Giant Microbe updates

North Pond 2017 video

posted Nov 13, 2017, 5:04 AM by Beth Orcutt

Our month long cruise distilled into five and half minutes of highlights, made by Annie Hartwell.

North Pond 2017

Diary of Microbe Hunter, episode 5

posted Nov 6, 2017, 3:23 PM by Beth Orcutt

By Rose Jones


As Atlantis travels towards land, the sea darkens from ultramarine to navy blue and birds begin to appear around the ship. In the labs, all equipment and microbe-filled samples are packed away ready for transport home. As with all such undertakings, the mess gets worse before it gets better. Suddenly, having your name on everything makes a lot of sense!


All of the things, ready for shipping home. Photo by Rose Jones.


There are also reports and lists to compile, check, and re-check. Special care is taken over precious samples so the microbes within get back safe and happy. They are the real VIP’s of the expedition, after all.


There is also some time for fun. Being on a small ship in the middle of the ocean with very little internet means making your own entertainment, but it isn’t dull. There’s the library, with books and comfy chairs. There are also lots of DVD’s to watch on the big TV screen and popcorn, so every night is film night. Some people came prepared with board and card games as well, with the all-important snacks left out by the super people in the galley.


Game night in the library. Photo by Kelli Freel.


The last day before making port is Halloween. Some people planned ahead and brought a costume, while others resourcefully make and borrow before the big day. Some even spent the whole cruise making theirs. The ship is decorated with spider webs, bloodstains and spooky decorations in the galley. Just for one day, a unicorn and the Flash work at laptops, while Jon Snow finishes packing, and a pair of sharks make last minute plans for arrival at port the next day.


Costume party on the bow. Photo by Ronnie Whims.


Then, after 30 days at sea, early dawn light finds Atlantis tying up at Barbados dock. Before long, all the crates and ROV Jason are offloaded and the ship feels quite empty. All the scientists, Jason crew and ship crew head on shore off for a celebration of a successful cruise. After all the hard work, we’ve earned it!

Offloading at the end of the cruise

posted Nov 3, 2017, 6:10 AM by Beth Orcutt

By Annie Hartwell


Happy November! We arrived in port in Barbados this morning. The work does not stop here though! First, we had to pack up, clean up, and offload. Then we head back to our labs for analysis and experimentation. 


The transit was four days long. During that time, we packed up all of the equipment and materials that we brought on board. Then we had to clean to the lab spaces and our state rooms for the next group of scientists to utilize the wonderful R/V Atlantis.


Lots of items were packed: the ROV Jason, the lab equipment, and the samples. Jason equipment (the robot, the crane, the winches, the viewing vans) are all packed into shipping containers. A handful of the scientists will also load the shipping containers with their items, all to be shipped back to the homeport in Woods Hole. The samples collected on the expedition are shipped directly back to the labs. Temperature sensitive material (the water samples that must stay frozen) are shipped with dry ice or super ice packs. The samples that do not have to be kept cold are often checked as baggage and fly home with the scientists who needs them.  Offloading of the shipping containers and pallets loaded with science equipment is done with a crane and the cooperation of many people working together. 


Back at the lab the samples will be processed. The fluid samples that my team were here to collect will be analyzed for geochemistry. These include the fluids collected from the CORK strings, from the ocean bottom, and from within the seafloor sediment. Just a few of the geochemical parameters we’ll look at are dissolved organic carbon, dissolved inorganic carbon, stable isotopes, organics, and metals.  The data will be crucial information for determining the answers to questions like: What are the microbes eating? What are they consuming? Are they producing extra cellular stuff? Do other organisms benefit from their output?


Thank you for reading my posts this cruise - I enjoyed having the opportunity to share science with you all! As the cruise wraps up, ask yourself: What kind of deep sea exploration is most interesting to you? What kinds of questions would you want to answer?

What happens to the samples after the cruise?

posted Nov 1, 2017, 5:29 AM by Beth Orcutt

By Kristin Yoshimura


During the cruise, we spent a lot of time collecting seawater from different depths in the ocean using the CTD Niskin Rosette. Some of the depths that we sampled: the surface ocean, the depth where a lot of photosynthesis occurs, the depth where there is very little oxygen, and deep in the ocean where there is no light. We filtered this water on board the ship to collect the microbes from these different depths. But what happens to these samples now that the cruise is over?


When I get back to my lab on shore, I will extract DNA from the microbes that I collected. DNA is the genetic material that codes for everything in the cell, from the structure of different parts of the cell to the cell’s function. This DNA will be sequenced to try to figure out what the microbes do in the environment by looking at their genes. Each microbe has a genetic fingerprint that helps us determine who they are, and the different genes can tell us what function they have in the environment, such as what types of carbon they eat or how they use different elements and nutrients like nitrogen or sulfur. When the DNA gets sequenced, it is transformed by a computer into short sequences like this: AGATCTCCGTCGATTAGC. We then use computer programs to stitch all of the pieces together, like a giant puzzle. Each complete picture represents the DNA from a different microbe, and there can be thousands and thousands of different microbes in a single sample.


Some of the questions that I am specifically trying to answer with the samples I collected are: Are the microbes that live inside of particles (floating pieces of dirt) different than those that do not? If so, do the microbes that live inside of particles have different genes than those that do not? And how do these change with depth in the ocean as light and oxygen concentrations change?


We know that microbes can be very sensitive to their environment and that each type of microbe has specific requirements that it needs to survive, so I expect that we will see distinct sets of microbes that live in the various depths and inside of particles. Different microbes will likely have different metabolisms, that is what they eat and what they produce in order to get energy to live, and therefore interact with the environment in different ways. We have studied the surface ocean extensively, but we still don’t have a good grasp on what happens in the deep ocean. These samples that we collected here will help us to have a better understanding of the identity and function of the microbes in the deep sea.

Diary of a microbe hunter, episode 4

posted Oct 29, 2017, 11:48 AM by Beth Orcutt

By Rose Jones


The last week on station starts with waiting and hoping as Jason combs the seafloor for the errant instrument string. Then, just after breakfast, the string is spotted on Jason’s long-range instruments!


Everyone crowds into the Jason control van to watch. Photo by Rose Jones.


The CORK instrument string is carefully tied to a new float, which rises to the surface without losing its precious cargo. It takes a few hours to travel to the surface from such a great depth. Excitement ripples through the crowd on deck when the float is spotted riding low in the water, as the weight of the CORK string pulls down on the float. A crowd of people collects on the bridge as spotters to make sure it isn’t lost from sight.


Can you spot the yellow float in the photo? Photo by Rose Jones.

There is more good news as the string comes on deck whole, with all samples attached. There are many days of careful sample processing in front of them, but the mineral and instrument scientists finish their part of the expedition happy.  


The water people haven’t been idle during this time, however. Another way to reach the seafloor involves the CTD. This device has a rosette of bottles that can be individually closed at a particular depth. The CTD is sent down again and again to collect water at different depths, for different microbe hunting activities.


Hurrying to collect water from the CTD on deck before its contents warm too much. Photo by Rose Jones.


Jason is sent down on a last mission to collect sediment and explore the seabed. Then, sadly, this microbe hunting trip comes to an end. All equipment is secured, and Atlantis turns her bow towards Barbados and the first dry land in a month.

Measuring heat flow below the seafloor

posted Oct 28, 2017, 9:08 AM by Beth Orcutt

By Tess Weathers


You know the feeling when you’re too excited to fall asleep? Maybe the night before your birthday, or before the first day of school? I had that feeling last night, because today is the day for my science!


You may have already read about the types of experiments going on here. Kelle has been part of the team collecting crustal fluids, Annie taught you about CORKs, Rose is growing microbes from rocks she retrieved. I have been patiently waiting for my chance: I’m going to measure heat flow!

Here I am with the heat flow probe before loading it onto ROV Jason. Photo by Jackie Goordial.


Why am I so excited? Measuring heat flow is a tool that we can use that will tell us what the sediment and underlying rocks are like, and how water and heat might be moving through them. If we know how water moves through these places, we can better understand how microbes are surviving.


How does it work? Jason uses a heat flow probe, which is a long metal rod. Inside the rod are thermistors, or temperature sensors, and a small heater. There are two parts of this tool that provide information:


1: Jason sticks the probe into the sediment while the thermistors record temperature. The probe will heat up a tiny bit because of the friction from pushing the probe into the sediment. It takes about eight to ten minutes for the temperatures to cool back down. This is how we measure the natural temperature in the sediment!


2: Once the temperatures are stable, I command the probe from the ROV Jason control van to fire a heat pulse. For 20 seconds, the probe heats up. The thermistors then record how fast it cools down. This can tell us the thermal conductivity of the sediment. Thermal conductivity is a measure of how easy it is for the sediment to transfer heat, as in, how fast it can cool down or heat up.


Here we are comparing the results of two probes tested at the same time. The Jason control van shows us three different images so we can see exactly how the probes were inserted.


By combining 1 and 2, we can start to predict how heat and water might be transferred through the sediment. For example, if it cools down quickly after the heat pulse, that might mean that cold water from the bottom of the ocean is flowing through the sediment.


This graph shows temperature over time. Each color is a different temperature sensor. Notice how quickly the temperature cools after the peak.


I was up all day yesterday taking these measurements during our final dive of this cruise! Hopefully we’ll be able to learn a little bit more about how water and heat move through the rocks below the ocean.


What's it like to be an ROV Jason pilot?

posted Oct 26, 2017, 3:21 PM by Beth Orcutt

By Kristin Yoshimura


Greetings, folks! Here is a picture I took of what it is like to sit in the ROV Jason control van and watch the pilots drive the ROV on the seafloor. I had the opportunity to sit down with Jimmy Varnum, one of the pilots, and ask him a few questions about what it is like to a pilot.


How did you become a Jason pilot?


“I began working for Benthos, a maker of underwater equipment in the 70’s. A year later, when they began designing an ROV, I said “I’m in. I want to get into this.” In 1982, I began piloting ROV’s. In 1993, Andy Bowen, a friend and former co-worker at Benthos who now works at Woods Hole Oceanographic Institution (WHOI), asked if I wanted to pilot ROV Jason on the Mid-Atlantic Ridge. I said yes, and I’ve been flying Jason ever since.”


Why did you get so interested in ROV’s and Jason?


“Benthos largely made single-purpose equipment like cameras and beacons. When they began building the RPV-430, it was great to finally work on the design of a system with many functions and parts. It was the challenge of creating a vehicle that would be so versatile and complex that really drew me in. I didn’t have much involvement in the original Jason other than piloting, but Bob Petitt and I designed many of the boards in the vehicle and I wrote the firmware for those boards. We learned a lot from Jason I, and built the current version to enable interdisciplinary science.”


What is involved in becoming a Jason pilot?


“There is no set program to becoming a Jason pilot. The most important thing is if you can be away at sea, live on a ship, and work with the same people over and over. If you can, then you get experience with the system over time. Later, if you express interest in becoming a pilot, you’ll get informal training and basic flying lessons. You learn basic manipulation, and then in time you’ll split a watch with a pilot. Eventually you should get your own watch.”


What kind of background is required to become a Jason pilot?


“Well, there are only a limited number of people at sea. Usually around 10, but there are more than 10 types of jobs that need to be done, so you have to be able to wear many hats. There are a lot of things you can learn on the job, but you have to be capable of learning how to do many different things. Being a good electrical or mechanical engineer or technician is a great start. You also have to have the desire to learn new skills. Lastly, we need more women in engineering!”


What is the coolest thing you’ve ever seen?


“I have two favorite dives, both of them at underwater volcanoes. Hydrothermal vents are cool, but underwater volcanoes are out of this world. At one, we watched the cone of volcano form, and at the other we watched the striations on pillow lava form. It was the coolest thing. There was another dive that was amazing; a molten sulfur pool with iron in it. It was jet black. The sulfur was much denser than the water so the two didn’t mix. There were sheets of sulfur ice and little flat fish that would sit on top of the ice. We dipped a bucket into the pool of the black bubbling, boiling sulfur and pulled it up to sample it, and the entire bucket immediately froze when we lifted it out of the pool. That was pretty neat.”


What would you say is the most rewarding thing about your job?


“Piloting never gets old. There’s a lot stuff that’s hard work about the job, but sitting in the chair and using the manipulators will never get old.”

The science of shrinking cups

posted Oct 26, 2017, 5:04 AM by Beth Orcutt

By Annie Hartwell

This figure shows a simplistic representation of the forces that enable the cup to maintain the shape. The magenta arrows represent the pressure from inside the cup pushing outwards on the cup walls. The blue arrows represent the pressure from outside the cup pushing inwards on the cup walls. The magenta arrows and the blue arrows are equal, but in opposite direction so the cup maintains its shape. You also see the size of seven cups exposed to different water depths, and the graph shows the corresponding volumes of the shrunken cups versus the exposure depth. Between 0 and 2000 meters, the volumes have big changes (the points are far apart), below 2000 meters the volume only changes a little (the points are closer together). 

Drawing on Styrofoam cups and sending them down to the bottom of the ocean to make shrunken Styrofoam cups is a lot of fun for ocean going scientists. For one, coloring is a great way to relax between all the science, and for two, the scientists get to make their own souvenirs that are unique from everybody else’s. 


Why do the cups shrink?


Before we get into the nitty gritty about why the cups shrink, let’s talk about Styrofoam. The key character of why Styrofoam cups shrink is air. Between all the white parts of Styrofoam, there are little pockets of air.  If you took all the air out of the white stuff, then the cup will get smaller.  This is precisely what is happening when the cups are brought down to the bottom of the ocean – the air is forced out causing the cup to shrink. 


How does all the air get removed from Styrofoam?


Styrofoam cups shrink when they are brought to the bottom of the seafloor because there is an enormous amount of pressure pushing on them from all sides. Remember what you have already learned about pressure at the bottom of the ocean, from the activity with stacking gallons of water? Both of these factors – that the pressure is high, and that the pressure is equal from all sides – are simultaneously important.


Pressure:  The pressure forces that are acting on the cup and forcing the air to leave is from the weight of the water.  As you descend deeper into the ocean, the weight of the water above becomes greater and greater, thus adding more pressure and forcing more air out. When a cup is placed in the bottom the ocean, the pressure from the weight of the water forces the air bubbles out, enabling the white part of the Styrofoam to contract (shrink). The deeper the cup is submerged, the more water weight it is subjected too, and the smaller it will get, until all the air is removed.

Pressure From all sides is important because it enables the cup to maintain its shape. If the pressure was only coming from above, the cup would get flattened. Same thing if the cup was pushed on either side, the cup will get squished. If all the pressure is coming from inside the cup, it would cause the sides to blow out. When a cup is submerged in the water, the cup fills with water, so there is a pressure acting from above, from the sides, from the bottom, and there is an equal amount of pressure pushing back from inside the cup. 


How small can the cup get? How deep does it need to go?


The Styrofoam cups will only shrink until all the air bubbles are removed, somewhere around 2000 meters. At that depth, there is enough pressure to force all the air bubbles out, so no matter how much additional pressure you add, the cup will not shrink any further because there is no more air to squeeze out.  In 2011 on the Research Vessel Endeavor, a scientist named Dr. Dave Ullman sent a series of cups down to different depths (150 meters, 300 meters, 800 meters, 1000 meters, 2500 meters, and 4000 meters), and he documented the volume of the un-shrunken cup at zero meters and compared it to the volume the cups shrunken at each depth.  He observed that the cups do the majority of the shrinking in the top 2000 meters of the water column and below 2000 meters the volume will decrease slightly, but much less than in the upper water column.



A little bonus about Density:


Remember what you learned last week about the density of different solutions (salt water versus freshwater versus rubbing alcohol)? Do you think that the density (mass per unit volume) of the Styrofoam cups changes when the size shrinks?


To explore this concept, let’s think about ping pong balls.  Imagine you have five ping pong balls that all together weigh 5 grams (this is the mass).


Scenario A: Now imagine the 5 ping pong balls are in milk crate that is 1 cubic foot (the volume).  If you wanted to know the density of ping pong balls in your milk crate, you calculate the value as the mass (5 grams) divided by the volume (1 cubic foot), so your density would be 5 grams/cubic foot.


Scenario B: Now imagine that you took the same five ping pong balls and put them in a milk crate that is bigger than the first one (2 cubic feet). The density of the ping pong balls in this second bigger milk crate is 5 grams/2 cubic feet = 2.5 grams/cubic feet.


Comparing scenarios A and B (5 grams per cubic foot vs. 2.5 grams per cubic feet) you see that the density of the ping pong balls in the smaller milk crate is larger than the density in the bigger milk crate. Both crates have the same about of mass (5 grams) but because the volumes of the crates differ, the densities do, too. 


In the case of the Styrofoam, a normal size cup has a certain mass of white stuff in the volume of the cup. If the air between the white is removed, the white stuff condenses and the volume of the cup decreases – but not the mass. When the air is removed from between the Styrofoam, there is essentially NO change in mass (no white stuff is lost). However, the volume of the cup does get smaller, so the density of the cup will increase. The shrunken cup will have a smaller volume than an un-shrunken cup, but they will both weigh the same.

Diary of a microbe hunter, part 3

posted Oct 22, 2017, 4:07 AM by Beth Orcutt

By Rose Jones


The deep subsurface water is all collected, and the water scientists start the week tired but happy. For those who are interested in instruments and mineral samples within the CORKs, the hard work is only just beginning. These experiments have been sitting beneath the seafloor for six years, hopefully providing a nice home for microbes (like the ones in the Adoption Center) to settle on. Once brought to the surface, these microbes can be coaxed off the minerals in a variety of experiments.


This stage of the expedition involves sending Jason down to take the stopper out of each CORK, then fish for the hook at the top of the instrument string. It’s rather like hooking a toy for a prize at a fair sideshow, but in total darkness using only a small flashlight. It’s a tricky thing to pull off, and there’s no way to know how much of the string has come up until it appears on deck.


The long instrument string comes up from the deep. Photo by Rose Jones.

The first string should be the longest, but only part of it appears on deck due to corrosion of some of the pieces. There is disappointment that only part was recovered, but relief that anything came up at all. These strings have been sitting in salt water beneath the bottom of the sea for six years, after all. Even though dawn is just breaking and some people have been up all night, processing the strings begins at once. Samples have to be in the fridge as soon as possible as the warmth on deck will cause changes in the strings, which up until now have been sitting in cold water. There is a frantic rush to get all samples processed before the next string is pulled up.


Cutting up yards of strings to get at the water and rock samples stored within. Photo by Rose Jones.


The weather turns unsuitable for a few days, forcing an anxious wait but supplying time to finish processing samples. Then, Jason dives once more. Again, the string comes up with the dawn, but again there has been trouble with corrosion and not all of the samples are recovered, yet the microbiologists get busy processing the samples that are recovered. Hope is pinned to the last instrument string to be un-CORKed. This time, the plan is to float the string up rather than have Jason pull it up underneath. Instrument string people gather on deck to spot the big yellow floats, which should be carrying a long tail of the instrument string. But when the float comes on deck, there is no sign of the string! The float rope parted somewhere between the seafloor and the ship due to abbrasion.


A reward poster for the lost CORK instrument string. Photo by Rose Jones.


Yet all is not lost, as the lost string should make for a good sonar target on the seafloor. Entering the final few days on station, the plan is to have Jason hunt for the lost string and finish up remaining tasks. Hope and optimism prevail.

Getting the job done, part 1

posted Oct 21, 2017, 4:10 PM by Beth Orcutt

By Tess Weathers


As you learned from Annie’s post about teamwork, there are a lot of people on the ship that need to work together to get everything done. I put on my journalist hat, and have interviewed some fellow seafarers about their jobs aboard Atlantis.


Scientist: Jackie

Jackie is organizing sample tubes that will be used for storing microorganisms! Photo by Tess Weathers.

Jackie is a microbiologist who is using water and rocks from the ocean’s crust to grow microbes like the ones in the Adoption Center. When she’s on the ship, her day varies depending on what’s happening! If Jason is in the water, every scientist has a four-hour watch every day (or night!) where they take notes on what Jason is doing and take photos or videos of the cool things the cameras capture. Some days, Jackie has free time when she can sit in the sun, play games, or watch movies. Other days, like when Jason brings crustal water to the surface, Jackie works non-stop to make sure the water stays sterile and as close to the original conditions as possible. This means Jackie has to be very careful about wearing gloves, making sure her workspace is clean, and keeping things cold so the microbes can be preserved before she starts doing her experiments.


This is Jackie’s first time on a research cruise! Before this, she was studying how microorganisms live in deserts with very little water. Even though this might seem like the opposite of what she’s doing now, she can apply many of the same skills and techniques. The hardest part of Jackie’s job is focusing on the big picture while she’s doing some of the small, repetitive tasks that you wouldn’t normally think scientists have to do: entering data into spreadsheets, or measuring, cutting, and draining “coils” full of samples. Even though that’s the hardest part of her job, doing those things is also the easiest! Her favorite part is when she has all of her information to make conclusions about how the world works; when she knows she was able to contribute even a tiny piece of knowledge to what humans know about our planet.

Jackie thinks that anyone who is making observations about the world around them and asking questions is already a scientist. If you stay curious, you could become a scientist too!


Jason Pilot: Akel

Akel is in the Jason control van. He uses a joystick shaped like Jason’s arm in order to control the manipulator while it is on the seafloor. Photo by Tess Westhers.


Akel is a Jason pilot, technician, and the lead navigator. This means he actually gets to drive Jason, which is his favorite part of the job! He can move Jason around the bottom of the ocean, land it on the sediments, use the manipulators, and take samples. He has two four-hour watches a day, when he drives Jason, makes sure everything is working properly by using computers that are remotely connected to the ROV, and helps get all of the scientific objectives complete. When he’s not on watch, he helps fix things that are broken, and if he has time off he likes to exercise and read.

Akel has been a pilot since this version of Jason’s first science trip. He likes that he gets to travel to a lot of new and beautiful destinations, even though the hardest part is missing his family while he’s at sea. The easiest part of the job is “Z-watch” or when Jason is heading to the bottom of the ocean or back up. On this cruise, Jason has to travel 4400 m from the ocean surface to the bottom sediments, which takes almost three hours! Because this part is automated, Akel’s job is to watch the remote computers and make sure everything is working correctly. Akel says if you want to become a Jason pilot, you should study electrical engineering! That might seem surprising, but it’s very important to be able to design and repair the electrical systems that communicate with the submarine.



Chief Mate: Jen


Jen is on the bridge. The bridge is the name for the top level of the ship that has all of the navigation and communication tools needed to drive R/V Atlantis. Photo by Tess Weathers.


Jen is the Chief Mate, which means she’s the second in command on the ship! She has a lot of responsibilities: she is in charge of driving the boat, she is the safety officer (which means making sure we all had safety training, she assesses safety conditions on board, and is also the medic), and she makes sure the crew and the scientists have all the tools they need. Jen’s schedule is different from the scientists’, she has two four-hour watches each day when she’s in charge of ship navigation. When she’s on the ship, she’ll sometimes work overtime if there is something big happening, like when Jason brings back a big set of samples.


Jen went to college to study biology; she didn’t even know that being a chief mate was a job! She ended up working as an Able-Bodied Seaman (or AS, we’ll interview an AS next time!), and has climbed the ladder to her job now. The hardest part of her job is making sure everyone stays happy and things keep running smoothly even in bad weather, with long travel times at sea without any Jason dives to keep things interesting, and when everyone is tired. Her favorite part is when she’s able to work with a deck team to bring in ocean samples safely and smoothly, without any mistakes on the first try. To be successful in this kind of job, Jen says you shouldn’t be afraid to look stupid or ask questions. That’s how you learn, and everybody else on the ship had to learn it too!


Do you know someone on land who has a similar job? How might their job on land be different while at sea? Would you like to do any of these jobs?

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