C-MORE Group Blog Post

On October 2, 2012, the Center for Microbial Oceanography: Research and Education (C-MORE) hosted the Virtual Workshop on Science Writing as part of the Science Communication module for the Professional Development Training Program for graduate students and post-doctoral researchers. One of the activities for the workshop was to write a 350(+/-)-word blurb about their own research for a broader audience. We are excited to share some of these blog posts. Thanks for reading!
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Life is tough: we live in a dog-eat-dog world, where it is every man for himself and those that prosper seem to be the smartest and the sneakiest. Life in the deep blue sea is similarly challenging: food is scarce, hiding places are few, and predators are always lurking in dark waters in search of a quick meal. However, all marine organisms are connected to one another through a network of feeding interactions called a food web. Marine food webs are whale-eat-plankton, squid-eat-shrimp, shark-eat-tuna kinds of places. All of these diverse organisms are engaged in an on-going arms race for survival.

So how do scientists know the structure of the marine food web? Who eats whom? Which organisms are the most important players in the web? What happens if human activity like large-scale fishing or trawling interrupts some of the links in the web? Anela Choy, a Ph.D. student studying Oceanography at the University of Hawaii, is trying to answer some of these very questions in Hawaiian waters. Traditional techniques like looking in the stomachs of marine organisms can be time-consuming, sample-intensive, and downright smelly. However, new biochemical tracers (e.g., stable isotopes, fatty acids and trace metals) are being used by Anela to elucidate food web connectivity. Ultimately, Anela hopes to shed new light in the dark ocean on understudied predator-prey relationships between deeper ocean animals and large marine fishes, many of which are commercially harvested at unsustainable levels.

Predator-prey interactions make up the backbone of a food web. While complex and confusing at times, the transfer of energy through these interactions allows for life to persist in the ocean. For example, without microscopic plankton there would be no large sharks – not because sharks dine regularly at the plankton salad bar but because plankton is food for small crustaceans called zooplankton, which are in turn food for small fishes, which then feed larger fishes that sharks eventually eat themselves. A change or break in any link of the food web ultimately means changes in the other links. A better understanding of marine food webs will provide a basis for ensuring that in an ever-changing ocean, people will still have access to fresh and delicious Hawaiian-caught fish for dinner!

Anela Choy is a Ph.D. graduate student at the University of Hawaii at Manoa. You can read more about her research here.
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On a November morning in Hawai’i, the ocean stretches out like a rippling sheet of glass before me – the surfers are surely disappointed, but it’s a perfect day for SCUBA diving. One hundred feet beneath the boat, colonies of “cauliflower” coral are clearly visible. As the name implies, they bear a striking resemblance to a certain hated vegetable. Once at depth, I’m amazed by the diversity of animals hiding in the reef – a startled octopus that immediately releases a cloud of ink, a moray eel defending his crevice, and even a pair of whitetip reef sharks resting in a shallow cave. But what about the corals themselves? They are as animated as rocks or trees. So, are corals animal, vegetable, or mineral?

The answer is that although corals are technically animals (so props to you if you guessed correctly!), they also have aspects that are “vegetable,” “mineral,” and perhaps most surprisingly, “microbial”. It has long been recognized that the coral harbors symbiotic algae (the “vegetable” part) that perform photosynthesis and pass most of the sugar products to the coral. Likewise, anyone who’s ever cut herself on a reef realizes that corals produce a hard skeleton (the “mineral” part). The “microbial” part of coral, invisible to the naked eye, has only received serious attention within the last decade.

But what a decade it’s been! Microbes on corals, including bacteria, viruses, fungi, and a domain of life known as the Archaea, have been found to play essential roles in both coral health and disease. For instance, certain bacteria are now known to provide nutrients to the coral host. However, other microbial species cause the deadly White Band Disease, which has decimated the elkhorn and staghorn coral populations in the Caribbean. These are only a couple of examples of microbial activities on coral reefs – the fact is, there are hundreds of millions of microbes on each square centimeter of coral and we know next to nothing about them. Scientists have their work cut out for them – so stay tuned for updates from the world of corals and microbes!

Dr. Christine Shulse is a postdoctoral scholar with C-MORE at the University of Hawaii where she studies coral symbioses with marine bacteria. Read more about her research here.
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How did life start on Earth? One idea is that organic molecules, the basic building blocks of life, were delivered to Earth by comet impacts. However, recent research at the University of Hawai’i suggests that organic molecules could be produced much closer to home, in craters at the Moon’s poles, as a natural result of exposing simple ices like water and CO₂ to radiation from space.

The craters at the Moon’s poles are never exposed to sunlight, so temperatures in these craters can reach as low as 25 Kelvin (about -248 degrees Celsius), as measured by the Diviner instrument on the Lunar Reconnaissance Orbiter spacecraft. These permanently shadowed regions are cold enough to trap volatile compounds like water, carbon dioxide, ammonia, and more from comets, asteroids, and the solar wind. These simple ices can combine to form complex organic molecules when they’re exposed to radiation—in fact, this is one process used to explain the presence of organic molecules on comets.

The Moon is constantly exposed to radiation from galactic cosmic rays, or energetic charged particles from outside the solar system. The only question is whether the trapped ices at the Moon’s poles are present long enough to acquire the high radiation doses that stimulate organic synthesis on comets, since the Moon’s tilt changes with time and today’s permanently shadowed regions probably weren’t cold enough to trap ices two billion years ago.

Researchers at the University of Hawaii used particle physics modeling to calculate the radiation dose received by ices at the lunar poles. In results submitted to the scientific journal Icarus, they discovered that the Moon’s cold traps could accumulate 36 eV per molecule of radiation over their two billion history—compared to only 10 eV per molecule required by chemists to stimulate organic synthesis in experiments.

These results suggest that organic molecules are not a rare resource in the inner solar system, delivered only by wayward comets. Instead, they could be continuously produced in craters on the Moon, Mercury, and asteroids, providing a wealth of ingredients from which life could have formed billions of years ago. If organics really are being produced at the Moon’s poles, it means that, as the closest place to Earth where we can study this process, the Moon would be a great natural laboratory for future robotic and human astrobiology missions to visit!

Sarah T. Crites is a Ph. D. student at the Hawaii Institute for Geophysics and Planetology at the University of Hawaii at Manoa.
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Similar to the way that a meteorologist predicts the weather, I predict the activity of phytoplankton (plant-like micro-organisms, or algae) in the ocean; I like to figure out where, when and how these cell-sized plants grow. I do this using numerical models. Some of these models are statistical (e.g., regression, correlation) or more mechanistic (e.g., fitting data to a specially shaped curve), while others are complex and deterministic (i.e., using fancy partial differential equations calculated over 3-dimensional domains).

Most recently, I have been able to investigate how phytoplankton interact and complement one another using a complex “trait-based model”. With this type of model, I first prescribe simple rules (or parameters) to each phytoplankton type: some types prefer lots of nutrients; some prefer low light conditions, etc. I put all of these different phytoplankton types into a model that simulates the tides and sloshing around of the ocean’s waters, watch the different phytoplankton types interact and compete for resources, and see where they end up (or “emerge”).

It turns out that the types that prefer nutrient-poor waters offshore may ultimately depend on those types that prefer growing in high nutrient coastal waters! All of these phytoplankton types together are called a community. Even though they are single-celled plant-like organisms, they grow and interact with one another in ways that parallel that of human communities. And like people, phytoplankton are complicated, their behaviors vary quite a bit, they come in all shapes and sizes, and sometimes they can be very unpredictable! Despite the challenges of measuring and predicting phytoplankton populations in the ocean, our ecosystem model of the California Coastal System does a great job at capturing seasonal changes in the low productive offshore waters and high productive coastal waters, as shown in this video:

Dr. Nicole Goebel is a post-doctoral researcher at the University of California, Santa Cruz.
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Food webs are all around us: ant caravans carrying food, deer nibbling leaves, bats snapping insects, and squirrels crunching nuts. Open ocean food webs are harder to spot, because in the oceans, all the action is microscopic! Whales, sharks, tuna, and anchovy alike are all ultimately fed by phytoplankton, plants that are too small to see.

Land plants grow by adding leaves or thickening trunks. Phytoplankton have less storage space and can’t just keep growing bigger, so they behave differently. Consider a teabag in water; inside the bag are particles like phytoplankton cells. The tea itself is water and various dissolved compounds, like sugars, proteins, caffeine, and amino acids. During phytoplankton photosynthesis, some of the new organic carbon material they produce from carbon dioxide, using sunlight energy, stays within their cells (growth of particulate stuff, basically making more stuff in the teabag); some of the new material becomes dissolved compounds like sugars, proteins, fats, and amino acids. Just like terrestrial plants, phytoplankton are eaten by other organisms called zooplankton. These zooplankton don’t eat neatly and so some of each cell they try to eat is spilled and adds to the amount of dissolved compounds; we call this “sloppy feeding”. Think of a baby first learning to eat, sometimes as much gets on baby and parent as goes into the child!

We can certainly drink tea and use the dissolved compounds it contains (caffeine!), but many ocean organisms can’t use dissolved material, because they swim in water. If they drank the water to get the compounds dissolved in it, they would be trying to drink the ocean. So, the dissolved stuff from phytoplankton is available only to bacteria, because bacteria are small enough to get the dissolved amino acids, and proteins, and so on without taking in the water as well. The bacteria then turn some of those dissolved compounds back into carbon dioxide as they respire, and some of it they use to build new cell material. That cell material now in the bacteria is then big enough to attract the attention of the zooplankton, and so that dissolved stuff can be recycled back into the food web.

How much new organic material is usually produced? Is it mostly inside cells or outside the cells? As part of my work with the Hawaii Ocean Time-series program, I try to measure how much dissolved material is produced by phytoplankton photosynthesis, what percent of the total photosynthetic production that is, and also how fast the bacteria are growing. I want to know if these production rates change with seasons, or the amount of light, or the amount of nutrients present. I am also interested in how ocean acidification affects the amount of dissolved material produced. As we add more CO₂ to the atmosphere and it finds its way into the oceans, does increased CO₂ make the phytoplankton produce more organic matter, and if so, will that new material be in the tea or in the teabag?

Donn Viviani is a Ph.D. graduate student at the University of Hawaii at Manoa. You can read more about his research here.
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Leaning over the railing of our 40’ research vessel, I notice a tug on the thick blue rope serving as our fishing line. “I think we’ve got one!” I yell to the crew, "Get the tagging gear ready!” From over 1000 feet below the surface of the ocean, we haul a live, 10-foot sixgill shark onto the boat.

Sixgill sharks live on deep slopes of islands and continents, where divers cannot venture and light hardly penetrates. So, how can we find out anything about them? Well, Kevin Weng and his team at the University of Hawaii tag them with small sensors, which collect data such as depth, temperature, and light. The tags pop off at a preset date, so we don’t have to catch the shark twice to find out where it's been.

Using these tags, we’ve discovered that sixgill sharks cover a lot of "ground"! They are amazing divers, diving over 1000' each day. Horizontally, they can cross hundreds of miles of open ocean. Sixgills could be moving all around the Pacific, or even beyond! This could mean that distant populations of sixgills may be connected by movements and breeding, which might make them less susceptible to local fishing impacts. But even with large-scale geographic movements, sixgill sharks could still be in trouble. Some studies indicate rapid declines in sixgill shark populations over short time scales, potentially associated with fishing pressure. Deep sharks often grow and mature quite slowly, so it might take a long time to replenish a population. Learning where sharks go and how they use their habitat can help us locate important nursery areas, which need to be protected to ensure continued survival of the species.

Returning to the deck of our research vessel, it’s time to tag a shark. On the count of three, we insert the sensor under the tough layer of skin and set the shark free. She points her snout downwards and with two tail beats, is diving back to her dark, cold home far beneath the surface.

Christina Comfort recently completed her M.S. degree in Biological Oceanography this semester at the University of Hawaii at Manoa.
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Each summer in the dark bottom waters off Louisiana, fish and crabs scatter to avoid suffocating in a 20,000 square kilometer dead zone. The Dead Zone is neither adjacent to the Twilight Zone nor crawling with zombies, but it does sit 70 miles southeast of New Orleans in the Gulf of Mexico. Hundreds of kilotons of nitrogen and phosphorous rich fertilizer runoff from the breadbasket of America drain in to the Gulf of Mexico via the Mississippi River, stimulating the growth of tiny aquatic plants (phytoplankton). These plants die and sink to the sea floor where bacteria devour the remains using oxygen in the process. It is this hypoxic (oxygen lacking) area that mobile animals flee from, searching for healthier waters.

What happens when there is no escape? What makes this low-oxygen layer a long-term threat? Don’t all those tiny plants make more than enough oxygen?

The answer to that is stratification: the sun-warmed, freshwater from the river sits on top of the salty, cold ocean water, due to density differences. The physical differences between the two water bodies prohibit movement of gases by creating a physical barrier called a pycnocline that prohibits oxygen from passing from the surface to the bottom. Beneath the pycnocline any oxygen produced is devoured rapidly with every microbial bite.

Yet, something in the dark survives, because the Dead Zone isn’t really “dead.” The Mississippi River’s persistent plunge to the sea has gone on for a thousand years and a hardy community of invertebrates has learned to thrive under these harsh conditions. In 2005, the passage of Hurricane Katrina threw the entire ecosystem for a loop. The physical havoc wreaked on the seafloor opened the door for a whole new set of invertebrates to move in and take over, but they could not adapt to the low oxygen levels ensuring a summer massacre on the sea floor. They just didn’t have the decades of adaptations to sit calmly in the dark and wait out the long rain of dead plants and wait for fall storms to mix oxygen back into the bottom layer.

Climate change is going to impact coastal ecosystems in many unexpected ways. Systems that function admirably under environmental stress can be devastated by the unexpected. The Dead Zone might soon resemble the horrifying corpse-ridden wasteland that its name suggests.

Dr. Clifton Nunnally is a post-doctoral research fellow at the University of Hawaii.
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The wind blowing over the ocean does not only produce surface waves that are enjoyed by surfers, but it also generates waves that propagate from the surface towards the deep ocean. For that reason, this type of wave is called “internal wave” or “internal swell” in an analogy to the surface waves people see on the beach.

The ocean can be thought of as composed of an infinite amount of thin layers of same density or temperature (“stratified”). Internal waves displace these layers up and down as they move from the surface to the deep. Because of this, researchers have long recognized breaking internal waves as key factors in controlling the amount of mixing between warmer near-surface waters and colder deeper waters.

The amount of mixing occurring in the interior of the ocean, which depends strongly on the energy of the internal waves, has important implications to Earth’s climate and its understanding remains as one of the biggest conundrums in climate science. For instance, it is still unclear how much of the wind energy is converted to internal waves, let alone how much of the wave’s energy is used for mixing in the deep ocean. Therefore it is important to map and quantify the sources of internal swells.

Similar to surf waves, most of the internal swell energy in the ocean has been known to originate from winter storms near the Westerlies region. However, researchers at the University of Hawaii suggest that powerful internal swells may be regularly generated in the tropics, more specifically off the coast of Central America.

In this region, an atmospheric phenomenon called the Easterly Wave is responsible for blowing strong winds over the ocean, repeating itself every 3 to 7 days with such perfect timing as to generate energetic, near-inertial (because their frequency is close to that of the Earth’s rotation) internal waves. Because of the particularly strong stratification of this part of the ocean, most of this energy inputted by the wind is carried away downward as big internal swells. Thus, the Easterly Wave can be a viable source of energy for mixing in the deep ocean, or for surfers to find the biggest waves yet, if only they could catch internal waves!

Saulo Soares is a Ph.D. graduate student at the University of Hawaii at Manoa.
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With our bodies bent at the waist, leaning dangerously over the rail, we watch in anticipation as the Secchi disk twirls in the purplish blue waters near Easter Island. The round, black-and-white plastic disk has been providing measurements of water clarity since its invention in 1865. The white sections of the disk flicker as sunlight penetrates to an astounding depth of 236 ft. Who lives down below, and how do they live?

Since phytoplankton use sunlight, carbon dioxide, and water to make their cells, one might think that the phytoplankton in this region would be happy campers. But phytoplankton, much like land plants, also need nutrients to make proteins, nucleic acids, and other cell parts for reproduction. Even though the South Pacific Gyre is full of light, it is one of the most “oligotrophic” (low nutrient) waters in the world. My goal during this expedition was to investigate the identities of a group of really small phytoplankton that have adapted to low-nutrient conditions, and to determine whether some species prefer to live in specific light levels at different depths in the ocean.

To obtain a census of the photosynthetic inhabitants of this region, I collect and filter about half a gallon of seawater from different depths onto a small filter membrane. Each filter is barely an inch wide, but contains ~3 million cells of my study organisms. When I'm back on land, the cells on the filter are extracted for DNA, molecules comprising genetic instructions for cell development. A specific gene (18S ribosomal RNA) in this extracted DNA is isolated using coding markers, and is compared to genes from other cells collected around the world. If I find matches, I will know that either the same, or related, phytoplankton species are living in certain regions of the world ocean. I can then piece together a larger picture, linking the types of phytoplankton to their environmental characteristics such as light intensity and nutrient concentrations.

With every expedition, one gene at a time, I am able to zoom into the life of the phytoplankton that make their home in the clearest ocean water on Earth.

Shimi Rii is a Ph.D. graduate student at the University of Hawaii at Manoa. She hosted the C-MORE Virtual Workshop on Science Writing.

Tags : carbon, CMORE, computational models, coral, dead zone, DNA, food web, Hawaii, microbial oceanography, moon, oceanography, photosynthesis, phytoplankton, predator-prey, sharks, South Pacific Subtropical Gyre, waves

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The man behind the video: Drew Berry is a biomedical animator who is responsible for the fascinating scenes in Bjork's music video.Courtesy John D. & Catherine T. MacArther FoundationIn the same vein as this Buzz post, here is another interesting blend of art and science. Bjork teams up with a biomedical animator to create a music video for her song "Hollow."

The animation is a mesmerizing, slightly creepy exercise of scale: it takes you down to the nanoscale, where you watch DNA replicate, then all the way back out to the macroscale, when you zoom out of Bjork's forehead. Interesting, indeed.

Tags : biomedical animation, Bjork, DNA, macro, micro, music video, nano, power beaming

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