Wednesday, May 7, 2014

The Plight of the Penguins

            Everyone loves penguins. From their distinctive waddle, to their tuxedo-like coloration, everyone can recognize these flightless birds. Mostly found on the frozen wastes of Antarctica, penguins are known for their swimming prowess as well as their ability to withstand the frigid conditions of their home. However, trouble looms on the horizon for these birds, as an international research team has discovered a strain of avian flu in the adélie penguin.

The adélie penguin
(Photo credit: George F. Mobley)

            The adélie penguin, Pygoscelis adeliea, is one of the more common species of penguin. Roughly 70 cm tall, these short penguins were discovered in 1840 by James Dumont d’Urville, a French explorer. The adélie penguin is typically found on small islands surrounding the coast of Antarctica, during the spring breeding season. Otherwise, they tend to spend most of their time out at sea, searching for food. Adélie penguins typically will eat krill and other small marine creatures, but will eat small fish and squid as well.
            While these penguins are incredibly good swimmers, reaching speeds of 72 km/hr. and diving to depths of 175 meters, they are also remarkably good walkers as well. Despite having the distinctive penguin waddle, these birds will walk 31 miles to go from their nests to the shoreline. The penguins’ main threat lies from predation by leopard seals and skuas, as well as the occasional orca.
            But there might be a new threat from these little penguins, one that could be much more dangerous, avian flu. This comes as a shock to Dr. Aeron Hurt, a senior researcher for the WHO Collaborating Centre for Reference and Research on Influenza, as no active strain of avian flu had ever been seen in Antarctic birds before. For this study, Hurt and his team collected swabs from the windpipes of 301 penguins and blood from 270 of those birds as well.
            Using real-time reverse transcription PCR, Hurt and his team found avian influenza genetic material in eight of the birds. Four of these viruses were able to be cultured, meaning that they were active and infectious. Not only that, but these strains of influenza all seemed to be H11N2 influenza viruses and were all very similar to each other. Worst of all, when comparing this genetic material to other known strains of influenza, Hurt and his team discovered that this strain was unlike anything they had ever seen before.

Dr. Aeron Hurt with an adélie penguin
(Photo credit: Aeron Hurt)

            Luckily, it seems that currently the virus isn’t doing any damage to the penguins and is not making the birds sick. It also appears to be exclusive to birds, as it couldn’t infect a species of weasel that the researchers used. However, it raises a lot of question for Hurt and his team. Namely, how often are avian influenza viruses being brought into Antarctica, whether animal ecosystems are allowing the virus to sustain itself, and whether or not the virus is being cryopreserved during the winter? For now, all we can try to do is keep trying to find where these virus strains are coming from and trying to find a cure before they mutate into something much more dangerous for the adélie penguin.


Tuesday, May 6, 2014

On the Origins of Life

            Four billion years ago, the Earth was just a floating ball of rock; insanely hot, an atmosphere of carbon dioxide, it’s amazing that life could ever exist here. But as Ian Malcolm said, “Life, uh, finds a way.” And indeed it did. Life started in the oceans of primordial Earth; a soup of amino and nucleic acids, lipids, and carbohydrates that just happened to be in the right place at the right time to become the original cell. Many believed that a bolt of lightning might have provided the original energy needed for this transformation, but a new study presents another possible origin.
            Recently, NASA scientists believe they may have found what provided the electrical energy needed to create life. Deep down on the bottom of the ocean floor, hydrothermal vents are spewing out sulfur, magma, and apparently, electricity. The hypothesis was first proposed under the name “submarine alkaline hydrothermal emergence of life”, but NASA has now managed to unify all of the data into one unified picture.

A "Black Smoker" Vent
(Photo credit: NOAA)

            But not every hydrothermal vent produces the conditions needed to create life. While it was assumed in the 1980’s when the hypothesis was first proposed that “black smokers”, vents that produce extremely hot, acidic water, were responsible, but this may not be the case. The vents that NASA scientists use in their new study produce cooler, alkaline water and are not nearly as harsh.

An alkaline vent, dubbed "The Lost City"
(Photo credit: The University of Washington)

            Michael Russell, the head scientist for this study, states that these alkaline vents created an unbalanced state, conflicting with the ancient acidic oceans. This imbalance created the free energy needed to create life, Russell believes. In fact, Russell believes that these vents could have created two imbalances.
            The first imbalance was a proton imbalance. This would have been caused by the alkaline fluids interacting with the acidic oceans that surround them. This gradient could have been used to produce energy in a fashion similar to how mitochondria function. The other imbalance could have been an electrical imbalance. The ancient oceans were loaded with carbon dioxide, which when coming into contact with the methane producing vent could have become more advanced carbon compounds, which are important for the formation of life.
            But life isn’t just electricity and carbohydrates, proteins are also needed. Will in the primordial soup that was Earth’s ancient ocean, enzymes could be found floating in the water. These enzymes could then come into contact with the rock chimneys of these alkaline vents, where two different “protein engines” could take over.
            The first would have harnessed the proton gradient from earlier in order to produce energy storing molecules which could be used later. The other used an element known as molybdenum, which can allow for the transfer of two electrons at once instead of one; a key concept needed in most key chemical reactions.

            So, this study presents a lot of interesting information. We now have a practical, new idea on the origins of life. This information could be applied to any rocky, wet planet in terms of identifying if life could exist there. So, while we are still not terribly certain on how life started on Earth, we now have a good idea of what may have happened. And while it may take decades to truly figure out how life started, Russell and his team while be willing to tackle these problems until they’re solved.


Monday, May 5, 2014

Battles Under the Sea

            A battle under the sea brings up iconic images; sharks and whales and other large animals fighting for their lives. However, this battle occurs deeper than what these animals could reach; roughly one mile below the ocean to be specific. In the deep darkness of the bathypelagic, a war is happening…a microbial war. It’s been recently discovered that viruses are attacking hydrothermal bacteria with one goal, their stores of sulfur.

A typical hydrothermal vent 
(Photo credit: NOAA)

            Bacteria and viruses have been enemies for as long as both have existed, but this is anew an interesting front in these battles. Deep-sea hydrothermal bacteria are still very unusual and not very well-known, and this is the first time that this sort of virus-bacteria relationship has been seen, since chemosynthetic bacteria are a rare lot.
            So, why do these bacteria target the sulfur in these bacteria? Well, the answer lies in the viruses’ desire to reproduce; turning the bacteria into a virus factory in a sense. What they do is they will force the bacteria to consume all of its sulfur reserves, and then use the resulting energy to create as many viruses as possible. The bacteria will inevitably die from this process, releasing all of the newly created viruses into the open to repeat the process.
            Interestingly enough, this sort of relationship has been seen before, namely in the shallow ocean water. There is a similar virus that target photosynthetic bacteria in order to reach the same end goal. So, it’s interesting to see the parallel between the two viruses, especially when it comes to their mechanism for reproducing.
            So, what are researchers doing about this? Well, currently Gregory Dick, a University of Michigan microbiologist and oceanographer, and his team are currently analyzing the DNA of the bacteria and viruses in order to better understand the mechanism of this invasion. After collecting samples from the hydrothermal vents found near the Gulf of California and the Western Pacific, Dick has begun taking a look at the DNA samples he’s gathered, and believes he may have found what the virus is doing.
            Dick and his team believe that the virus is targeting the SUP05 genes found in the bacteria. This comes as no surprise to Dick, as the SUP05 genes are responsible for creating the proteins necessary to use sulfur to create energy. By targeting this gene, the virus can overexpress it, forcing the bacteria to burn through its supply of sulfur faster than it would ever need to naturally.

Riftia pachyptila, a polychaete typically found around hydrothermal vents have an organ with chemosynthetic bacteria instead of a gut.
(Photo credit: Wikimedia Foundation)

            So, what does this mean, what can be gained from this research? Well, Dick believes that this shows that these viruses are actually very important in the long term survivability of these bacteria. Dick and his team believe that these viruses act as “agents of evolution”, allowing for gene transfer between the chemosynthetic bacteria, a theory first proposed about photosynthetic bacteria found in the shallows by David Garrison, a program director for the National Science Foundation. Without these viruses, the bacteria would rarely receive gene transfer, and a disease could cause catastrophic damage to the bacterial population, which could cause an entire collapse of the hydrothermal vent community, since they rely on these bacteria for primary production.


Sunday, April 27, 2014

New Carnivorous Sponges
The above image shows the typical anatomy of a sponge.  These use the whip-like tails (flagella) of their collar cells to create a current of water.  This current of water allows the sponge to filter out bacteria and other food.  However, four new species of sponges (two species of Asbestopluma and two species of Cladorhiza) have adapted a different feeding strategy.  These new species inhabit the food-poor waters of the deep sea in the northeast Pacific.  Therefor it is not cost-effective for them to have this constant motion of cells to create a current.  Instead these sponges have a carnivorous feeding strategy.  When small crustaceans bump into the spiny sponge, they become trapped in their microscopic hook-like spicules.  A picture of the spicules from the species Abestopluma rickettsi can be seen below.

The sponge then proceeds to digest the crustacean.  A picture of the progressive decomposition of a crustacean by the species Asbestopluma monticola can be seen below.

These sponges are also often found in chemosynthetic habitats.  These are habitats where bacteria utilize the chemical-rich water as an energy source as opposed to sunlight.  The species Asbestopluma rickettsi was discovered in one of these habitats offshore of southern California where the bacteria use the methane that seeps from the seafloor.  Another species, Cladorhiza caillieti was discovered near a hyrothermal vent along the Juan de Fuca Ridge.  The fourth species, Cladorhiza evae was also discovered near a hydrothermal vent in the Gulf of California and is pictured below.

There is still much to learn about these sponges.  Researchers believe that these sponges may also be able to utilize the chemosynthetic bacteria as an additional energy source to the crustacean prey.  Only further research with these sponges will be able to confirm that hypothesis or not.



Better ways of protecting Coral Reefs?

With coral reefs being destroyed by bleaching and ocean acidification new methods of conservation must be approached.  One of these approaches is by not putting all efforts into the coral reefs directly buy by better conserving the land around the reef.  Researchers Carissa Klein, Stacy Jupiter, Matthew Watts and Hugh Possingham tested six different conservation techniques on coral reef ecosystems in Fiji.  The primary objective of each approach was to achieve terrestrial conservation or to minimize land-based runoff.  They also compared these results with other conservation plans on how well they benefit coral reef conditions.

The researchers found that when terrestrial conservation was the primary goal that the reefs benefited by  7.7-10.4% greater than other protected areas that weren't focused on terrestrial conservation.  However, 31-44% of the terrestrial conservation was not achieved which means that there could be a higher percentage of benefit if terrestrial conservation can be achieved better.  These results are being used by the Fiji's protected area committee to better define conservation boundaries on land.

Another method that is being researched is to take more of a gardening approach to the reefs.  Studies are being done on how successful coral reefs, grown in labs, that are modified to withstand current oceanic conditions.  Artificial reefs such as concrete structures are also being used.

A more abstract study looks into if electrical currents can stimulate coral reef growth.  On Vabbinfaru Island, Maldives a 12 meter metal cage that weighed 2 tonnes was placed in the ocean and a small electrical current ran through it.  The electric current stimulates a chemical reaction that draws calcium carbonate out of the water and gets deposited on the cage.  Studies have also been done that found that the electric current helps them filter and adapt to warmer conditions because less energy is needed to form a skeleton.  One of the steel cages used is hard to distinguish now because of all of the colorful reef growth on the cage.

Unfortunately using these steel cages on a global scale would be extremely costly.  The only benefit of these artificial reefs would be from tourist areas or areas that are hit by temporary damage such as oil spills or boat impacts.  Many of the coral reef researches believe the only way to save the reefs is to greatly slash carbon dioxide levels across the globe, but they don't see that being accomplished.  Researcher Peter Sale said "By 2050, we may still have corals, and things we'll actually call 'reefs', but they will be massive limestone structures that were built in the past, with tiny patches of living coral struggling to survive on them." He adds "The world will go on without reefs, but its going to be very much inferior to the planet we have now."

  • Saturday, April 26, 2014

    Barreleye Fish

    In our last class lecture, we discussed much about the adaptations of deep sea animals. This fascinated me because the mystery behind these creatures is worth looking more into. While scrolling through an article discussing the 25 most terrifying deep sea creatures, number 8 struck me as truly interesting. This organism is known as the barreleye fish. In the family Opisthoproctidae, it is scientifically known as Macropinna microstoma, and more commonly known as the spook fish. The reasoning behind its common name can clearly be seen below through the obvious observation that they have a transparent dome head, which indeed looks strange and spooky.  The barreleye fish have two upward facing eyes that allows them to specifically search for potential predators around them. What we would think would be eyes on this species (which are the two spots on its mouth) are actually nasal organs (equivalent to the nose in humans). I found that fact interesting because it definitely made me think that the two spots on its face were its eyes, when actually its eyes are the two green glands in the transparent portion of its head. The history of its existence has been described since 1939 but it wasn't until about 2008 that the true understanding of this species had been further discovered.

    Originally thought to have eyes that are fixed in place to only look up above, it was believed by marine biologists for quite some time that this was their disadvantage to not see what what in front of them. According to an article by Bruce Robison and Kim Reisenbichler, there is now a complete understanding that these fish eyes are tubular. Not only that, but the eyes are meant to peer through their transparent membrane to look straight above in search of potential predators. According to Robison and Reisenbichler, they used machinery known as remotely operated vehicles to study these deep sea fish off the coasts of central California. They reportedly caught one and examined its physiology. Their flat fins allow them to take advantage of being nearly motionless in the water and to maneuver efficiently. This is interesting because it allows them to save their energy. 

          Figure 1. The barreleye fish with its transparent head and tubular eyes (as green glands) shown above.

    In addition to their strange physiology of their eyes, the fact remains that their eyes show green pigments when the remotely operated vehicles (ROVs). These pigments are speculated to filter out all the sunlight above them and allow them to detect prey through bio-luminescence. This is a very interesting adaptation because it allows this species to stay protected by seeming quiet and vulnerable. Its small mouth makes it a predator who relies on getting energy/food effectively. The barreleye fish feed on jellyfish, which is effective and a positive thing considering they live within the same habitat as the jelly fish at these deep depths (2,000-2,600 feet). According to this article, Apolemia colonial jellyfish have stinging tentacles that can extend as long as thirty-three feet long, which can be deadly to other organisms within that area. As means to have a defense mechanism, the barreleye fish have adapted in protecting its eyes with a the ability to avoid the tentacles and also to rotate its overhead eyes. The fact that they can protect themselves in this way shows their ability to have adapted to the challenges of the deep ocean. The fact that it was the Monterey Bay Aquarium who discovered this species fully intact for the first time in its dome shaped head. I think what really was interesting to learning about this species was the fact that there are so many more organisms in the deep ocean that I hope to learn more in the future. 

    B.H. Robison and K. R. Reisenbichler. Macropinna microstoma and the paradox of its tubular eyes. Copeia. 2008, No. 4, December 18, 2008.

    Monterey Bay Aquarium Research Institute. Researchers solve mystery of dep-sea fish with tubular eyes and transparent head. February 23, 2009. 

    It's a Squid... It's a Worm.. It's a Squid Worm?

    Have you ever seen a creature so disgusting or bizarre that you were in shock? This is what happened to researchers at Woods Hole Oceanographic Institute. In a November 2010 expedition to the deep, marine scientists thought they had seen a worm eating a squid, or a squid eating a worm. This sight turned out to be neither of these things, but in fact a brand new species called the squid worm from the genus Teuthidodrilus. The squid worm is living proof that there are a massive array of undiscovered and incredibly strange organisms living in the largely unexplored depths of the ocean.

    The squid worm feeds on plankton, uses bristles to swim, and has pseudo-arms on its head which are primarily used for sensory function. The squid worm can grow to lengths of up to 9 cm. The squid worm resides in the depths of the ocean and has been found as deep as 6,200 meters in the Celebes Sea. Even the marine scientists responsible for the discovery were very surprised by the appearance of the squid worm.

    Perhaps the most perplexing thing about this organism is the fact that it is so common. This worm appears to be very abundant at the depths. This speaks volumes about our knowledge of the creatures that reside in deep marine ecosystems. With recent findings of creatures that are common and incredibly large creatures that would seem impossible to miss such as the giant squid, our knowledge of what exists on our own planet seems limited.

    The hadal zone of the ocean, named after Hades in Greek mythology, begins at about 6,000 meters - well within the range of the squid worm - and continues to the point where life no longer exists in the depths of the sediments. Currently, there is enough unexplored space in the hadal zone to equal roughly the size of Australia. This seems absurd considering our exploration of the moon and the heights of the earth such as Mount Everest.

    The ocean should not remain an enigma for very much longer. Advances in technology allows for scientists and unmanned vessels to explore the depths much more readily. James Cameron recently completed a voyage to the depths of the Marianas Trench, the deepest solo dive on record, and there is a current expedition exploring the Kermadec Trench which is one of the deepest and coldest trenches in the world. The outlook for future exploration is bright. The depths are predicted to contain diversity matching that of the coral reefs. One thing is certain, in the near future we will have a much better knowledge of the deep.


    Howard, Jacqueline. "Researchers Take On Kermadec Trench Dive To Find Unknown Deep-Sea Creatures." The Huffington Post., 13 Apr. 2014. Web. 26 Apr. 2014. <>.
    Sample, Ian. "'Squid Worm' Emerges from the Deep." The Guardian. Guardian News and Media, 24 Nov. 2010. Web. 26 Apr. 2014. <>.
    Than, Ker. "James Cameron Completes Record-Breaking Mariana Trench Dive." National Geographic. National Geographic Society, 09 Mar. 0040. Web. 26 Apr. 2014. <>.
    "To Hades and Back: Exploring the Deepest Part of the Ocean | Expeditions, Scientific American Blog Network." Scientific American Global RSS. N.p., n.d. Web. 26 Apr. 2014. <>.