July 29, 2012
WE JUST FINISHED THE LAST STATION!!!!!!!! The final station of the cruise is done and we are steaming back to Barbados. There is still a lot of work and clean up that needs to be done but the hard part is over. Everyone is pretty psyched about how things went and emotions are high. Another successful cruise for the books.
Once we get back we have to process a lot of samples and data. This can take a really long time, some times years to get through it all. When you are out here you try and do all you can and take all the samples and data possible because who knows when you or someone else will be back. I have a lot of work ahead of me myself. Collected a lot of samples and data. Next goal is to make sense of it all and figure out what is going on out here. Try and answer some of these questions. Even come up with some new ones.
But for now I am going to relax!!!!
Another milestone is reached. This cruise has definitely been a fruitful one. On the first of the three ANACONDAS cruises (the one that I was not on), tons of DDAs were found. That information, along with previous cruises to the ocean further north of here, lead to the hypothesis I discussed earlier. That the DDAs were helping to draw down CO2 from the atmosphere making the Amazon River plume a net sink and therefore possibly affecting climate change.
Last cruise however we did not see many DDAs and the few times we did there were not many. However we did see lots and lots of Tricho throughout the cruise and they were in areas that you would not normally expect to find them. They tend to like the low nutrient, high salinity open ocean but we found them in the mesohaline (kinda middle of the road for salinity) plume where the nutrients can vary but are usually high. I was able to measure nitrogen fixation and they appeared to be limited by phosphorous because when I added some to my incubations they would fix more compared to Tricho I did not add any phosphorous. This combined with finding them in areas we did not expect was pretty interesting. But not finding DDAs where we thought they would be was perplexing.
This cruise we found lots of Tricho in the open ocean areas and the plume again. They were fixing but did not seem to be limited by phosphorus. An interesting finding though is that they are fixing when there are other sources of nitrogen in the water. Fixing nitrogen costs a lot of energy so it is thought that they would not waste the energy to fix if they did not have to. Pretty cool.
Anyway, we had been looking for them all cruise again with no luck. I was kinda thinking that they might not exist. Then just to top off an incredible cruise we find them at the last station! What luck! They were pretty abundant as well. We found two diatoms, Hemiaulus and Rhizosolenia, with the nitrogen fixing symbiot Richelia inside. I was able to concentrate a water sample and measure a rate of nitrogen fixation. This is the first time I have ever measured nitrogen fixation on DDAs!!!! It was a great day. Now hopefully my stable isotope probing incubations work as well and then I will win twice brother. We will see. For now things just seem great.
July 26, 2012
So I said it would be interesting; I was wrong. It is hell. I am being overly dramatic but it’s really tough. I have to admit that I was not properly prepared for this at all. There is so much mud in this water. Even water from the surface that is nowhere near the bottom is full of sediment. I filter my water that I incubate onto a filter that is 0.2 µm mesh (really really tiny) because I want most of things that are in the water. Plankton and bacteria. Pretty much everything but the viruses. Normally I can filter about 2 liters of coastal water in about one and a half hours. The water near the mouth took forever. I had to change the filters seven times and it took 6 hours!!! Plus, only 600 ml filtered which is about a forth of what I normally can filter. This is discouraging because I need a certain about of DNA to do the stable isotope probing that I discussed earlier. Unless the biomass is really high here I don’t think my methods will work. Higher biomass (more organisms in the water) will mean more DNA is less water. But this in relatively unexplored territory so if any experiment works around this area it would be unique results that would be publishable in a scientific journal so I am going to try my hardest and tough it out. Even though sometimes I just want to quit and get some sleep for once. It’s worth my time and effort because the reward is so high. Plus what else am I going to do…
Same applies for this post. After 3 years of trying we made it. We are at the mouth of the Amazon River and it was spectacular. The water is completely brown, like coffee with some milk in it. Nothing like I have ever seen before, especially in the ocean. But the most amazing part was that the salinity was less than 1 ppt (parts per thousand) at about .05. The average for the ocean is about 35 so that is really low. It is basically fresh water. What makes it even crazier is that we were about 12 miles from the river itself, out in the ocean. Now this may not seem that cool at first but it is difficult for me to wrap my head around. The ocean for miles and miles and miles around us was brown and fresh. The ocean! Goes to show you even further how much influence this river has on the ocean out here. It made the trip even more worth it. Thanks Tish and Doug! Dr. Patricia Yager is co-chief scientist on this cruise (the big cheese) and she is the person that gave me the berth on this cruise and Doug (my advisor) sent me out here.
Anyway, it’s pretty muddy out here. I just filled some of my bottles with “water” (and I am using that term loosely) to start my incubations and there is about an inch of mud sitting on the bottom. Should be interesting trying to filter these samples…
July 22, 2012
Now get your mind out of the gutter! This is a great and sought after day on any cruise. It is the midpoint of the cruise. You are halfway home…kinda. This usually picks up the spirits of the cruising party. This time however, spirits are pretty high already. We are in heavy plume waters now. Even though we are still a hundred miles away from the mouth, you can see so much silt and mud that the water is brown, not blueish greenish brown, but brown. It is amazing! The river has such a huge impact on the areas that it feeds into that it is able to change the entire ocean (well as far as we can see) around us. Just think about that for a second. We are no where near the mouth of the river and the OCEAN is a different color. Can’t wait to see whats next.
Also, I got my first 5 hours of straight sleep last night. Most of the entire cruise! I am feeling much better.
July 20, 2012
WE DID IT!!! This may not seem like a huge feat at first glance but for us it really is. We have been trying for three years now to get samples in Brazilian waters and now it is happening. There is a huge hole in our data set that we can now finally fill. Everyone is in pretty high spirits. We just got done with our first set of sample collection and now we are processing. The last station (We call each part of the ocean that we sample at a station. They are based on GPS coordinates and each station gets its own number.) was an open ocean, blue water station (high salinity with not a lot of life in it) and now we are heading back into the plume. Soon we will start zigzagging in and out of the plume until we get the mouth! I am pretty excited!!!! Then we will cross the equator. More about that later…
Also, I feel a little bit better. Still sick though.
July 19, 2012
I usually have trouble sleeping. I am a very light sleeper and I can only go to bed when I am really tired. Can’t just lay down and go to sleep because I have to get early; can’t nap. I don’t understand how other people can do it. So when I go out to sea I have to get up around sunrise because the Tricho I talked about earlier get up around then and they will not wait. Everyone else that gets up with me for the net tow usually just goes to bed early the night before so they can be up and ready to go. I, for some reason or another, do not have this luxury. I try to go to bed, don’t get me wrong. I will lay there and lay there and lay there. Then my mind starts racing, Did I set everything up? Did I remember everything? I start thinking that even though I could not sleep on the last cruise in the beginning, this one will be different. Then I start pleading with myself. Listen brain, I don’t like you and you don’t like me. We have to get up at 430 a.m. no matter what time we go to bed so lets just do it. This seldom works. My brain does not listen. I toss and turn. Sometimes because I am not comfortable, other times because the boat is rocking and rolling. I try not to look at the clock anymore, that just makes me sad to know how little sleep I am actually going to get. Maybe I should have laid down earlier, I never do though. I get caught up in preparation, double checking things, and the casual conversation. Maybe one last glimpse of land; won’t see that for awhile. Then acceptance. It is happening again. Almost no sleep the first night. Things are starting off badly. You need to be alert on the first day. The boat is rocking back and forth and you are not used to it. Things always go wrong somehow during the first day of sampling. Here I am again, laying in the dark, hours before I have to get up thinking, here we go again.
This usually continues for at least another night. I am used to it by now. The way I deal with it is to run myself ragged. Work hard all day. The little amount of sleep the night before plus a full days work may do the trick. I’ll be so tired tonight I will have to sleep. Usually works. This time it has not. The first three nights I barely slept at all. I was taking a couple hours to fall asleep and then I would just keep waking up. I don’t think I slept for more than four hours any of those nights. It was not fun. I got something from another scientist to help me sleep and even that did not work completely. Still took awhile to fall asleep but when I did I slept through the night. I was beautiful but still not enough.
Another scientist was sick. And now I am. Sickness spread rapidly on a boat. You are always at least 270 feet from another person. I have a sore throat, I’m all stuffed up, my head and sinuses feel like there is a lot of pressure building up, plus I am a little groggy. But I still need and want to work. We only get a few chances like this. This cruise can never be repeated. The waters are constantly changing. This is a short cruise; only 17 days. And at $30,000 a day for ship time, I better give it my all. Plus, I do want to graduate one day. Anyway, enough complaining. I have to go to bed. Not sure when the next post will be because I have to try to sleep more and there is always work to do. There goes what little free time I have. I’m complaining again. Goodnight.
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…