the water to reach the ship's deck. They must have really wanted to say "Hello!"

Boobies have effectively taken over the bow of the ship. Those are seabirds, for those of you with your minds in the gutter. 

Perched atop the foremast the squawking, pooping birds make a mess of the foredeck. Just as they begin to to annoy you, one takes flight and you are reminded of their majestic beauty as they soar around the ship.

One booby got up close and personal with Adrian's GoPro. He was so inquisitive!

What other visitors have we had, you ask... Whales!

A small minke whale came up to investigate the ship and Lena Albers managed to snap some excellent photos of the moment she shared with this amazing animal.

The whale visited us on two separate days, we believe that he may be attracted to the chirping of the pinger on our sampling gear as he came in quite close to investigate.

The usual suspects have been showing up in our box cores, and we've managed to collect some fairly large ophiuriods [brittle stars] and xenophyophores [forams]

Ophiuriod pictured on the top of a boxcore sample.

Xenophyophore collected from a boxcore by Andy Gooday's team.

Written by: Cassandra Turner, University of Hawaii at Manoa

Thursday, March 5, 2015

I have to wear What?

What's the number one rule on a ship? Safety First!

When at sea, the guidelines for keeping safe can be very different from those on land, and aren't always as intuitive as one might expect. Here are some tips and tricks about what to do and what NOT to do to stay safe at sea.

My first tip for you: The Three Rules of Ship-safe Style

Rule #1

Hard Hats Rule

Hailey Farah is keeping it safe and stylish!

On the ocean, safety is in style! A hard hat may not be your preferred fashion accessory, but on this boat they are a necessity. Stickers, markers, and other means of modifying a hard hat turn this piece of safety gear into a fashion statement.

Rule #2

Steel toed boots will be your new favorite shoes.

They're sturdy, they have good grip on the deck, and they keep your feet dry. When you spend your day maneuvering around heavy equipment on a swaying vessel or pouring muddy water through sieves on a windy deck, those qualities are really all you need in a shoe. 

Rule #3

If it can't get wet, don't bring it on deck!

From an accidental spray down with a rogue water hose to finding yourself elbow deep in hundreds of pounds of mud, it is guaranteed that if you're working on deck you will get wet {and likely very muddy}. Period. It is best to keep this in mind every single day when you get dressed.

Your clothes may get destroyed, but Science thanks you for your sacrifice. Expect to go home with far fewer items than you arrived with, and you won't be disappointed when you lose a few shirts to mud stains and holes that mysteriously appear.

The Dos and Don'ts of safety at sea:

DO wear a work vest [life jacket] if you will be anywhere near the edge, especially if the lifelines are down. Didn't bring your own life jacket? There is no shortage of work vests to borrow on the Life Jacket Wall.

DON'T be embarrassed, embrace the hard hat / life jacket / steel-toed boot combo. Everyone is doing it!

Bin Qi Gan sorts samples from the EBS on the back deck.

DO tie everything down. When the ship rolls, you don't want your things to roll off the table, or onto someone's foot. On this ship, you will find rolling chairs with the wheels removed and a colorful assortment of lines, bungees, and ratchet straps used to hold everything in place.

DON'T put your coffee mug on the Formaldehyde table! This should be self explanatory, but the table is so enticing for coffee mug holders, that we have had to write warning signs on it...twice.

Formaldehyde table for preserving samples on deck, foreboding messages courtesy of Craig and Cassie.

DO braid your hair. If you have long hair, it will blow in your face and get tangled in your hardhat. Bring your A-Game for hair braiding and you will save yourself lots of hair being ripped out by snagging on things.

Astrid Leitner sports gorgeous braids by Kirstin Meyer

Thank you for reading, I hope these tips will help you stay safe next time you find yourself braving the open sea in the name of Science!

Written By: Cassandra Turner, University of Hawaii at Manoa

What are we pumping from the deep sea?

The Plankton Pump is currently our most efficient means of collecting demersal [near-bottom] plankton from the deep sea. 

This includes both holoplankton (organisms that live as plankton their whole life) and meroplankton (organisms that live in the plankton only during one part of their life, such as larvae of benthic organisms).

Generally, the holoplankton is dominated by copepods (>50%), but other substantial groups include chaetognaths, ostracods, and polychaetes. Meroplankton, on the other hand, is very small and present at very low densities, which means that a very fine filter (mesh) size and a large sampling effort is needed to catch these organisms. However, the meroplanktonic component is of special interest because larvae of benthic organisms or other dispersal stages are very important for the supply and dispersal of benthic populations. Therefore, data about meroplankton is useful for estimating recovery abilities of benthic populations after a disturbance event, such as a mining operation. 

Oliver Kersten, the proud papa of the Plankton Pump free vehicle, flashes a look of satisfaction after a successful recovery.

After the acoustic release is contacted from the ship, the lander floats to the surface with the aide of 8 hard-hat glass floats.

When it is due to surface, everyone gathers on deck to watch for the flash of the strobe in the darkness.

After it is spotted, the captain maneuvers the ship alongside the lander, which is referred to as the "package" so that it can be snagged with a  grappling hook.

It is then walked around to the a-frame, where the winch is used to bring it back on board the ship.

 Recovery of the plankton pump free vehicle through the R/V Thompson's A-frame, made possible by the helpful hands of the ship's exceptional crew. They make even the trickiest of recoveries look effortless.

In order to sample the bentho-pelagic zooplankton community, a free-vehicle was outfitted with two plankton pumps that filter seawater 3 m above the abyssal plain (seafloor) for about 23 hours on each deployment.

Oliver really "dives in" to his work!
After recovery, the samples of each pump are split into two subsamples to allow for both a morphological analysis and DNA analysis. Based on the analysis type, these subsamples are then fixed and preserved in either formaldehyde or ethanol, and further analyzed (sorting, identifying organisms, DNA extraction etc.) back in the lab on land.

Written By: Oliver Kersten, Hawaii Pacific University

A few simple numbers: The tale of the respiration lander

The moonlight shone on the water in a bright streak, like a yellow brick road to the horizon. Various crew members chatted amongst themselves as they loitered on the deck. Just a few yards away, two scientists crouched beneath a ring of bright orange floats, making some last-minute adjustment that nobody dared to interrupt.

With one signal to the crew and a few frantic triple-checks, the lander was ready to go. The massive metal frame with her crown of floats was lifted over the side of the ship, released with a tug, and sent on her way to the deep.

The respiration lander is now in her fourth deployment of the cruise, and she is bringing back valuable data. The lander houses three benthic chambers – white plastic boxes that are pushed into the seafloor. By penetrating the sediment, the chambers effectively seal off an area of the seafloor, and we can measure the decrease in oxygen concentration over time in this isolated area. Oxygen concentration shows us the respiration rate, and the respiration rate shows us how active the organisms are.
Deep-sea sediments are filled with all sorts of organisms that cannot be seen with the naked eye. Prokaryotes, foraminiferans, nematodes, harpacticoids, polychaetes – the list of multisyllabic names goes on. Our job is to figure out how much carbon these animals consume and how much oxygen they respire, then compare our numbers to similar measurements from other areas of the ocean.

Andrew Sweetman, my adviser, has been developing his respiration lander for years. It’s been specifically designed to not only measure respiration but also run in situ experiments at the deep seafloor. Let’s say you want to figure out what path carbon takes as it gets worked through the benthic food web. Where does the energy go? Who eats whom? There’s a simple way to find out – well, as simple as engineering a 3-ton, quarter-million dollar lander and deploying it to the abyssal plain.
While the lander is sitting on the sediment and the optodes are measuring away, we artificially add some carbon to the benthic chambers. The added carbon is chemically labeled with heavy isotopes – carbon atoms that have 13 neutrons instead of 12 – so we can find it later and tell whose bodies it ends up in. You are what you eat, right?

Kirstin Meyer beams after a successful recovery of the respiration lander.

The lander is a complicated piece of equipment, and the data it collects are both rare and valuable. Standing on the edge of the deck, watching the lander sink away in the moonlight, we can only hope she will return to the surface again. Just a handful of samples and a few simple numbers allow us to push back the frontiers of science, one step at a time.

Written by: Kirstin Meyer, University of Oregon/International Research Institute of Stavanger