& when all is said and done… WHALE SHARK! – B. B. Cael

We’ll leave you all with a little video that we weren’t able to upload while at sea, of a majestic little friend that stopped by to say hello. Angel heroically had the prescience to tape a go-pro to a pole & dunk it in the water while most of the rest of us stood around oohing, ahhing, & drooling. Tom estimated 36 ft in length! While there are many joys of being at sea, this is undoubtably one of the more special ones for all of us. Safe sailing everyone!

 

Conducting research at sea: challenges, solutions and jury-rigging – Abigail Bockus

Even after months of preparation and meticulous planning, likelihood is a research cruise isn’t going to go exactly as planned. And sure enough, every scientist on the R/V Kilo Moana had their own stories of previous shipment delays, gear malfunctions, or (worst of all) the time that prized piece of equipment sank to the ocean floor. Whatever the situation, research at sea poses the unique challenge of being out of sight and out of reach of even the closest Home Depot.

This requires oceanographers to apply their creativity not only to their research but sometimes to their jury-rigging skills as well. This cruise was no exception. Albeit a far cry from the disaster of losing a multimillion dollar piece of equipment, on day seven of our ten-day research cruise the zooplankton team (ahem… my team) lost a piece of our MOCNESS net during an overnight tow. Specifically, one of our ten nets came up without its cod end – the end piece that collects the animals being trapped by the net. Whether this was due to user-error or just bad luck, we found ourselves missing an essential item for our science operation. Scavenging a mis-sized cod end from a smaller surface net, and some appropriately sized mesh lining, we retrofitted a solution using more duct tape than I’d like to admit. Thankfully, our makeshift net lasted through the end of the cruise and we were able to complete three more invaluable 6-hour tows.

After basking in the glory of our little MacGyver moment, I looked around the ship and noticed that the scientists and crew were finding innovative uses for all kinds of household items. One scientist had fashioned plastic sheets into a semi-enclosed “bubble” or clean space for work on trace metals, sensitive sampling that can be effected by the introduction of small particles of dust or other contaminants. Another had built her own water filtration system with some PVC pipes and impressive carpentry. Even the crew had put recyclables to good use, reusing an old water bottle as a protective sheath for an atmospheric CO2 intake port / meter. Not to mention the countless examples of tie downs, string ups and other temporary supports holding our scientific equipment in place against the rocking of the ship.

I guess the take away is – in oceanography, impressive ideas are sometimes supported by even more impressive means… just don’t forget the duct tape.

Thoughts from a first-time research cruise participant: it is, and is not, like a family vacation – Aspen Reese

Filtering water samples with a view. (Image credit: Abigail Bockus)

 

Once in my youth, I went on a family cruise near Baja; this was really my only frame of reference coming into the Chief Scientist Training cruise. My field work mostly keeps me on land moving about by car with the occasional plane or (once) helicopter thrown in. It turns out, though, in more ways than one might expect, that a research cruise is not so unsimilar to what I remember from that long-ago trip.

True, there are no water slides or towel origami animals on the Kilo Moana, and there is definitely no happy hour. There are however quite good buffets and, perhaps even better, stocks of late-night snack foods for in between trawls or instrument deployment.  There are bunk beds in each cabin with—an improvement that Carnival might consider integrating—great little curtains around each bunk to help you sleep during the day. Tucked in amongst the sleeping quarters are a conference room and a gym and a lounge for when you need to feel like a normal person for a bit. You can even do laundry. The boat is much smaller than a cruise ship, but still I got lost going everywhere the first few days. And, as is true on any boat, the best place to be is up on the deck watching the waves go by. Scientists get just as excited as tourists when a pod of whales appears.

There is a lot new though. So much vocabulary for instruments and techniques and spaces. Unlike on a tourist cruise, sometimes the crew fish off the stern while the boat is parked taking water samples. They take meals with us in the mess and help with engineering problems (and crossword puzzle clues) too. There are whole rooms of freezers and incubators and seemingly endless equipment for filtering seawater. We spend a lot more time in those rooms than in the lounge. We wear hard hats frequently; swim suits never.

We have to return to Hawaii on Monday for the next group of researchers to load up. Everything must be finished before then, so we cram it in at all hours of the night (hence the need for all those snacks). It is tiring, and we look a bit worse for the wear. We’ve gotten to know each other quite well for having only met a week ago though. There are long conversations about our upbringings and now many inside jokes mixed in with the science. At the end of the day everyone is really excited to be here, for all that it is not a vacation and would never be mistaken for one. We appreciate seeing the waves outside the portholes, but then look back down at the bench and get to work.

 

What a day!: Oceanographers working around the clock for the love of science – Paulina Pinedo

Left: McLane pump. Right: filter before and after pumping ~200 liters of seawater at 45 meters depth.

It is midnight. Sunday has just begun and I find myself, once more, very busy aboard a research cruise in the middle of the Pacific. The name of my home for the next ten days on the seas is the Kilo Moana. Whenever I tell my family and friends that I’m going on a research cruise, they picture me sitting by a pool on a sunny day sipping a tropical cocktail from a glass with a little umbrella. Not so on the Kilo-Moana! Real-life here is quite the opposite –  it means very long hours of intense physical and metal activity and abbreviated showers and meals.

About seventy percent of our beautiful watery world is covered by the oceans, yet much about them remains a mystery. We have tried for centuries to unravel the enigmas of the marine realm, but ocean exploration is difficult: The ocean is a challenging environment in which to operate. Research expeditions are expensive and funding is a constant struggle. Hence, we scientists need to make the most out of our time at sea. This expedition is not the exception and aboard the Kilo Moana we are taking advantage of the entirety of our days. Our research plans are very ambitious: collect samples for a large number of analyses and deploy more than 9 different instruments multiple times during our 10-day expedition. We need to accommodate the needs of the 21 scientists on board, so we are on a 24/7 working schedule.

Sunday is a typical example of our round-the clock, crazy-busy, work-days:  Our operations start at midnight with the zooplankton team deploying their nets (read Rebecca Asch’s post to learn more about the fascinating creatures they collect!). This requires 3 marine technicians and 3 scientists. Meanwhile, another team prepares a CTD (read Eric Orenstein’s post to learn about this and other pieces of equipment) –  it has to be in water by 2AM. All seems to be OK when, UH-OH, a problem with the CTD’s electronics is detected! Malfunctions of instruments at sea are frequent and we need to work under pressure to troubleshoot them without disturbing our tight schedule.  Finally, after a few very stressful minutes, the CTD is ready for its first cast of the day! An hour later, it emerges triumphantly from the water carrying water samples from different depths. A swarm of scientists rushes to deck to collect their samples. They only have 35 minutes to get their water and prepare the CTD for its second trip to the deep ocean. After the second CTD cast, the ship steams a few miles away from our sampling station to empty the grey water tanks. Since this activity takes between 1 to 1.5 hours from our precious research time, it’s a good opportunity for us to eat, take a short nap and organize our thoughts.

Back at our sampling stations, my colleagues work on four different pieces of equipment that are scheduled to be deployed back to back as the day’s operations continue.

In a research cruise there is always something that has to be done, but every once in a while we take a break to admire the beauty and vastness of the ocean –  a breathtaking sunset, or with a little luck, some playful marine animals like whales and dolphins.

It’s dinner time! But first, it’s time to deploy one of my favorite instruments, the McLane pumps. These pumps are submersible, so they allow researchers to filter large volumes of seawater in-situ. Essentially, they are like vacuum cleaners. The pumps are lowered to the ocean and spend several hours “vacuuming” the waters, collecting marine particles at specific depths. At the end of the deployment, scientists collect the biomass accumulated on the filters. Check out the picture of the McLane pumps and filters before and after deployment!

It is midnight again.  Operations are still going but it is time for me to go to bed. But first, a quick visit to the galley: I wonder if there are any donuts left…

Day in the life of a scientist at sea – Harriet Alexander

Hello, I am Harriet Alexander. I am one of the early career scientists participating in the training cruise. On this cruise, I am part of the higher trophic level group (HTL), which working to characterize the contribution of larger organisms (meaning larger than microbes, read: small fish and zooplankton) to carbon flux in the North Pacific Subtropical Gyre. In particular, I have been running a series of assays to assess how animals at depth might metabolically compensate for lower quality food (the dregs, if you will).

Here is a day in my life at sea:

Tuesday, June 18, 2019

0700 Wake up on the top bunk (childhood dream sleeping arrangement) of the state room that I share with another scientist and get ready for the day.

0715 Pop down to the CTD bay to see what is going on and check if the schedule has shifted at all. Cruise schedules are prone to change, what with equipment failure, or slow recoveries. This time, nothing has changed. Our big operation for the day, the MOCNESS, is still scheduled to be deployed at 0900. Hunt down my designated coffee mug and head to breakfast. 

0730 Breakfast! Huge selection of fruit, eggs made to order, bacon, lots of coffee. The food this cruise has exceeded my expectations. Hats off to the steward. 

0800 Back to the back deck to prep the MOCNESS (Multiple Opening Closing Nets Environmental Sampling System). The MOCNESS (or MOC for short) is basically a series of fine-meshed butterfly nets that collect and concentrate organisms at a particular depth. The MOC we are using is a series of 10 nets that are sequentially opened and closed as the MOC travels from the surface to 1000m and back, capturing and storing animals from a particular depth range. Getting it in the water requires quite a bit of careful preparation as once the MOC is in the water there is no fixing or changing it. Nets have to be cocked, cod ends (or buckets that catch the animals) securely attached, the associated computer turned on and checked, and the nets organized for deployment. Check lists are involved, and all six people from the higher trophic level group are required.

0900 The MOC is ready to be deployed! However, we are informed by the bridge that we are not in the ideal location to deploy it, and we need to steam North a bit more. A nice example of how the schedule is prone to change. HTL team crossword time! Almost finished our Sunday crossword puzzle.

0930 The bridge gives us the go ahead to deploy the MOC. The CTD gets carefully guided off the ship, each of the nets is tossed over in order to keep them from tangling, and off the MOC goes to sample the depths. It won’t be back on board for at least 6 hours.

1000 Back to Lab 1 which houses the operations console for the MOC. Here we can communicate with the bridge and the winch operators who dictate the speed of the MOCs vertical traverse and we will be able to watch its progress on computer read outs, tracking changes in depth, temperature, pressure.

1030 Quick team discussion. We have a second MOC deployment later tonight where we have different goals and we want to make sure that we agree about the speed of the net, and depths that we are targeting.

1100 Depths agreed upon, I head back to the lab to do a bit of data entry from an assay that I am running on board. It is good to have a lot of redundancy in data acquired at sea. Here, I am taking a scan of the original handwritten copy and manually transferring numbers into a spreadsheet to back up the data.

1115 Lunch time! Meals are a bit early and very regimented at sea. Meals occur at set times and if you want hot food—you eat at those times. Of course, not everyone is on a breakfast-lunch-dinner schedule—lots of people work night shifts. So, meal leftovers are abundant and kept in an easily accessible fridge. I am not starving, but head down for lunch (big salad and delicious pasta dish). Meals are a great time to catch up with other cruise participants who you might not see all the time otherwise. It is really staggering how even though we are on a small ship—you can still not see someone all day long.

1145 Back from lunch to do more data entry. Happy for my headphones and some good tunes.

1300 Naptime. One unique aspect of working at sea is how common it is for people to be napping or sleeping at random times. I know that we are going to have some late night / early morning operations going on later, so it is important that I try to catch a bit of sleep while the MOC is in the water and things are calm. Operations on a ship are 24-hours so scheduling sleep is very important.

1515 Alarm goes off. It is time to get ready for the MOC’s return. I head to the galley to grab some coffee and head back to Lab 1 to see where the MOC is.

1530 The MOC is getting near to the surface. I chug my coffee and prep for the MOC retrieval—turning on a machine I will need for running samples and making sure all of my sampling containers are labeled and I have printed off a log sheet.

1600 The MOC is back and we guide it on board. Once back on deck it is mad dash to carefully put each of the numbered cod ends into buckets and move the back to the lab. Again, this is quite the operation requiring all six of the HTL team members and lots of focus.

1630 Now the fun begins. Someone turns on the dance tunes and we are off beginning the slow process of carefully and quantitatively splitting each of the discrete samples caught in the cod ends to be processed differently to answer different questions: Who is there? How much do they weigh? How much carbon do they have? How hard are they working to live?

1730 Dinner time! Dinner waits for no wo(man) and happens on a fixed schedule. However, team HTL is arms deep in zooplankton and fish and not even half way done processing the MOC. So, we begin a tag team operation to make sure everyone is able to get some food to keep them going. I tag out with Aspen and go to grab a quick bite.

1800 Come back from dinner and processing is still in full swing. My main job is grinding up zooplankton to look for an enzyme that helps them acquire nutrients they need. Coming from a microbiology background, working with zooplankton is a new territory for me… I think I am still getting used to it.

1830 Still processing. Our group keeps up the energy with occasional dance breaks, speed chess competitions, and an endless stream of “would you rather…” questions. 

1950 We have finally finished processing the first MOC of the day and it is time to start my enzyme assay. Tom and I start pipetting furiously and watching the data roll in.

2100 Cleanup time. While the assay is running we tidy a bit and get ready for the next round of samples.. and get more coffee.

2230 Time for MOC #2. We now repeat what we did in the daylight—prepping the second MOC to go down. Nets need to be cocked, cod ends attached, etc. This is our fourth cast so we have a developed a pretty good system.

2300 Hurry up and wait (round 2). There were delays throughout the day—and everything has shifted back a bit. Again, we spend some time in the CTD bay waiting for the go ahead to deploy. 

2345 The second MOC is in the water and headed to 1000m. We will see this one back on deck in about 3 hours as we are trying to sample something that degrades very quickly…

0010 The second MOC is in but I am still processing the first MOC. Back to the assays I go, pipetting away.

0100 Finally done with the assays I check back in with the HTL team in Lab 1 to watch the progress of the MOC. All of us are crammed in there watching numbers slowly tick by on the screen. We have another rousing round of “would you rather” to keep us awake while the MOC follows her slow traverse. Example question, for you: Would you rather have teeth like a beaver that never stop growing, or teeth like a shark that are continuously replacing? I am team beaver.

0145 Someone breaks out a crossword to help pass the time while we watch the MOC. 

0200 We reach 1000m and it is time to head back up! Aspen communicates with the winch and bridge and we fire our first net. This net will cruise between 1000 and 700m gathering all the organisms that are too slow to swim away in it.

0315 The MOC is nearing the surface so it is time to head back to the lab to prepare for her landing. On this cast we are attempting to sample for RNA which can be contaminated easily. Every piece of equipment that will come in contact with a sample gets thoroughly cleaned and disinfected. 

0345 The MOC is back! There is organized chaos as we grab the MOC and bring it back on deck under the light of the moon. Samples are quickly placed on ice and moved back into the lab for processing.

0350 Someone turns on some dance tunes and we are off, splitting and size fractionating the MOC tow as quickly as we can. The organisms caught in our nets from 1000m (big red shrimp) are so different those caught in the surface (small copepods and jellies).

0430 One hour later and all the samples are processed and frozen. We can now start cleaning up and I can start in on my enzyme assays.

0500 Group selfie time! We made it through another MOC!

0530 Sunrise spotted through the porthole. It is shaping up to be another beautiful day.

0600 I keep sampling the enzyme assay. This type of assay requires many time points after the initial sampling to determine the rate of a particular reaction—meaning I need to be up for quite a while longer.

0645 Almost done with my enzyme assay—but still have probably another hour to go. I am starving after being up all night and wish that breakfast was 30 minutes earlier.

0715 Taking a break between time points for breakfast. I am starving and load up on French toast, scrambled eggs, bacon, fruit, and coffee. It all tastes amazing.

0730 Last time point! I write down the numbers, cleanup, and prep for the next APA assay.

0800 Back in my room, take a quick shower, and hop into my bunk. Time for some well-earned sleep.

Tools of the trade – Eric Orenstein

Clockwise from left: The zooplankton team deploying the MOCNESS (look closely to see the doors that open at different depths); a riot of plankton collected with the MOCNESS; an image of an arrow worm, or chaetognath, taken at Station ALOHA by the Scripps Plankton Camera; the author assembling the SPC aboard the Kilo Moana. 

Ocean scientists have all sorts of tools and toys they use to sample the ocean. There is a huge variety: from satellites to remotely operated vehicles to good ol’ fashioned binoculars. We have had the opportunity to play with an assortment of them on our cruise to Station ALOHA.

Broadly speaking, there are two ways of getting data from the ocean: bringing water into the lab or putting an instrument in the drink. Oceanographers spend a lot time thinking about which is most appropriate to get at their scientific question. We have had the chance to do a bit of both to accommodate the diverse interests of our science party.

We’ve already heard about a few ways to look at sediments and particles. The sediments traps, McLane pumps, and bottles are all great examples of pulling samples out of the ocean. The traps accumulate sinking particles over several days, the pumps filter living organisms, and the bottles capture whatever happens to be suspended in their volume. All three methods bring material back on board for further analysis on the vessel or in the lab.

The team that I am working with is looking at slightly larger objects: the zooplankton. These microorganisms are an important part of the marine ecosystem. At Station ALOHA, they are responsible for much of the carbon export from the surface to the deep ocean. Without them, life would not be possible much below the surface.

Observing these organisms is a challenge. They are sparsely distributed relative to their phytoplanktonic cousins and can move great distances over the course of a day. To study their behavior, we had to think about ways to look at them at different depths and times.

The humble net is the workhorse of zooplankton research. Different types of nets have been in continuous use since the early days of biological oceanography. Over the years, scientists have refined net-based sampling strategies, adding bells and whistles to better answer their questions. Since we are interested in observing the Diel Vertical Migration, we decided to use a Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS).

This specialized tool is much more than just a fine-mesh that is dragged through the water: it has multiple nets stacked on top of each other coupled with a suite of environmental sensors. As the MOCNESS is towed behind the Kilo Moana, an operator triggers it to open and close nets based on where it is in the water column. When the system comes back on deck, we end up with 9 discrete depth bins that give us a snap shot of the community structure.

To get a different perspective on the zooplankton assemblage, we have also been deploying the Scripps Plankton Camera (SPC) to look at plankton without pulling them out the water. The SPC is an imaging microscope that goes right in the water; essentially a light and a camera sealed inside a pressure housing. The system can go down to 500 meters to image the tiny denizens of the ocean. Besides taking pretty pictures, the SPC can spot fragile organisms that might get damaged in a net and resolve community differences at very fine depth intervals.

Together, the MOCNESS and the SPC let us ask interesting questions about how these microscopic creatures influence the larger environment and ecosystem. But they are just a few tools of the trade; the ocean is too dynamic a place to be observed with a just a few instruments and it takes lots of effort to come up effective methods. That to me is part of the fun of being an oceanographer. We get to spend our time thinking of new, creative ways to understand what is happening on two thirds of our planet!

Vision and bioluminescence – Tom Iwanicki

 

 

Figure 1: Zooplankton collected from Station ALOHA using a MOCNESS net. The community of zooplankton emit bioluminescence as they are disturbed in a tube. The likely emitters are various copepods from the genus Pleuromamma.

When you close your eyes and think of bioluminescence what do you see? People often see the twinkle of fireflies on a warm summer night, or the ethereal blue glow of bioluminescent bays. I see a glowing blue trail of dinoflagellates behind my dog as he chases a stick off the coast of Vancouver Island. Although these cases are striking, there is much more to bioluminescence than meets the (human) eye. Bioluminescence has evolved more than 40 times across living organisms and is found in creatures as different as bacteria, mushrooms, shrimp, fish, and squid. It is used to attack prey, defend from predators, and find a mate. Many tricks humans have devised through technology and cunning have been invented by evolution long before we arrived on the scene.

Researchers studying animal behaviour want to do so without distracting the animals with lights, sounds, smells. We can watch animals in the dark with cameras equipped with infrared light and sensors. This allows us to see natural behaviours without blinding or surprising the animals. We aren’t the only ones with night vision though, stomiid fish have a trick up their sleeve. Most animal eyes in the deep sea are sensitive to blue light only. Stomiids have the unique ability to detect red light and they also produce red light from bioluminescent patches under their eyes. As they swim through the deep, dark water they shine their red flashlight. This secret red channel, not visible to most other animals, can be used by stomiids like night vision goggles to search for and capture unsuspecting prey.

To be seen or not to be seen? Hunters wear patterns of green, brown, and black to hide from deer in the forest. The camouflage patterns or materials we have developed are quite sophisticated. It may seem counter intuitive, but rather than color or pattern, many ocean dwelling animals actually shine light to hide! The ocean gets dark as you dive deeper, but up to about 1000 meters deep there is still faint light filtered from the sun. In these conditions animals swimming through the water will cast a shadow visible to predators below. Some shrimp, fish, and squid have bioluminescent organs on their underside and, based on the light above them, will produce light just as bright to hide from predators below. From a hungry predator’s perspective, the camouflaging animal above doesn’t look like a meal but faint sunlight shining down.

Even the best camouflage in the world can’t keep you hidden forever. If by chance or by the ingenuity, unwelcomed guests can find even the most hidden hovels. People have developed a number of ways to alert ourselves to unwanted guests and call for help when needed. The burglar alarm does just that. Dinoflagellates, tiny unicellular protists, also use a burglar alarm system in response to unwanted attention. If a predator, say a small shrimp, comes nibbling, dinoflagellates will defensively emit light. When done en masse this creates enough light to draw the attention of large fish in the area. Dinoflagellates are not on the fish’s menu, and so the fish will come to the rescue and slurp up the unwanted shrimp now illuminated by the bright burglar alarm.

Defense mechanisms come with different costs. If you were eating a steak in the woods and found yourself face-to-face with a hungry wolf, your first instinct may be to throw the steak at the wolf allowing you to escape! You would go hungry and have wasted hard won pay on a gourmet dog treat, but you live to dine another day. Brittle stars go a grisly step further when confronted with a similar situation. When brittle stars are being attacked by a predator, a crab for instance, they forcibly remove one of their appendages. The removed arm begins to writhe and bioluminesce to draw the crab’s attention while the brittle star, perhaps a little distressed but still alive, quietly escapes.

There are countless more examples of different forms and functions of bioluminescence in nature. One of the reasons I am participating in the Chief Scientist Workshop is to learn how to lead a successful research cruise at sea. I am fascinated by vision and bioluminescence, how it is made, and how animals use it. In some areas of the ocean more than three quarters of all animals are capable of bioluminescence. It is a major ecological trait and I want to learn how light, bioluminescence, and vision structures where and what animals are doing in the Earth’s oceans.

Vision and bioluminescence – Tom Iwanicki

 

 

Figure 1: Zooplankton collected from Station ALOHA using a MOCNESS net. The community of zooplankton emit bioluminescence as they are disturbed in a tube. The likely emitters are various copepods from the genus Pleuromamma.

When you close your eyes and think of bioluminescence what do you see? People often see the twinkle of fireflies on a warm summer night, or the ethereal blue glow of bioluminescent bays. I see a glowing blue trail of dinoflagellates behind my dog as he chases a stick off the coast of Vancouver Island. Although these cases are striking, there is much more to bioluminescence than meets the (human) eye. Bioluminescence has evolved more than 40 times across living organisms and is found in creatures as different as bacteria, mushrooms, shrimp, fish, and squid. It is used to attack prey, defend from predators, and find a mate. Many tricks humans have devised through technology and cunning have been invented by evolution long before we arrived on the scene.

Researchers studying animal behaviour want to do so without distracting the animals with lights, sounds, smells. We can watch animals in the dark with cameras equipped with infrared light and sensors. This allows us to see natural behaviours without blinding or surprising the animals. We aren’t the only ones with night vision though, stomiid fish have a trick up their sleeve. Most animal eyes in the deep sea are sensitive to blue light only. Stomiids have the unique ability to detect red light and they also produce red light from bioluminescent patches under their eyes. As they swim through the deep, dark water they shine their red flashlight. This secret red channel, not visible to most other animals, can be used by stomiids like night vision goggles to search for and capture unsuspecting prey.

To be seen or not to be seen? Hunters wear patterns of green, brown, and black to hide from deer in the forest. The camouflage patterns or materials we have developed are quite sophisticated. It may seem counter intuitive, but rather than color or pattern, many ocean dwelling animals actually shine light to hide! The ocean gets dark as you dive deeper, but up to about 1000 meters deep there is still faint light filtered from the sun. In these conditions animals swimming through the water will cast a shadow visible to predators below. Some shrimp, fish, and squid have bioluminescent organs on their underside and, based on the light above them, will produce light just as bright to hide from predators below. From a hungry predator’s perspective, the camouflaging animal above doesn’t look like a meal but faint sunlight shining down.

Even the best camouflage in the world can’t keep you hidden forever. If by chance or by the ingenuity, unwelcomed guests can find even the most hidden hovels. People have developed a number of ways to alert ourselves to unwanted guests and call for help when needed. The burglar alarm does just that. Dinoflagellates, tiny unicellular protists, also use a burglar alarm system in response to unwanted attention. If a predator, say a small shrimp, comes nibbling, dinoflagellates will defensively emit light. When done en masse this creates enough light to draw the attention of large fish in the area. Dinoflagellates are not on the fish’s menu, and so the fish will come to the rescue and slurp up the unwanted shrimp now illuminated by the bright burglar alarm.

Defense mechanisms come with different costs. If you were eating a steak in the woods and found yourself face-to-face with a hungry wolf, your first instinct may be to throw the steak at the wolf allowing you to escape! You would go hungry and have wasted hard won pay on a gourmet dog treat, but you live to dine another day. Brittle stars go a grisly step further when confronted with a similar situation. When brittle stars are being attacked by a predator, a crab for instance, they forcibly remove one of their appendages. The removed arm begins to writhe and bioluminesce to draw the crab’s attention while the brittle star, perhaps a little distressed but still alive, quietly escapes.

There are countless more examples of different forms and functions of bioluminescence in nature. One of the reasons I am participating in the Chief Scientist Workshop is to learn how to lead a successful research cruise at sea. I am fascinated by vision and bioluminescence, how it is made, and how animals use it. In some areas of the ocean more than three quarters of all animals are capable of bioluminescence. It is a major ecological trait and I want to learn how light, bioluminescence, and vision structures where and what animals are doing in the Earth’s oceans.

Enigmatic organisms in the ocean – Wei Qin

Microbes are the most abundant form of life in the ocean, the largest biological system on Earth.  While they are generally too small to be seen by the unaided eye, there are 100 million times as many microbes in the oceans (13 × 1028) as there are stars in the known universe.  However, for every creature on earth, big or small, there is a time to be born and a time to die.  Death sustains new life in the ocean and microorganisms are essential for converting the products of decay into the nutrients of life.  They grow by assisting digestion in guts of marine animals, by consuming animal waste and decay, and by capturing the energy of the sun.  They too are eaten, and their small bodies and the nutrients released at death sustain all life in the sea.  A very important nutrient is ammonia, a form of nitrogen that is used to make protein and DNA essential to all life.  For over a century we did not know what marine microbes were responsible for converting ammonia to other bioavailable forms that can close the circle of life in the oceans.  We now know because of research conducted at the Seattle aquarium by investigators at the University of Washington.  These scientists isolated the responsible microbe from a tropical marine fish tank at the Seattle Aquarium in 2005.  Remarkably, this organism is only very distantly related to other forms of sea life.  It is a member of the Archaea, an evolutionary branch of life that diverged from animals, plants, and bacteria over three billion years ago.  This novel microbe was named Nitrosopumilus maritimus, a Latin name that translates to “the dwarf nitrifier of the sea”.  Nitrifiers oxidize the ammonia originating from decay into nitrate, a form of nitrogen sustaining most microbes and algae in the sea. 

Although very small (4 million could fit on the head of a pin), because marine ammonia-oxidizing archaea are among the most abundant organisms in the ocean, accounting for 20% of total marine microbes, they control the production of nitrate.  Their remarkable success is attributed to the ability to grow on only a whiff of ammonia, just one teaspoon of household ammonia added to an Olympic size swimming pool would keep them actively growing.  Besides their prominent role in nitrogen cycle, ammonia-oxidizing archaea also make a significant contribution to the marine carbon cycle through CO2 fixation, the production of the greenhouse gases nitrous oxide and methane, and the provision of vitamin B12 to primary producers like algae in oceanic systems.  Beyond the marine environments, members of ammonia-oxidizing archaea have also been found in a wide variety of habitats, including soil, freshwater, wastewater, and hot springs.  They are now considered as one of the most widely distributed organisms in Earth`s biosphere, reflecting their remarkable ecological adaptation.