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.

Petri dish full of mesopelagic fishes caught in the MOCNESS.  Organisms marked with yellow stars are Cyclothone; fish marked with red stars are myctophids, and; the fish marked with green stars is a rather beat up hatchetfish.  Note that not all Cyclothone, myctophids, and hatchetfishes shown in this picture are marked.

Those of you who are regular readers of this blog will know that one of the key foci of this research cruise is to develop a greater understanding of how the biological pump functions.  The biological pump refers to a set of processes in which atmospheric CO2 enters the ocean and is taken up by phytoplankton during photosynthesis and then converted to organic matter.  If this organic matter is transported to depth quick enough, it will be “sequestered” there, meaning that it will stay at depth and won’t return to the surface ocean where the organic carbon can be remineralized and converted back into CO2, which can in turn contribute to global warming. 

It is hypothesized that certain fishes may contribute to the biological pump.  More specifically, the fishes that may affect this process are mesopelagic fishes that generally live at depths between 200-1,000 m.  Many of these fishes participate in diel vertical migration (DVM), in which they hang out at deeper depths during daylight hours but then travel to surface waters at night to feed on organisms found there.  By eating at the surface, but respiring and pooping at depth, these fishes may serve as a vector for carrying organic carbon to deeper into the water column. 

During this cruise, I’m conducting research to explore this hypothesis.  We are collecting mesopelagic fishes at both and night with a MOCNESS net.  MOCNESS stands for Multiple Opening/Closing Net and Environmental Sensing System.  The MOCNESS can collect zooplankton and fishes from 10 discrete depths during a single deployment, allowing us to better understand the depth range inhabited by particular organisms.  After the cruise, I plan to identify the fishes collected to species, dissect them removing their stomachs, and then measure the total organic carbon in their gut contents.  By doing this, we will be able to see how much of the food eaten by these fishes at the surface makes its way down to depth.  This will provide us with some initial information about these fish’s potential contribution to the biological pump.

Some of the mesopelagic fishes that we are sampling have a fairly cosmopolitan distribution and are found across wide swathes of the Pacific Ocean.  However, one notable pattern that we see at Station ALOHA is that the mesopelagic fishes found here are tinier than those in many other regions.  This is noteworthy because most mesopelagic fishes are not very big to begin with.  Typically, sizes are 2-10 cm, whereas on this cruise we are capturing fish at the smallest end of this range.  This reflects the fact that the area around Station ALOHA has relatively little nutrients.  When nutrients are scarce, smaller sized phytoplankton tend to be more competitive.  These small phytoplankton are eaten by small grazers, which are in turn consumed by small fishes.  As a result, the whole ecosystem is miniaturized.

Below are some “fun facts” about common fishes found in the mesopelagic realm of the ocean:

Cyclothone spp. These fishes, whose common name is the bristlemouths, are the most abundant type of vertebrate on planet Earth.  They have an elongate body and a large mouth relative to their body size.  Having large mouths is fairly common mesopelagic and deep-sea fishes.  This is because such fishes live in environments with relatively little food.  By having a large mouth, these fishes can capture food of a variety of sizes, allowing them to eat whatever sized meal they encounter. 

Another characteristic of Cyclothone that is shared among other mesopelagic fishes is that their body is covered with photophores.  Photopores are light producing cells.  Photophores can help fishes camouflage with their environment by mimicking downwelling light from the sun.  This is why Cyclothone and many other mesopelagic fishes have their photophores concentrated on their belly.  That way they won’t be easily seen by predators looking up at them from below.  Among some mesopelagic organisms, photophores can also be used to detect and capture prey and may be involved in attracting mates. 

Talking about mating, an interesting aspect of the life cycle of some fishes in the genus Cyclothone is that they are protandrous hermaphrodites.  That is a technical way of saying that these fishes start off life as males but, as they grow, they will switch sexes and become females.  This life history characteristic is common among many fishes, including clownfishes, which are the fish that Finding Nemo is modeled off of.

Myctophids. Myctophids are the second most common group of fishes that we have been sampling during this research cruise.  Their common name is the lanternfish, because, like Cyclothone, myctophids also have photophores that can produce bioluminescent light.  Myctophids are an incredibly diverse family of fishes, with ~250 species found worldwide.  Most myctophid species engage in DVM.  As a result, they possess a variety of adaptations to help them migrate between the mesopelagic ocean and the surface.  These adaptations include having a more muscular body than many other deep-sea fishes.  Their swim bladder is filled with fat to increase their buoyancy and reduce the energetic cost of migrating to the surface.  Lastly, they have adapted to tolerate the broad range of temperatures that they encounter along their migration route.  Although myctophids do not grow to be very big in size, there are fisheries that catch them in some parts of the world.

Hatchetfishes. We have caught a few hatchetfishes during this cruise, but they only seem to be captured in a few depths fished by the MOCNESS net.  This may reflect the fact that most hatchet fishes do not engage in DVM, so they may be more limited to inhabit a narrower range of depths.  Hatchetfishes have a particularly distinct body shape.  Their body is compressed side-to-side, but their body is rather deep when looked at dorsoventrally.  Their sides tend to be silvery and covered with photophores.  Their silvery color helps them blend in with their environment, making them harder for predators to detect.  Most hatchetfishes have a short gut, which is indicative of a carnivorous diet.  They are also characterized by upward pointing eyes and an upward pointing mouth, which allow them to better hunt organisms found above them in the water column.  Some fishes in the hatchetfish family have two sets of retina and lens in each eye, allowing to both look upward and sideways without moving their head. 

So far we have only deployed the MOCNESS net during the day.  We have a bunch of nighttime deployments coming up, so we will likely see new things in the coming days.  Stay tuned!

Me with the MOCNESS net in all of its glory.

How many Tums are in the ocean? – Adam Subhas


A planktic foraminifera, species G. ruber.  This foraminifera is about 0.3 mm across, with spines that extend another 1 mm or so.  Both the shell and the spines are made of calcite, a form of calcium carbonate.  Foraminifera are animals, and must hunt their food.  Here it has caught a shrimp in its spines — a tasty lunch!  Image credit: A. Subhas and S. Oron

Heartburn, or acid reflux, has a common and simple remedy: take antacid tablets, which dissolve in your stomach and neutralize excess acid.  You may be asking yourself: what does this have to do with the ocean?  In fact, the ocean as a system uses antacids in exactly the same way.

Many marine organisms grow calcium carbonate shells, the active ingredient in TUMS.  These shells make up the basis of limestone rocks, and are abundant all over the world, and on the ocean floor.  The white cliffs of dover are made up of the “liths” of tiny algae known as coccolithophores; the pyramids of Giza were built with rocks chock-full of calcifying organisms known as foraminifera.

These rocks all got their start with microorganisms growing in the surface of the ocean, those organisms dying, and their shells settling to the ocean floor. As the world oceans become more acidic due to fossil fuel burning, these shells — the TUMS of the ocean — will dissolve back into seawater to neutralize the excess acid. I study this cycle of calcium carbonate formation and dissolution in the ocean, and how it regulates the ability of the ocean to take up and release CO2.

One fun fact: The ocean holds 60 times more carbon in it than the atmosphere does.  This is because of the large buffering capacity of seawater, which is regulated by the formation and dissolution of calcium carbonate shells in the ocean.  The amount of buffering capacity, or alkalinity, in the ocean, is equivalent to about 200 billion billion dissolved TUMS tablets — yes, that’s right, two times ten to the power of 20 TUMS tablets.  And yet — even with all of that buffering capacity, we are still changing ocean pH by burning fossil fuels.

On this cruise, I am collaborating with my colleague, B.B. Cael, to test how adding alkalinity will affect organisms growing in the open ocean.  Depending on what we find, we will better understand how alkalinity affects the growth of marine organisms and their shells.  With enough research and experimentation, we may be able to add more alkalinity to the ocean to help counteract global warming and ocean acidification.

I am also studying the role the enzyme Carbonic Anhydrase plays in the formation and dissolution of organisms’ shells. This enzyme drastically speeds up reactions crucial for both calcification and calcium carbonate dissolution.  For instance, pteropods grow calcium carbonate shells, but also produce a lot of carbonic anhydrase.  Pteropod shells are abundant in the surface ocean, but dissolve very quickly once the organisms die.  It is possible that carbonic anhydrase is catalyzing this dissolution reaction, and I hope to measure enzyme activity to link its presence to this dissolution reaction.


Volume of the oceans: 1.332 billion cubic km = 1.332e21 cubic dm, dens is 1.025 kg/dm3, alk = 0.0022 eq/kg, mass of caco3 in tums is 0.75g, or 0.015 eq alk per tablet, so we get 2.0e20 tums tablets in the ocean

How this training cruise is impacting early career scientists and the future of oceanographic field research – Matthew Rau


A research cruise is quite an operation. Speaking as someone who is fairly new to oceanographic field research, it is amazing how much planning, coordination, logistics, and manhours were necessary to fill the Kilo Moana with scientists and equipment to get us all out to sea for a ten days of research. Training to carry out this sort of planning is not something you typically get early in your career (if ever). As scientists, even early-career scientists, we’ve all become pretty skillful at asking relevant and important scientific questions. How we answer those questions is a whole different story. The ocean is big, dynamic, and complicated. Many of the most important questions we have about our oceans’ function and health cannot be studied remotely. The answer? Conduct field research on a cruise. The only problem is that proposing, planning, and implementing a research cruise is far from simple.

In general, research takes a lot of planning. Ideally, your preparation will help ensure that your efforts test your scientific hypotheses and yield valuable new scientific knowledge. I typically work in a lab. Planning experiments takes a lot of work and consideration. Planning a research cruise takes this to a whole new level. Not only must you plan your own sampling and measurements, but you also must decide what kind of ship best suits your science needs, when and where to go to answer your hypotheses, coordinate the science plans of the other scientists, and logistically determine how everything will be safely managed on board. And we haven’t even considered the ship yet. Who will crew your vessel while you conduct your research? What kind of cables, winches, cranes, and other ship-board equipment will you need? What is the safest way to deploy that new instrument you just acquired? Luckily, the University-National Oceanographic Laboratory System (UNOLS) is there to handle the bulk of the actual ship management, but training young scientists on how best to manage these resources is still important to ensure their effective use in future oceanographic research.

This training cruise is meant to do just that. Myself and the other participants are getting a behind-the-scenes look at what goes into cruise planning and management so that we can lead future research at sea. This cruise has already been an invaluable experience and it is hard to imagine taking on the role of a chief scientist aboard a research vessel without this exposure. As oceanographers and marine scientists, we are incredibly lucky to have these scientific facilities available to our research and experiences like this will help ensure we know how to use them!

The most important aspects of cruise planning – Katherine Heal


It’s easy to get caught up in the pace of sea going operations and not recognize all of the work it takes to plan and prepare for a cruise. Of course there is the proposal writing and requesting ship time through UNOLS. Then there is the ordering of equipment, the shipping, the permits, and a myriad of other logistical steps necessary to make an operation like this happen. After deploying a free floating array at 4 am this morning (pictured), Tara Clemente and Matt Church shared their thoughts with me on important aspects to cruise planning. Combined, Tara and Matt have served as chief scientists on somewhere in the order of 40 cruises, so I figured their insight into the matter was worth sharing. They landed on two main pieces of advice, communication and managing resources. Communication-wise, both agreed that having clear overarching goals for the cruise while balancing individual objectives were key for setting the stage for making making the most of our time at sea. They advocated for having clear lines of communication to the captain as well as the land- and sea-based marine technicians and starting those conversations early. The second aspect of managing resources is more obvious to me – as a team of scientists moving aboard a ship, we have to think carefully about the dance to get the right equipment, deck space, wires, and time to make this all come together. This involves being aware of each piece of equipment, having a clear vision of where and how it will be deployed, and recognizing the time each effort will take. Sitting in the staging bay after a full night of successful operations (ahead of schedule!), I can easily say that being prepared pays off.

The beating heart of the ocean – Nick Hawco

Caption: Left) A surface ocean phytoplankton, Trichodesmium. Right) The remains of surface ocean phytoplankton: a particle sinking to the deep ocean. Taken by the Scripps Plankton Recorder. Photo credit: Jaffe Lab, Eric Orenstein

The heart wants what it wants, but what it wants most is to pump. The thump thump squeeze of atria and ventricles pass blood fresh with oxygen into arteries, organs, cells.

Out here, in the heart of the sea, the ocean wants to pump too. This one, though, is a bit harder to see or hear. I’ll explain: the ocean creates a habitat for microscopic phytoplankton at the sea surface, where a miraculous reaction takes place: sunlight and air transforms into stuff. Specifically, phytoplankton capture light energy to transform carbon dioxide gas (a.k.a. CO2) into organic carbon (the di-oxide part from carbon dioxide is released as di-oxygen gas – what we breathe in, what flows through our blood, our bodies).

But there’s a catch. Unlike carbon dioxide gas and light, the organic carbon that makes up phytoplankton biomass feels the tug of gravity. It starts to sink. Phytoplankton may sink slowly at first, but their descent quickens as they are grazed, digested, compacted, and (ahem) expelled back out. In this new state, biomass sinks out of the sunlit ocean and down into the abyss.

Still, the ocean is very deep and it might take several months for biomass to sink from the ocean’s surface to the seafloor. Many such particles will never get there. Like leftovers spoiling in a refrigerator, someone’s trash is another’s treasure. The deep ocean is the world’s largest food desert, and so when something digestible passes by – no matter how gross – its thanksgiving to the microbes living there. Like us, these microbes eat organic carbon, breathe in oxygen, and burp out carbon dioxide (which dissolves in deep ocean seawater).

So the ocean’s heart – its carbon pump – moves carbon dioxide from the surface ocean into the deep sea. This deficit of carbon dioxide gas at the sea surface allows CO2 from the atmosphere to dissolve into surface waters, where it too can get pumped down into the abyss.

We’re all hoping that the ocean’s carbon pump is resilient to global warming and climate change – in fact we’re relying on it to take much of the atmospheric CO2 that we humans have released and sequester it in the deep sea. But there’s still reason to be vigilant. There’s evidence from the past that the carbon pump can change, and that these changes have global consequences. In fact, an unusually strong carbon pump tens of thousands of years ago led to an ice age, storing more carbon dioxide in the deep ocean, with less in the atmosphere. The opposite of modern climate change where high CO2 leads to global warming, lower amounts of CO2 in the atmosphere of the past cooled the planet, helping to build massive glaciers worldwide.

Although a number of phytoplankton species can grow at freezing temperatures, if the ocean gets too warm, many won’t survive. A major worry about modern global warming is that overheated phytoplankton might make the carbon pump less efficient, and that this will slow CO2 removal from the atmosphere. Warmer oceans might also inspire bacteria to degrade organic matter more quickly – similar to food left out in the open will go bad fast compared to food in the fridge – and so fewer particles may sink to the deep ocean.

What we’re doing out here, in essence, is a check-up. Scientists have been coming to this location – Station ALOHA – for the last 40 years, tracking how many phytoplankton are growing in the surface, and how much is sinking to the deep. We’re here to pitch in: continuing this vital record of ocean health will allow changes in the biological pump to be diagnosed early on. The moving parts of the ocean’s carbon pump may be too small to see, but its too important to ignore.


When you’re working at sea, safety is key – Erin Black

Andddd go! The first mate throws a flagged buoy off the back of the ship. It hits the water with a crash and begins to bob in the waves. “Man overboard!” someone shouts. Right away, two scientists point, full-armed, at the buoy. It’s their job to be the spotters. No matter where the buoy goes, they point. The captain is notified to slow the research vessel so that a rescue boat can be launched to pick up the ‘man overboard’. By the time the rescue boat makes it to the buoy, it’s been 10 minutes and the buoy is barely visible as the waves move up and down between the vessel and the buoy. The buoy is recovered and the new ship-goers have learned a valuable lesson. This is the best-case scenario that could happen if, perhaps, you reached too far out to grab some research equipment or walked too close to an unsecured opening and toppled overboard. The sun is shining. Two spotters are watching you. The entire crew is mobilized to come pick you up while you tread water. The take homes from this drill: safety first, always have one hand for the ship, and tell someone where you are. If you take risks, fall off the back deck at nighttime, and you didn’t tell your bunk mate that you were quickly checking on some scientific samples…you may be in the water a very long time or worse.

Thinking about safety is a large part of your everyday job when you do science at sea. There are the obvious dangers, such as the winch wire, ship cranes, and large oceanographic equipment. You stay away from these unless you’re properly trained and wearing a hardhat. However, something as simple as stairs can become a hazard at sea if the boat rocks at the right time. Try to imagine doing everything that you do in a day while swaying side to side. Sleeping (back and forth), eating (back and forth), and showering (back and forth). Moreover, ocean scientists must perform their research while the boat is inconsistently shifting this way and that. Imagine pouring a mixture from one beaker to the next under these conditions. Imagine that mixture is a dangerous acid. As scientists, we take steps to minimize ‘typical’ science actions like pouring, because one sharp roll of the ship can mean a spill. We secure everything we use with ties and straps. A ‘secured’ lab might look a bit silly with bungee cords on this and ratchet straps on that. It’s certainly annoying to remove the ties each time you need to do something. However, at sea, safety is serious business and is the key to successful research.