Sunday, November 30, 2014

Life, uh, Finds a Way

A few hundred years ago we believed that nothing could live in the deep sea. Even as our understanding of the world grew, in some ways we lost our imagination. We began to understand that the deep was incredibly cold, very low in oxygen, and subject to astonishing pressures. So we assumed that this environment was just too inhospitable . Boy were we ever wrong.

A mile and a half down (2560m), on the vent field of an active volcano.
Courtesy NOAA Ocean Explorer via Flickr

More and more, we're seeing that life not only exists in the darkness, but thrives. A few weeks ago we talked about animals up in the water that survive with little light, but now we're headed to the bottom. The above image comes from a deep sea hydrothermal vent community, which in the last few years has become relatively well known. Thanks to programs like Blue Planet and Planet Earth, there is beautiful footage of these ecosystems readily available to the public.

But hydrothermal vents are a small part of the ocean bottom. Other incredibly diverse ecosystems exists, and with the prevalence of the internet, researchers are starting to show them as they're discovered. Some of the coolest environments being found are cold seeps.

There are several types of cold seep ecosystems, but what defines them all, is gasses escaping from underground into the water. Seeps have been found all over the world, from as shallow as 15m (easily diveable) to over 7000m (not easily anything), and even in inland bodies of water. Generally seeps are found on the edges of continental slopes where the earth's crust is bending and folding. Unlike hydrothermal vents cold seeps are not due to magma heating seawater and expelling it back out of the ground. Seeps form in places where a lot of plant and animal matter has settled to the bottom, become buried, and decayed. As that material breaks down it makes a lot of methane gas. Then as the ground bends it squeezes the gas, pushing it closer to the surface through the soft sediments on top. My apologies for being crass, but yes, the earth does fart.

A stream of bubbles escapes from the ground at a cold seep
Courtesy Deepwater Canyons 2013 - Pathways to the Abyss NOAA-OER/BOEM/USGS

The gas alone is not enough to establish an ecosystem; some organism needs to harvest the gaseous bounty to start a food chain. On land and in the surface waters, plants convert the sun's energy into chemical energy using CO2. At cold seeps bacteria and archaea convert the energy in the methane (CH4) coming from underground, and sulfate in seawater, to a type they can use. In a spectacular bit of symbiosis the archaea manipulate the methane and the bacteria manipulate the sulfate, then they use one another's products to complete their energy conversion. The exact nature of this back and forth isn't well understood, but scientists do know it produces hydrogen sulfide.

The hydrogen sulfide is then used by bacteria living inside animals to produce even more energy. These animals (some types of mussels, clams, and tube worms) have little to no digestive system. They get their energy straight from their symbiotic bacteria. At many cold seep sites large mats of bacteria and archaea are surrounded by these animals. Sometimes they even form a bulls-eye of different colors radiating out from the center.

Bacterial mats (white) and mussels (brown/orange) thriving at a cold seep
Courtesy NOAA Photo Library via Flickr

These large sedentary animals draw in small animals that take shelter in the jumbled chaos of their shells. Predators of those small organisms then come hunting. Many animals also feed directly on the bacterial mats, so there don't even have to be larger organisms around them. Entire ecosystems develop from the toots of the planet. Some of the animals that take advantage of cold seep environments are even ones that we eat, like sablefish and crabs. King crabs have even been observed feeding on bacterial mats, leaving, and coming back only after enough time has passed for the mats to regrow!

All of this biological activity helps contain methane (a potent heat trapping molecule) in the sea, keeping the temperature of the earth from rising even more. Also many seeps found in very deep water have low enough temperatures and high enough pressures for solid ice crystals to encase methane molecules. These "methane hydrates" also help keep carbon out of the atmosphere. You can see the biological and geological carbon traps interacting in this adorable video below.

Cold seeps are a good number of deep sea ecosystems, but there's more talk about, and even more to discover. Clearly the ocean bottom isn't quite so lifeless as we once believed. And probably it's even more full of life than we currently understand. Jurassic Park's Ian Malcom knew what he was talking about.


Levin, Lisa, "Ecology of Cold Seep Sediments: Interactions of Fauna with Flow, Chemistry and Microbes", Oceanography and Marine Biology: An Annual Review, 2005, 43, 1-46, Taylor & Francis

Niemann et al., "Methane-Carbon Flow into the Benthic Food Web at Cold Seeps- A Case Study From the Costa Rica Subduction Zone", PLOS ONE, Oct. 2013, DOI: 10.1371/journal.pone.0074894

"Discovery of a New Chemosynthetic Community" NOAA Ocean Explorer

Wednesday, November 26, 2014

A Ray of Hope

Courtesy kathleenreed via Flickr

It's a story that lends itself to hyperbole. An unknown disease causing the literal disintegration of a large group of animals across a wide geographic area. Sea star wasting disease has been on the minds of every marine science professional for the last two years. And amazingly...wonderfully, this issue has captured the attention of the general public as well. Through traditional media, the internet, and personal experience, sea star wasting has become, I think, the most visible issue facing the oceans today.

In case you haven't heard, throughout the North East Pacific, from Alaska to California sea stars have been dying off in large numbers. The animals begin to show signs of distress by curling their rays in unusual ways. Then white lesions (any kind of damage to tissue) appear on the outer skin. These lesions then disintegrate further until holes appear. Eventually the holes grow so large that limbs separate from their bodies, and the animals crumble into piles of skeletal plates. Some reports have stated that the disease causes the arms to walk away from the body, but that is a blatant exaggeration. Partly because stars don't have brains, their limbs can survive for a surprisingly long time after they've been separated from the central disk. So while the disease does cause the arms to come off, it's not what's causing them to keep moving. Sea stars can even deliberately drop off limbs in an attempt to protect the rest of their body from disease and predators. Then they grow a new ray in it's place.

 "We can rebuild him, we have th...." "No that's okay he'll do it himself"
Courtesy Jill Siegrist via Flickr

So why can't the stars regenerate from the damages of the disease, and what the heck is causing it in the first place? Well for the last two years the answer has been a big, fat, "I dunnuh", but that's because researchers have been furiously looking into it, and good experimentation takes time. There has been amazing collaboration between aquariums, research labs, and everyday folks to study the spread and cause of wasting. From this collaboration a new study has identified a virus that is associated with sick stars.

Last year a team of researchers discovered the first virus associated with echinoderms. They found the pathogen inside the tissues of sea urchins on Hawaiian coral reefs. This virus was a type of densovirus which are most commonly found infecting arthropods, like crabs, shrimps, and insects. In the urchins the virus wasn't causing any disease, but as the outbreak of sea star wasting became more severe the scientists wondered if something similar might be at fault. 

First they needed to see if there were any viruses in the stars at all, so the scientists separated virus sized particles from the tissues of sick stars and injected healthy ones with this material. They also boiled samples of those particles before injecting other healthy stars; doing so destroys the DNA that viruses could use infect the organisms. Sure enough the stars that received potentially active viruses became sick with wasting and the ones that received the boiled samples did not.

MMMM Nothing like a nice hard-boiled virus to start the day
Courtesy michelle@TNS via Flickr

From there the team ran a viral DNA analysis on the sick animals and found a densovirus that is unique to stars. They named the pathogen Sea Star associated Densovirus or SSaDV for short, and the more copies of the virus the stars were carrying the more likely they were to start wasting. Interestingly the team found that for most stars, the larger the animal, the greater the viral load, but the opposite was true for the sunflower star (Pycnopodia helianthoides). Sunflower stars were one of the first and most heavily impacted by the disease, so I'm curious if this association may have something to do with that. Through this, and some other lines of evidence, these researchers have found a compelling correlation between this virus and sea star wasting.

So is that it? Can we all wash our hands of this and get on with out lives? In short, no. The study confirms the existence of a virus associated with wasting, but it doesn't look at how the virus interacts with the sea stars' cells. It's extremely likely that the virus alone isn't what's causing the stars to die. Especially since the researchers looked at samples of stars collected as far back as 1943 and found the same viral DNA. And when you think about it that makes sense. When you contract a virus you don't get sick purely because the virus is in your body. You get sick because the virus combines with your stress from work, and the bacteria in your environment, and the fact that you stayed up late having drinks, to tax your immune system until it can't suppress the virus anymore and you get symptoms.

There has been extensive coverage of this study, but the problem is that many news outlets are claiming the answer has been found and they have ignored an important takeaway from the paper's conclusion. From the paper itself: "However it remains to be seen how infection with SSaDV kills asteroids, what the role is for other microbial agents associated with dying asteroids, what triggers outbreaks, and how asteroid mass mortalities will alter near-shore communities throughout the North American Pacific Coast." (Hewson et al. 2014). Essentially the author's are saying " this is a good start, but we have a lot to look into."

It's even possible that disease is a normal means for the
environment to handle overpopulation of echinoderms
Courtesy US Fish and Wildlife via Flicker

It all seems a bit bleak, but like I said before there has been an incredible amount of collaboration, and unprecedented visibility to the plight of West coast stars. Knowing the densovirus is associated with the disease won't stop it, but now we have jumping off point to further our understanding. This is a unique opportunity for you, as an interested person, to participate and keep this research alive.

So if I could ask one thing of you all it's this: Keep paying attention. Stay up to date, visit your local aquarium and ask questions, follow researchers on twitter. You can even go out and survey beaches for wasting stars yourself and scientists will use your data. Together we can develop a strong understanding, citizen and scientist alike, of what this disease is and does. So if you make statement about stars, or upload some pictures to social media I encourage you to attach the hashtag #RayOfHope, and we'll see if we can keep the momentum going.

For more information on the study that identified the virus check out this great summary from Ed Yong with National Geographic. Or read the paper yourself for free on the National Academy of Sciences website. 


Hewson et al., "Densovirus associated with sea-star wasting disease and mass mortality", Proceedings of the Natural Academy of Sciences, Oct 2014, DOI 10.1073/pnas.1416625111  

Sunday, November 16, 2014

Suspiciously Helpful Drifters

I can't contain it any longer! The blog has been active for three months now and we've barely talked about the most amazing, most important, most spectacular group of living things on the planet! Well no more. Prepare yourselves to meet the very reason for life on earth as we know it...

Oh look it's even waving hello
Courtesy Lindsay Waldrop via Flickr

Well not that specifically, that's just a baby barnacle, we'll come back to him/her (I'm not being politically correct, barnacles are hermaphrodites) in little bit. What I'm talking about is plankton. And I'm not exaggerating when I say that plankton are why we have the planet that we do. They've shaped evolution since the beginning of life, and they continue to do so today. So this week we're going to take some time to learn about our magnificent, mostly tiny, benefactors.

The word plankton itself has a pretty cool story. It comes from the same Greek word as planet, Planktos, which means wandering. Planets seen from earth look like stars and they do this weird thing where they kind of meander across the sky. Because of this, the ancient Greeks called them "wandering stars" in their own language. A couple thousand years later a German physiologist named Victor Hensen saw all these living things wandering on currents around the Baltic sea and gave them the name.

Another important part of plankton is the fact that it's not a term to describe how things are related to each other genetically. Saying something is plankton isn't like saying something is a mammal; it's more like saying it's a carnivore. The word describes behavior not biology. That's how algae (referred to as phytoplankton) and animals (called zooplankton) can both be plankton. Any living thing that is moved around by currents, tides, and waves more than it can move itself is plankton.

Pictured: Plankton
Courtesy Ian Sanderson via Flickr

That's right any living thing, so even giant jellyfish are technically plankton. Naturally being very small makes it a lot harder to resist the movement of water so the vast majority of plankton are pretty tiny. Sometimes this means that zooplankton are baby versions of the familiar species we find on the beach.

Take that baby barnacle that we met at the beginning for instance. He/she is a perfect example of meroplankton (they're plankton for merely part of their life). Gravid (the egg-laying version of pregnant) barnacles launch out those tiny babies when they hatch. The babies are then free to spend the next couple weeks cruising the currents eating and growing strong; before settling down to stay in one spot for the rest of their life. These baby, or larval forms as they're known, are actually really important for scientists trying figure out how animals are related to one another. We thought barnacles were related to snails until the mid-1800's when we had good enough microscopes to see that the larvae are more like shrimp.

Of course just because something is small doesn't mean it's a baby. Many living things are plankton permanently. These are called holoplankton (they're plankton for their whole life) and they are incredibly important to the ocean's food web. The two classic examples of this are copepods (pronounced cope-uh-pods) and krill. Both are crustaceans, just like the barnacle, and between the two of them they directly or indirectly feed almost everything in the ocean.

 A copepod (on the left) and a krill (on the right), you've probably seen them in TV and Movies
Courtesy NOAA Great Lakes and Norkrill via Flickr

What these two groups of animals lack in size, they make up for in numbers. Around Antarctica alone it's estimated there are around 500 million tons of just krill! One krill weighs about seven tenths of an ounce. There are literally uncountable numbers of these animals in the ocean. There are so many that we get into numbers that human brains actually have a hard time comprehending. You start to understand how something as massive as baleen whales can live off these two animal groups almost exclusively.

So zooplankton are clearly important to the health of the oceans, but what about the algae, those phytoplankton from before? Well we wouldn't have things like krill and copepods without those phytoplankton, and in fact we probably wouldn't have ourselves either. Like plants on land phytoplankton are at the bottom of almost every ocean food chain. They take sunlight and carbon dioxide and turn it into sugar, which things like krill and copepods love to eat. So the copepods gobble up the phytoplankton, and then they're gobbled up by fish, and on and on, all the way up to you. When you eat a fish you're eating everything that fish ate, plus everything that fish's prey ate, plus everything that fish's, prey's, prey ate. It starts to look pretty important to keep the plankton's tiny ecosystem healthy doesn't it?

Not only do phytoplankton make life work because they're food for other living things, but they provide complex life with something extremely important. Go ahead and take two really deep breaths for me. Nice, long, slow, relaxing breaths from your diaphragm. Feels good doesn't it? All that fresh oxygen to your brain and muscles really does you good. Well amazingly the oxygen in one of those breaths came from phytoplankton.

"You're welcome!"
Courtesy NOAA Photo Library via Flickr

It's been calculated that about half of the oxygen in the earth's atmosphere comes from the ocean. That means that phytoplankton are at least as important as all the terrestrial forests, all the savannahs, and all the shrub lands, combined. Remember how I mentioned that we can't even count the number of krill or copepods? Well to make that many animals you need even more of these algae. There are so many phytoplankton in the ocean that they actually dye huge swathes of the ocean green during the summer, which can be seen from space! Not only does phytoplankton sustain us complex organisms, it's partly responsible for us being here in the first place. 

On the very ancient earth most of the oxygen in the atmosphere was tied in with other gasses, like carbon dioxide, and what was escaping, quickly came out of the air to rust the metals in rocks. But then a group of photosynthesizing bacteria evolved multi-cellularity. All of a sudden there were way more organisms using up the CO2 and dumping out a lot more oxygen than the rocks could absorb, and BAM! They created an atmosphere full of an element that's essential for biological processes in animals.

So that's it for this week. I could write even more about plankton: how they have the single largest migration on earth, how they provide food for the deep ocean with their poop, and I will eventually; but for now let's just appreciate the incredible, essential plankton by looking at this wonderful picture of a spring bloom in the Atlantic.

For scale: that's Ireland at the top middle. This is a real color photo
Courtesy NASA Goddard Space Flight via Flickr


Carefoot, Tom, "Learn About Acorn Barnacles", A Snail's Odyssey

Sessions et al. "The Continuing Puzzle of the Great Oxidation Event" Current Biology 19, 2009, DOI 10.1016/j.cub.2009.05.054, Accessed via:

Shirrmeister, et al., "Evolution of multicellularity coninsided with increased diversification of cyanobacteria and the Great Oxidation Event." Proceedings of the Natural Academy of Sciences, vol. 110 no. 5, pg. 1791-1796, DOI 10.1073/PNAS.120992710 Accessed via:

Krill Facts Center, International Health and Science Foundation

Sunday, November 9, 2014

Drop the (Antarctic Research) Bass

Exterior shot: Antarctic research station over the Ross Ice shelf. Except for a single lamp right outside the door it's the complete inky blackness of the southern winter. Motes of snow billow past through the light and we hear only the sound of rushing wind. The camera slowly zooms in on the entrance. Cut to Interior: Two researchers, a man and a woman, are settling onto cots. There's a dull orange glow from the lamp outside over everything. The woman looks over to the man.

Woman: I can't believe how quiet it is here. Back in Seattle I got so used to hearing the noise from the street that I'd forgotten what it's like in the field.

Man: Yeah everybody reacts a little differently. Some people love the isolation, others start to go a little nuts, start to think they're hearing things. Either way all you'll be hearing for next couple months is wind and creaking ice, so get used to it quick. 

Woman: I'll be fine, I've had enough of civilization lately. I'm ready for the silence.

Man: Good. I wouldn't want you going cracked on me with just the two of us down here. Let's get some rest.

They both settle into their cots and rest their heads on their pillows. The camera pans across the room and settles on the woman's face. She looks slightly unsettled, but calm as she slowly closes her eyes. The camera lingers on her face and all sound from outside dissapears, suddenly we hear this:  

And our heroine's eyes snap open! End Scene.

While that may sound like the first scene from yet another reboot of The Thing it's a situation that can actually happen in Antarctica. As ruined by the image on the clip; that sound is not an alien horror, nor the intro to the latest club sensation, but a cuddly seal. (Disclaimer: No wild animal should ever be cuddled, seals have no way of knowing that your hug isn't a grip of death and they will defend themselves, also they usually smell like fish and pee.) Specifically that sound comes from the Weddell seal (Leptonychotes weddellii) which breeds farther south than any other mammal. And they'd have the record for all animals too if it weren't for those meddling penguins. They were first reported on the ice above the Weddell Sea but they have what's called a circumpolar distribution. Basically that means they're found all the way around Antarctica on coasts and ice shelves.

Weddells live much closer to shore than the other Antarctic seals. Although they generally prefer shallower water Weddell seals have been found diving 600 meters down in search of prey! To give you an idea of how far that is, the deepest dive ever done on SCUBA equipment was only half as deep (332m Ahmed Gabr). While it may not be noticeable to us there is a big difference in ice real estate for Weddell seals.

Perfect example; no one wants a bedroom right next to the road
Courtesy Sandwich via Flickr

 Breeding age females and males hang out on ice closer to land than juveniles. The ice closer to shore is called fast ice because it's locked fast and doesn't shift around much. On the ocean side is the more familiar pack ice which gets packed onto and removed from the sheet pretty regularly. As you can imagine a constantly shifting environment isn't great for rearing babies. There's some contention among scientists as to whether or not the adults migrate from the fast to the pack ice, but it looks like most Weddells are pretty site specific.

One of the lines of evidence for this is the presence of the sounds you heard earlier. The trilling noise is unique to male Weddell seals. That sound is thought to be a territorial display since males use it all year round, but ramp up how often during the breeding season. Of course it's always possible that these seals just really love Doctor Who. Either way we know that, during the breeding season, males guard cracks and holes in the ice that females use to access the water.

How you doin'?
Courtesy Sandwich via Flickr

Of course those holes in the ice are also very important for breathing. Even though they can go without fresh air for up to 80 minutes at a time, being mammals means they still need to breathe between dives. In fact both male and female seals put quite a bit of effort into keeping the holes open. Fast ice has fewer gaps than pack ice, so the ones that are free need to be maintained. Weddell seals use their teeth to literally carve out thinner sections of the ice.

It's easy to assume the seals would keep breathing holes to themselves but they've been seen sharing these spaces. So scientists think that some of the underwater vocalizations are seals communicating about the breathing holes. Decoding the Weddell seals' language requires a lot further study; but it could be that seals approaching the surface are letting those already on the ice know they're coming, or seals at the holes telling those underwater where they can be found.

Weddells are the most well studied of all of Antarctica's seals, but we still know so little about them. Why do they have up to 30 different vocalizations? What are they trying to say? Do they get more inspiration from Depeche Mode or Daft Punk? Thankfully, Weddell seals have been relatively unaffected by the loss of ice in Antarctica so far, so there's lots of opportunity to learn the answers to these questions.


Weddell Seal (Leptonychotes weddellii), Wildscreen Arkive

Leptonychotes weddellii: Weddell Seal, Encyclopedia of Life

Doiron et al. "Proportional underwater call type usage by Weddell seals (Leptonychotes weddellii) in breeding and nonbreeding situations." Canadian Journal of Zoology, 2012, 90(2): 237-247, 10.1139/z11-131

Lake et al. "Spatial utilisation of fast-ice by Weddell Seals (Leptonychotes weddellii) during winter.", Ecography, Vol. 28 Issue 3 pg 295-306,  June 2005, DOI 10.1111/j.0906-7590.2005.03949.x 

Sunday, November 2, 2014

Lighting Up The Deep

Happy just after Halloween everyone! And Feliz Dia de los Muertos if you're in Central America! This is one of my favorite times of year, not least of all because I've always had a lot of fun on Halloween. It's one of those few holidays that stay awesome no matter how old you get. When you're young you get to have all the fun of trick-or-treating, and when you're older you get to have parties. I remember one of my favorite things about trick-or-treating was getting to use glow-sticks.

Yeah these things!
Courtesy Timo Newton-Syms via Flickr

Most of the time we humans get to glow for fun, but there are animals in the ocean that glow entirely to survive. So this week we're going to explore some of the beauty of deep sea bioluminescence.  

As I'm sure you know the further down you go in the water the darker it gets. Eventually you lose all light but for a long ways, up to about 1000 meters, small amounts of light still get through. Not all light is created equal though. Different colors have different wavelengths, and therefore have different amounts of energy. Colors like blue and green are very energetic compared to colors like red and orange, so they travel farther through the water. Many a scuba diver can tell you that you don't have to go that far down before everything becomes awash in only blue. This property of light is very important to animals in the deep sea, because it determines what color their bodies are and what  colors their bioluminescence. Watch the video below and see how many different colors of animal made light you can see.

Also, revere the master David Attenborough!

So how many did you count? I'm guessing maybe two if you've got really good eyes or like to be pedantic about blue vs. blue-green. So why do we see basically one color down there? Is the deep sea just racist? Well it comes back to those properties of light; blue literally goes a long way down this far. Communication is one of the important uses for bioluminescence in the ocean and you can signal over a much longer distance with blue light.

Alright so attracting prey and communicating with your own species is a great use for bioluminesence, but there's more you can do with living light. Believe it or not many animals use light to blend in. Even though this seems counter-intuitive animals that do this are using an extension of matching their background like traditional camouflage. Many animals in the region where a little bit of light still lingers, sometimes called the twilight zone, have light emitting organs called photophores on their bodies. The photophores give off the same color of blue that makes it through the water, breaking up their silhouette and blending them in. This is especially true when they're viewed from below because the light comes down from the surface. Many animals do this: from the incredibly numerous lantern fishes (Myctophiformes), to one of my favorite animals, the firefly squid (Watasenia Scintilans

Seen here in a festively appropriate form. 
Actual pictures can be seen here.

Now that we know the things most animals ocean animals do with biolumiescence, let's look at an interesting exception. Three genera (one grouping less specific than a species) of dragonfishes (Stomiidae) have photophores that make red light instead of blue. These special light organs, which are just beneath their eyes, actually beam ahead of them like headlights. The reason they use red instead of blue is two fold. One, most animals in the deep have no reason to see red. Dragonfishes' prey evolved in an environment where red light doesn't exist, so they have no need for the eye proteins that see it. And two, many deep sea animals are red. Weird right? But red is great camouflage against everything except for those three groups of dragonfish. Since there isn't any red light, animals with red skin appear completely black in the depths. These three genera of dragonfish are pointing lights that their prey can't see at animals that are lighting up like beacons.

Why are you weirded out? Only two of them have no bottom on their jaws.
By Erich Zugmayer (died 1939) [Public domain], via Wikimedia Commons 

Even more amazing is the fact one of the species in this group of fish, the Northern stoplight loosejaw (Malacosteus niger), regularly eats copepods (open ocean relatives of shrimp) which eat a bacterium that makes a type of chlorophyll that picks up red light. The stoplight loosejaw takes this chlorophyll and produces the pigment its eyes need to see red light. Think about that for a second; this fish uses the food, of its food, to make what it needs, to find food. Cue the theme song from Inception!



Douglas et al., "Enhanced retinal longwave sensetivity using a chlorophyll-derived photosensitizer in Malacosteus niger, a deep-sea dragon fish with far red bioluminescence", Vision Research, Vol. 39 Issue 17, Aug. 1999, DOI 10.1016/S0042-6989(98)00332-0, Accessed via:

Moser, H. Geoffry & Watson, William, "Order Myctophiformes: Blackchins and Lanternfishes" From NOAA, accessed via:

Malacosteus niger: Northern Stoplight Loosejaw, Encyclopedia of Life

Watasenia scintillans: Sparkling Enope Squid, Encyclopedia of Life