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
July 16, 2012
If you guys are interested in following us along on our journey to the mouth of the Amazon river, and I know you do, you can look at our ship tracker:
This can give you an up to date position of where we currently are and the route we have taken to get here. You should check it out from time to time and follow us throughout our journey. If you look now you will see the route we took from Barbados and that we are out in some deep open water. Its pretty cool, or at least I think so.
Things are in full swing now so it is going to be harder to make new post but I promise you I am trying. I should have a new one at some time today because we are only coring the seafloor and I don’t do that so keep an eye out.
July 14, 2012
The clearance came through!!! The cruise is happening!!! We left this morning and are almost at the first station. I am just trying to finish setting everything up so I can go to bed. I have to be up at 530 for my net tow. Ill explain more later. The fun is just getting started…
July 13, 2012
So I left something really important out…
As I mentioned before the cruise leaves out of Barbados, heads to some open water sites, than toward the mouth of the Amazon River near Brazil. However there is a catch. What I did not mention is that currently this cruise is only tentative. WHAT??? But you are already there on the boat, I am sure you are all thinking. We first must get clearance into Brazilian waters and getting clearance from any country is not always straightforward. We have actually tried to get this clearance twice before, for each of the last two ANACONDAS cruises, and failed. NSF will only pay for the ship time if we get the clearance, if we don’t, the boat will head back to the U.S. and our cruise will not happen. We are all moving forward as if we are setting sail on Friday. I don’t think it’s affecting anybody really. Some of us speculate that they may let us go out anyway because we have shipped all our equipment here, the boat is already here, and so are we. But that was not the agreement so we will just see…
Tick, Tock….Tick, Tock…
July 12, 2012
What are the elusive and mystical ANACONDAS??!!
Sorry, the answer is not a swarm of mythological creatures that grant wishes to anyone able to find them deep beneath the Amazon River plume, though that would be pretty sweet. Maybe next cruise. ANACONDAS is actually the name of the project we are working on here. It is an interesting acronym that stands for: Amazon iNfluence on the Atlantic: CarbOn export from Nitrogen fixation by DiAtom Symbioses (ANACONDAS). One or two liberties may or may not have been taken with that acronym but cut us some slack, we’re scientists not word…people.
The very broad goal of the ANACONDAS project is to try to understand the influence the Amazon River has on the ocean. The Amazon River is very different from the Tropical Atlantic Ocean it feeds into. Other than the most obvious difference: the river, unlike the ocean, is fresh water, the river is loaded with nutrients (e.g., nitrogen and phosphorous) and organisms that differ from those found in the open ocean. The “open ocean” refers to parts of the ocean where there is no land around, go figure. Land is a source for nutrients, so the open ocean is usually low on nutrients and therefore life, which is a stark contrast to the water flowing out of the river. When these waters mix it allows organisms that can take advantage of this increase in nutrients to grow and outcompete the organisms that are normally found in the open ocean. We want to get a first hand look at this.
Now, getting a little more sciencey, the cruise aims to understand how nitrogen is cycling and in turn, use this information to better understand how the carbon cycle is working. This can give us an idea of the balance between how much carbon is being taken up by photosynthesizing organisms and how much is being respired by organisms. We can then determine whether the Amazon River plume is a source or a sink for CO2 from the atmosphere. By “sink” I mean taking CO2 out of the atmosphere. This is where the DAS of ANACONDAS comes in and DAS ist gut. Sorry about that, just could not resist. DiAtom Symbioses is referring to an interesting relationship between a photosynthetic plankton and nitrogen-fixing bacteria. Though we do not completely understand the complexities of their relationship, we believe that they have some sort of symbiotic association where the bacteria fixes nitrogen and supplies it to the diatom (a small plankton) while the large diatom possibly provides protection from smaller predators that could graze on the tiny bacteria. Isn’t nature just amazing? Sometimes I just can’t believe how beautifully evolution works. Anyway, these larger–now I feel I should qualify the use of this word here. When I use the word “larger” here, I mean that relatively; these diatoms are on the order of micrometers, which are about a million times smaller than a meter. Again something that is so bewildering; such complexity at such a small scale.–Anyway, these “larger” diatoms are made of silica (pretty much like glass), which is somewhat dense, and so with their size and makeup they sink faster than some other plankton. If they pull CO2 from the surface water and use that to fix carbon (something like fixing nitrogen as I discussed in an earlier post) into their biomass and grow, they can then sink out of the surface, bringing that carbon with them where it can be stored for thousands of years. This makes less total carbon in the surface so more must diffuse in from the atmosphere to replace it. This removes CO2 from the atmosphere and makes the area a CO2 sink, which can help mitigate the effects of climate change. Less CO2 in the air, less heat gets trapped, a slight decrease in temperature can occur over time. We will try and collect more data on this area to determine if the Amazon River plume is a source or a sink of carbon.
How do you do all this? You get in a boat and ride down to the mouth of the river. We can than use parameters like salinity (how much salt is in the water) to orient ourselves in and around the plume and roughly determine at a given point how much water is coming from the river and how much is from the ocean in a given area. This gradient can allow us to navigate through the plume and measure what things are like in the more saline low nutrient open ocean and how they change along a gradient as the two water masses mix until you get into the eventual low saline high nutrient river water.
You can get more information about the project if you go to this website:
I do not believe it has been updated in awhile but there is still a lot of background information on the science and some of the people along for the ride. Check it out if you have some time. However, I do not think I am on there so don’t get your hopes up.
Lastly some of the detail about the cruise. It leaves shortly, July 13 out of Barbados and returns to the same port on July 30. So that makes the cruise 17 days. The past two cruises I have been on have been double that, 35 days, so I think this one should be a breeze. Cruises are normally very hectic at first, as you’re trying to set everything up and make sure it all works. That first week usually goes by quickly, then you settle in and just hit a rhythm, and things continue to go by swiftly. But by the end of week 3, I usually hit a wall, realizing that I pretty much have to repeat the same amount of time and work before it is all over and I can step on dry land. Time starts to slow to a halt. On this cruise though, at that point we will already be sitting on the beach in Barbados. 17 days should go by relatively quickly…
Back to work!
July 6, 2012
Welcome to WordPress. This is your first post. Edit or delete it, then start blogging!