Hydrophone arrays, FTW!

Figure 1. Photo of Amy and Emily deploying the array off the back deck of the R/V Ocean Starr.
Figure 1. Photo of Amy and Emily pulling in the array at the end of the day.

We do a lot of things out here on the CalCurCEAS cruise – we play cribbage, we eat cookies, we ride the stationary bicycle – but mostly we do these two things, A LOT:

1) Look for whales and dolphins.
2) Listen for whales and dolphins.

Part 1, the “Look” part, is within the realm of the visual team, who stand bravely in wind and cold and rain (and sometimes gorgeous, balmy sunshine) and scan the surface of the ocean for animals that might pop up to say hi and or take a quick breath of air.

Part 2, the “Listen” part, exists because, well, it’s pretty difficult to see what animals are doing once they dip down beneath the waves. And we all know that’s where the fun stuff happens (synchronized swimming practice? underwater tea parties? you never know!).

Since I’m on the acoustics team, I thought I’d give a little overview of how our operation works.  We eavesdrop on the animals using a pair of hydrophones, which are basically underwater microphones. If we just used one hydrophone, it would be okay, we could hear the animals. But adding a second allows us to not only hear them, but figure out where they are.

Figure 1.  Top: Array geometry, showing how we can tell which direction a sound is coming from. Bottom: Signals measured on each of the hydrophones.
Figure 2. Top: Array geometry, showing how we can tell which direction a sound is coming from. (The poor creature pictured is my sad attempt at a striped dolphin, if you were wondering) Bottom: Signals measured on each of the hydrophones.

The pair of hydrophones are built into the end of a cable that is spooled onto a winch on the back deck. Every morning we head out there, don our life jackets, hard hats, and boots, and reel out the cable until the hydrophones are 300 meters behind us. The hydrophones are spaced one meter apart, and once the vessel is up to speed, they are roughly at the same depth.

The upper part of Figure 2 (blue) shows a cartoon schematic of the hydrophone setup. Here’s what it all means:

H_1 and H_2 – hydrophones #1 and #2

Known quantities:

d_h – distance between H_1 and H_2. For our array this distance is 1 meter

c_w – measured sound speed in water (approximately 1500 m/s, but depends on temperature and salinity)

Measured/derived quantities:

\Delta t – time delay between when the signal arrives at H_1 and H_2

d' – distance associated with the time delay \Delta t, derived using c_w

Unknown quantity:

\theta – angle between the incoming ray path and the array baseline. This is what we’re solving for!

OK, that seems complicated. But feel free to ignore the math, of course. The basic idea is that depending on where the sound comes from, it can arrive at the hydrophones at different times. For example, in the image above, it hits hydrophone 1 first, and after some amount of time, it hits hydrophone 2. The signals from each of the hydrophones are sent upstairs to the acoustics lab (see bottom part of Figure 2). The call shows up at slightly different times on each of the hydrophone channels, and we can measure that time delay \Delta t very precisely.

Using the time delay \delta t and the measured sound speed c_w, we can obtain distance d' using:

d' = c_w * \Delta t

So now we’ve got a right triangle where we know the hypotenuse and one other side, and you know what that means – trigonometry time!! Everyone’s favorite time! We finally have what we need to solve for the angle \theta.

\theta = acos( \frac{d'}{d_h})

We now know what angle the dolphin is at relative to the array. Huzzah! But wait. There are just a couple of little details that you need to remember (see Figure 3). First: you don’t know how far away the dolphin is. Second: there’s this pesky thing called “left-right ambiguity” *.


From the perspective of the array, there’s no difference between an animal calling from an angle \theta to the left and an animal calling from an angle \theta to the right.

Figure 3. Left-right and range ambiguity.
Figure 3. Left-right and range ambiguity.

These are fundamental limitations of the method, but we can (sort of) overcome them. As the vessel moves along, and we estimate angles at different locations, we end up with a location where most of the bearing lines intersect. If the vessel is traveling in a straight line, we can get a good idea of range – how far the animal is from the trackline. We just won’t know which side of the trackline it’s on. But if the vessel makes a turn, the new bearings estimated after the turn will resolve which side of the line it’s on!

Figure 4. Bearing estimates (red lines) taken at different locations along the track line. Probable location is where most of the lines intersect.

At this point you might be wondering, Michelle, what assumptions are you making when you do these calculations? So here they are:


  • The array is horizontal
  • The animals are calling at the surface
  • The animals are staying in approximately the same location for the duration of the measurements

So there you have it. That’s how we locate animals underwater with a towed, 2-element hydrophone array.


* Yin, one of the amazing visual observers on the cruise, thinks “Left-right ambiguity” would be a great name for a band, and I agree.

** assumptions are made to be broken

Harmful algal bloom forecasting: Chasing toxin producers

It started with “drunk” pelicans. While studying aquatic sciences at the University of Santa Barbara, Liz Tobin noticed that there was something wrong with the fish-gulping birds.  They exhibited unusual behavior, getting hit by cars, and sometimes simply falling out of the sky. The pelicans suffered from seizures induced by domoic acid poisoning, a particularly dangerous affliction when it hit mid-flight.  Biologists traced the source of the poisoning to rapid springtime growth (bloom) of Pseudo-nitzschia, a tiny, single-celled organism, distantly related to the giant kelps thriving in nearby coastal waters.  Small fish and shellfish consume these algae, and although they are not harmed, they store the toxins produced by algal cells and pass them on to their predators, including seabirds and marine mammals.

Scientists refer to these incidents as harmful algal blooms, or HABs.  They are not restricted to the waters of southern California, though.  And Pseudo-nitzschia cells are not the only culprits.  There are a number of other algal species that can cause trouble for local marine ecosystems. HABs occur in coastal waters around the globe, with larger and more frequent blooms being linked to a warming sea surface [1] and also to increased nutrient runoff from land [2], which is a common by-product of animal or plant agriculture.  Local economies suffer due to tourism losses and local residents can’t harvest shellfish from their beaches.

After wrapping up a bachelor’s degree at UCSB, Liz moved on to graduate school at the University of Washington so that she could study harmful algal species in Puget Sound.  One of the species she’s interested in is Alexandrium catanella, another single-celled marine alga that produces a suite of deadly neurotoxins causing paralytic shellfish poisoning, or PSP.  Alexandrium blooms can become so intense that they give the water a reddish-brown tinge, often called a “red tide” (although they don’t always cause water discoloration).


If you eat a shellfish that has accumulated Alexandrium toxins, a series of unpleasant events unfolds. First, your fingers and toes will tingle and your lips will feel numb.  Next, you may become nauseous and unsteady on your feet.  If the toxins hit you at full force, your diaphragm will become paralyzed, which means that you are unable to pull oxygen into your lungs.  Without prolonged artificial respiration, a severe case of PSP can lead to death in a matter of hours.

In recent years, poisoning cases in Washington State have been rare, but they do happen. Washington Department of Health aims to prevent outbreaks by regularly testing shellfish along Puget Sound beaches.  Commercially harvested shellfish are tested exhaustively before hitting the markets. Unfortunately, it’s tough to predict the severity, location, and timing of an Alexandrium bloom ahead of time. That’s where Liz’s work fits in: she’d like to improve our ability to forecast where those blooms will happen ahead of time so that public health officials, fisheries managers, and the shellfish industry have more time to react.


Alexandrium cells have a comfort zone, she explains.  They grow and divide furiously when the days are long and the surface waters are warm.  Once the spring bloom ramps up, zooplankton, fish, and shellfish feed on the algae, eventually decimating Alexandrium populations by early to mid summer.  Less Alexandrium cells means less food for their predators, and their predators begin to die off or find food elsewhere.  By late August, with newly lowered predation pressures and plenty of sunlight, a second bloom typically occurs.  As the season draws to a close, Alexandrium  algal cells feel the effects of shorter days and less sunlight.  They struggle to grow and divide and at some point cut their losses and transit down to the sediment to wait out winter.  -Settled into the muddy seafloor, they shift to survival mode, also known as the “cyst” stage.  The exact conditions that send them into their cyst stage are poorly understood, as are  the details of how they wake up and make their way to the surface come springtime.

Liz is particularly interested in how the Alexandrium cells swim, even though they are mostly at the whim of the currents.  Tides rush in and out twice each day, racing through narrows and washing languidly over mud flats.  Rivers pour into Puget Sound with irregular pulses of freshwater from rain and springtime snow melt. Alexandrium algal cells propel themselves through the water using a small whip-like appendage called a flagellum, but because of their tiny size – only about a third of the width of a single human hair – they can’t overcome even the weakest currents. However, if Liz knows their vertical swimming capabilities, she can better understand how quickly Alexandrium cells migrate from the seafloor to the surface (where blooms occur) and back again.

A lot of researchers, Liz included, study Alexandrium in the lab.  They blend solutions of water and various chemicals to imitate seawater, and observe how the cells behave and react to a variety of environmental triggers.  One of the labs she works in is a tiny bunker-like space on the second floor of the Ocean Teaching Building.  Two long black tables running along either side of the room are covered by a hodge-podge of beakers, elaborate video recording setups, and circuit boards sprouting nests of red and white wires.  At the back of the room, a giant insulated door opens to a fully programmable walk-in refrigerator, where algal cells can be subjected to controlled shifts in temperature and light.

Even at their best, however, lab experiments can’t possibly recreate the many complexities that exist in the natural world.  Liz knew that if she could monitor the emergence of the Alexandrium cells from the sediments she could combine those observations with detailed fluid flow models to better predict where the cells would eventually concentrate.  The only problem was that there were no “off-the-shelf” instruments that were capable of doing what she wanted.  So she set out to build her own.


When she starts describing the instrument she’s working on, I interrupt.  Pushing my notebook and pen across the table, I ask her to sketch her design for me.  She draws a tube a few inches in diameter, sitting upright on the seabed.  On one side of the tube a camera in waterproof housing points into a tiny window to capture any Alexandrium cells swimming past.  The end of a plankton trap sits on top, ready to catch any upward-swimming cells so they can be later compared with the video. She pauses her drawing to look up at me.  “It’s just like what we would do in the lab,” she says, “but instead of a camera looking at a tank, I have a camera looking into a chamber on the seafloor”.

As of mid-July 2013, Liz’s prototype of her seafloor camera was nearly ready to be deployed for testing.  If it works, she’ll try to capture Alexandrium cells emerging from the seafloor just prior to the late-summer bloom.  Her vision for the future, she tells me, is a network of these instruments deployed across Puget Sound, monitoring cyst emergence in real time.  Instead of only knowing about blooms once they are in full swing, they could be predicted days or weeks in advance, avoiding unnecessary closures and potentially saving lives.

[1] Climate change and harmful algal blooms, NCCOS http://www.cop.noaa.gov/stressors/extremeevents/hab/current/CC_habs.aspx

[2] Anderson, Donald M., Patricia M. Glibert, and Joann M. Burkholder. “Harmful algal blooms and eutrophication: nutrient sources, composition, and consequences.” Estuaries 25, no. 4 (2002): 704-726.


Diatom survival: It’s in their genes

Please welcome Sara Bender to the Science+comics interview series!  This week we’re taking a peek into the world of diatoms, and how they take up nutrients. Check it out!

Diatoms are tiny, single celled organisms that live near the surface of the ocean.  They are a type of phytoplankton, which are small, drifting organisms that form the base of the marine food web.  Many of them are so tiny that they can’t even be seen with the naked eye – even smaller than the width of a human hair.  Although they are not plants, they use photosynthesis to drive their metabolic processes, taking in carbon dioxide and releasing oxygen.  Also, like plants, they need nutrients such as nitrogen and phosphorous to survive.  Because of coastal upwelling and runoff from land, shallow, coastal regions tend to have the highest nutrient concentrations, and also the highest diatom concentrations.

Sara Bender studies phytoplankton ecology with the Armbrust Lab, and is a PhD student in her final year of Biological Oceanography at the University of Washington.  One of the things that Sara has looked at is how diatoms take up nitrogen. How do they do it, and how have they adapted to the conditions that exist at different locations? Sara has looked at three species in particular, all from very different environments. In a way, these species are sort of like the “lab rats” of the diatom research world, and many researchers have used them for experiments in the past and present. Let’s meet Sara’s special “pet diatoms”, shall we?


Now, here’s where Sara’s research gets really interesting: she uses cutting edge techniques developed for the medical field, and applies them to her pet diatoms. Her advisor, Ginger, along with a team of researchers, actually sequenced the very first diatom genome (Thaps) in 2004! Since then, both Fracy and Psemu have also had their genomes sequenced, and the number of diatom genomes is on the rise!

So how does Sara use these genetic sequences to learn about diatoms? Well, let’s back up a bit and talk about what is in a genome. DNA is made up of a specific sequence of nucleotides. You can think of these nucleotides as a very short alphabet – one with only four letters: A, T, C, and G. These letters are grouped together into genes that form the genome, which contains information that the cell can use to carry out different operations. Sara is interested in a particular type of operation: she wants to know how diatoms pull nitrogen out of the water. She asks questions like: how have different diatoms adapted to different conditions? And how might diatoms respond if conditions change in the future, as a result of climate change, for example?


Sara looks for similarities and differences between genes from her three test species. And as it turns out, just because different organisms have some of the same genes, it doesn’t mean that they express them in the same way – or at all. After looking at which genes are present, Sara is able to form hypotheses. For example, let’s say that one diatom has ten of a specific type of nitrogen transporters, and the other two diatoms only have one of those, you might guess that the diatom with the ten transporters had to adapt to some particular condition in its environment.


To test her hypotheses she looks at the next step in the process: the gene transcription step. This is where the information contained in genes gets transcribed into RNA. If this happens, the RNA can be translated into a protein, which can then be used to carry out some cell function. Sara looks at whether particular genes get transcribed in order to better understand how the cell functions under certain conditions. She can simulate different environments in the lab and then look at how the diatoms react based on the level of gene transcription.

Since diatoms play such a significant role in the marine food web, it’s really important to understand how they might be affected by changes in the ocean – whatever happens to them can have cascading effects on other organisms higher up in the food web.

Sara will be graduating this summer, and after that she’s going to the Woods Hole Oceanographic Institution (WHOI) to do a post-doc in Dr. Mak Saito’s lab. While she’s there, Sara will take her knowledge of diatom transcriptomics and translate it into studying phytoplankton proteomics- making the transition from genes to proteins. But fear not, she plans on continuing to unravel the mysteries of phytoplankton nutrient uptake in her future endeavors.

Krill and the Carbon Cycle

Krill And The Carbon Cycle 2013-01-14 (07.17.03-407 PM)

What do krill have to do with the carbon cycle?  Well, maybe I should start with, “What the heck is the carbon cycle? (oh, and why do I care?)”.  As many of you readers out there know, the carbon cycle is immensely complex and I couldn’t hope to explain it all in one measly blog post.  But in a nutshell, it’s the cycle that describes the overall budget of carbon, in its many forms, on/in our planet – that means, in the earth, the ocean, plants, animals, the atmosphere, everything.  The carbon is balanced in such a way that our planet can sustain life – excellent!  I don’t know about you, but I think that’s pretty great.

The ocean plays a huge part.  There is a constant exchange of carbon between the atmosphere and the ocean.  And it turns out that if there is an increase in atmospheric carbon, the ocean can suck it down… to a certain extent, at least.  Why? Well, blame it on chemistry (I blame most things I dislike on chemistry, but that’s just me).  The ocean can take up that CO2 because of chemical reactions that happen relatively quickly near the surface.  The uptake relies in large part on the weathering of rocks, which provides an input of ions that drive the chemical reactions.

Once the ocean reaches its limit, it just can’t take up any more CO2.  What then?  That’s when the krill (and, okay, some other helpful zooplankton) come to the rescue.  They eat up phytoplankton that have converted dissolved inorganic carbon (DIC) at the ocean’s surface to organic carbon (part of the whole photosynthesis thing).  Turns out krill are really messy eaters, spitting out spitballs containing clumps of uneaten phytoplankton.  They also have really inefficient digestive systems, and their fecal matter contains a lot of carbon and other nutrients.  These spit balls and fecal strings (yes, they kind of look like strings) sink WAY faster than individual phytoplankton, which means that those carbon packets sink deep into the ocean.

Source: Uwe Kils.  In this image you can see the feeding basket formed by the anterior legs (thorecopods).  The small red dot near the feeding basket is probably a small copepod (lunch!).  There’s a spit ball in the lower right corner, and a fecal string in the lower left.

This is an important way in which carbon is exported away from the surface waters, where it can be stored at depth, drifting with the deep ocean currents or being deposited on the seafloor to be incorporated into sediments.  Krill of the world:  thank you!

Sadly, if atmospheric CO2 continues to rise, the ocean will not be able to handle it, even with the help of the amazing krill.  And another very significant effect of just shoving the excess carbon into the ocean:  the ocean becomes more and more acidic, which is harmful to many of the animals that live there, especially corals and those with shells.

Which brings us to the “why do I care?” question from the beginning.  You might want to consider caring because your livelihood depends on it.  And if not yours, then certainly your children and grandchildren. If CO2 in the atmosphere continues to rise, the climate on our planet will be seriously affected.  In addition to this, the devastating effects of ocean acidification will have cascading implications for the ocean ecosystem – which in turn will have implications for us terrestrial types.

I’ve glossed over a lot here, and kind of ended on a downer.  So here’s something to cheer you up – Ernst Haeckel’s drawings of copepods (my new favorite thing ever since Tuesday, thanks, Owen and Anna).  No, copepods aren’t some kind of krill.  But they are zooplankton, and they’re pretty, aren’t they?

Copepoda – by Ernst Haeckel

If I’ve made any mistakes, whether they’re small, or total doozies, be sure to let me know so I can fix them up and not confuse people!

Krill and other zooplankton … and sequential hermaphroditism.

Have I mentioned this before? Fin whales love to eat krill. It’s a huge part of their diet (along with other types of zooplankton, small schooling fish, and sometimes a squid or two). Since zooplankton are so important to my animal of study, I’m taking a course on marine zooplankton ecology. Understanding more about them will help me understand more about fin whales!

It’s the second week of class, and we’re already giving presentations – phew! Luckily they are fun – we were encouraged to be creative, sing songs, write haikus – so long as we included the actual science in there somewhere. Here’s mine…

People gave really great talks today – one fact in particular that I found fascinating was that there are several types of animals (zooplankton and fish, at least) who are not only hermaphroditic (crazy in itself!) but that belong to a category of hermaphrodite that is sequential – they start off life as either male or female, and then at some point they switch genders. Amazing! (here’s the wikipedia page describing sequential hermaphoroditism)