July 17, 2012
Other than take up space…I have responsibilities on the boat. First and foremost, I am in charge of measuring nitrogen fixation from a cyanobacteria (bacteria that photosynthesizes) called Trichodesmium. Why is the nitrogen broken? Well it isn’t! It’s just in a form that most organisms, including us, cannot use. Certain organisms can change nitrogen from its inert form to an unusable form of N2 gas, into ammonium which can be made more easily converted amino acids. (Building blocks for proteins, organisms need them to carry out metabolism and grow.) All nitrogen fixers are prokaryotes; this means they are bacteria and archaea that are for the most part single-celled aka really really small organisms. Perhaps you are thinking, “Eww gross! Bacteria are scary and icky!” This is a common misconception. Actually, most will either not affect you at all or be beneficial! Even crazy is that in and on our own body bacteria cells out number human cells 10 to 1! So we are technically more bacteria then human. Think about it. Without nitrogen fixers, the life on this planet would have a serious shortage of new nitrogen and that would be a huge problem. A small portion of new nitrogen comes from lightning, but we couldn’t wait around for lightning to strike! Most new nitrogen comes from these nitrogen fixers, which makes them pretty important if you like continuing being alive. They are pretty important. So next time you see a bacterium, you should thank it for making life possible…it would appreciate some credit.
So how do you accomplish such a feat? Measuring nitrogen fixation in the middle of ocean? By taking a big net, about a meter across and tow it through the ocean off the back of the boat and collect the Trichodesmium. We’ll call them Tricho for short. Even though these Tricho are bacteria, you can see them with your naked eyes because they form long filaments of many bacteria, linking one after the other. Think saw dust people. This allows me to pick them out of a net tow that concentrates all the organisms that go through it because the net has really tiny holes that let water through but not the Tricho. I then run an assay that tricks them into thinking they are fixing nitrogen but in reality they are just converting an analogous substance that I can easily quantify with a gas chromatograph (or GC). Suckers! I pretty much sit in front of this machine all day and walk back and forth from the incubators. This technique can give us an idea of how active these guys are out here.
Now, my thesis work is a little different. The previous work I was describing is work that I am doing for my advisor. I use a technique called stable isotope probing. You may have heard this before on the Simpsons, Springfield’s baseball team was called the Isotopes. See, nerds are normal people, we watch TV too! Which is one of the only things to do on the ship. These isotopes are a little different and definitely not as funny. They are different forms of an element, like nitrogen, that have different amounts of neutrons. Other than that they are exactly the same. Isotopes with more neutrons are less common, usually only found in nature less than 1% of the time, and these different amounts of neutrons change the element’s masses. We can take advantage of this and identify organisms that are taking up substrates (something used to carry out a particular process) that are labeled “heavy” isotopes (the substrate has the rarer isotope with more neutrons which we call labeled). So I add a substrate that is labeled with heavy isotopes to a water sample and if the organisms can use it, they will take it up and when the reproduce or double they will incorporate it into their DNA. I can then filter the incubation, extract the DNA, and spin it really fast in an ultracentrifuge. This can then separate the heavier DNA with the label from the lighter, unlabled DNA. I then determine the sequence of that heavier DNA. Each organism has a unique DNA sequence and allows me to identify which organisms are actively taking up that substrate. Certain substrates can be linked to certain metabolic processes, so if an organism taking up that substrate, it is most likely participating in that process. It is an elegant way of getting at some really