Hello all, sorry I’m not feeling particularly creative at the moment. Yet again it seems like time is slipping by way too fast, and with the prospect of spending more time in the lab I know it’s just going to go faster. I’ve started in-lab work with Blair, but I think I’m going to use this post to give a little background on exactly what goes into the subject of Marine Biogeochemistry.

First, the Biology: The microbes we are interested in are two phylogenetically distinct groups of Archaea referred to as ANME 1 and 2, which play a key role in methane oxidation in the global methane cycle. Aerobic bacteria are able to oxidize methane by using oxygen, which is highly efficient and gives an energy yield of about 720 kJ/mole. However, the Archaea we look at are anaerobes, and oxygen is one of the few things that can easily kill them. The general equation for their oxidation uses water: CH4 + 2(H2O) → CO2 + 4(H2), which requires energy input to run to completion and thus can’t be used on its own to provide the microbes with energy to survive. These Archaea are therefore found in consortia with sulfate-reducing bacteria, and together the two metabolic pathways generate just enough energy for both to survive. At this point, exactly how this syntrophic arrangement functions is mostly unknown – for example, we don’t know precisely how the molecules are shuttled back and forth between the sulfate reducing bacteria and the methane oxidizing Archaea. From what I understand, most studies of live microbes have to be done on the sea floor in anoxic conditions, because once they are taken to the surface even a tiny bit of oxygen can kill them. Hence, trying to grow colonies of live microbes involves lots of attention to detail and machines that don’t ever break (good luck with that one, says Dave).

Within the Biology you have the Viral: marine viruses account for a significant amount of the evolution that these microbes go through, with the exception of occasionally beneficial mutations in DNA replication. Viruses are basically protein capsids enclosing genetic material. They replicate and spread through two cycles, called the lysogenic and lytic cycles. In the lysogenic cycle, viruses inject their genetic material into the cell, which becomes incorporated into the genome. In this cycle, the virulence function of the virus is benign, and the cell goes through repeated cycles of division without hindrance, which also duplicates the viral code. Eventually the virus receives a signal from the environment that activates the lytic cycle, which causes the virulence portion of its genetic material to activate. This causes it to induce the cell into forming its protein capsid, and then lyses the cell, allowing the virus to leave and infect other cells. When this happens however, the virus often picks up bits of the original cell’s DNA and brings it to the next cell it infects. This is called horizontal gene transfer, and it suggests that a large percentage of microbial adaptations to extreme environments could be from their corresponding viral communities. This doesn’t just apply to our anaerobic microbes either; for example, it has been estimated that about 60% of the psbA genes (needed for photosynthesis) in all marine environments (whose origins could be identified) originally came from phage.

Oh goodness, this is getting long and I don’t want to lose your attention! The Geology and the Chemistry: The environment plays an important role in oil and gas formation. First you need an area that can collect and trap organic material in an area where it will not immediately be degraded. Tectonic movement and accumulation slowly buries the organic matter, and it is heated through a natural thermal gradient. Rule of thumb, the temperature increases by about 25 degrees Celsius for every kilometer you go down, but this does depend on the environment. Once you get to about 75-100 degrees you have a more or less sterile environment and you start losing oxygen and nitrogen from your organic matter as it forms hydrocarbons. The hotter it is, the faster this process goes, but too hot and it breaks apart into gases. New oil is about 5-10 million years old, which eventually makes it back to nearer the surface and can sometimes escape into the water column, where it undergoes physical, biological and chemical degradation.

Well, that’s not quite all I wanted to talk about, but I don’t want to bore you. Now hopefully you have a general background so when I start explaining my research you’ll have a reference point to base your understanding off of. In other news, ALL my free time has been dedicated to applying for summer programs. If you’re interested in getting involved in research it’s so incredibly easy – just Google “REU” or Research Experience for Undergrads. Since I’m feeling very nice today, here you go: http://www.nsf.gov/crssprgm/reu/reu_search.cfm. This is where you can search for REU programs in any area that you’re interested in. The summer is a great time to get started, when you don’t have schoolwork to distract you, plus hello stipend for Fall Quarter books. Get started soon because applications are due February through March, good luck!

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Posted in 2010-2011, EUREKA

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Alex Iteen is a second year student majoring in Biology. He is interested in bioengineering and synthetic biology. He is currently working in Dr. Fygenson's lab on DNA nanotubes.
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David Wallace is a third year student majoring in Biochemistry/Molecular Biology. He is currently working in Professor Weimbs's lab studying the pathogenic mechanisms of Autosomal Dominant Polycystic Kidney Disease (ADPKD).
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