We’re in full on science mode now. We have finished sampling at 3 of out 11 stations. Some of these stations take only a few hours to collect water while others are scheduled to last 26 hours. Whenever we get to the station we start sampling. I was up until 4:30 am and then back up at 8:30 for station 4. The transit to station 5 should take about 7 hours – enough time to finish up, take a shower, eat dinner and take a nap. I’ll be waking up at 10 to sample at station 5 and when we’re done with that, it’s only a 2 hour transit to station 6 which is scheduled to be the 26 hour station. Now, that doesn’t mean we each need to be up for all the sampling, but we do need to be around when our science gets done.
We’ve been working efficiently and are ahead of schedule a bit, which feels good because you never know when something could go wrong and set you back. I spent most of the day trouble-shooting the RNA sampler, which worked well once and then started misbehaving. I think we’ve finally got it working again though, so I’m looking forward to trying it out at the big station tomorrow.
Sampling last night was especially fun because the light from the ship attracted a huge school of flying fish, some small squid, and a decent sized shark, all visible in the water right next to the hull. There was also some bioluminescence flickering on the breaking waves. That kind of made up for the lack of sleep!
We actually did some science today and it was pretty exciting. You can tell how eager everyone is to get started because we were all crowded around the instruments and the computer screens even though this was only a test site. The idea behind a test site is to make sure the gear all works and we have our sampling procedures down before we get to the actual site of interest. If anything had gone wrong with today’s instrument deployments we would have the next 20 hours to make adjustments before we get to the first site within the oxygen minimum zone.
The exciting part of the day for me was that we got to deploy a new device created by my advisor and the cruise’s chief scientist that is designed to filter water and preserve it for RNA at whatever depth you want. The chief scientist had never seen the instrument in person so I was responsible for giving him and his group the run down, and if things go wrong it falls to me (with help, hopefully) to figure out why.
The traditional way this type of sampling has been done is to collect water in what is called a Nisken bottle at your desired depth, bring the water to the surface, filter it, and then preserve it. This method works fine for DNA because the composition of which microbes are present in the water isn’t going to change much in a few hours. However, RNA is probably a very different story. RNA records what a cell is actually doing (what genes it’s using that moment) where as DNA is a record of all the genes an organisms has, regardless of what it’s doing. RNA is much shorter lived and changes much more frequently. It’s entirely possible that we are not getting an accurate picture of what organisms are doing in the water column when we bring them up from depth (changing their temperature, pressure, light exposure oxygen exposure…) and then preserve samples for RNA analysis. Hopefully the instrument we deployed today (nicknamed the PIMPR or prototype in situ microbial preserver of RNA) will allow us to get a more accurate picture of what these organisms are actually doing when we haven’t disturbed them. The trial run went well after a few initial hiccups. Having to troubleshoot an electronic instrument is a new challenge for me, but so far I’m enjoying it!
Tomorrow we start collecting samples – woohoo!
Our second day at sea is approaching its end. Seas are still calm and I remain seasickness-free!
I have unlisted the help of a good friend to receive my posts via email and upload them on my behalf since I can’t seem to access WordPress from the ship. Thanks Roxie! Here is yesterday’s entry:
Not much happened today. I slept through breakfast – which was a bit strange because I was sure I’d wake up when I heard people moving around. I did a bit of reading before lunch. After lunch I pre loaded 300 tubes with preservative in order to have one fewer things to do when we start collecting samples. I also labeled 75 tubes for a different set of samples. I think tomorrow will be another full day of just cruising, and the the evening of the day after we will supposedly hit our practice station. From there it’s about 20 hours to the actual stations where all the fun really starts.
Dinner was pretty awesome: flank steak, crab cakes, and poke. After dinner we were called outside by one of the crew to see a large pod of dolphins, maybe 20 of them, playing at our bow. That was pretty exciting. I also saw a couple of flying fish. I’ve never seen them alive before, and I was surprised how far they can fly!
Tomorrow is our last full transit day. We should make it to out test station by the end of the day Sunday.
I’m writing this from the galley of the R/V New Horizon, somewhere off the coast of northern Mexico. We set sail (figuratively) around 11am after waiting for a last minute FedEx shipment. One group’s gear got stuck in customs and a fairly epic effort was made to round up a minimal amount of supplies from various people at Scripps as well as many of out home institutions, and a family connection in a local pharmaceutical company. I can’t imagine how frustrating it would be to show up for a cruise after months of prep only to find that your gear isn’t there and have to re-think all of your science plans! The delay set us back a day, but we may be able to recoup that on the return by coming in a day later.
So far the seas are surprisingly calm. I guess I am used to the less calm northern Pacific Ocean. I’m hoping that bodes well for my seasickness. So far so good though – no signs yet! After lunch we did a pirate drill, which they apparently only rarely do on this boat, but since we’re headed into Mexican possibly (but not likely) drug smuggler infested waters it was decided that the crew would practice the pirate drill, just in case. What is my role in the case of pirate attack you ask? I play a pivotal role by hiding in a locked room with the other scientists – no complaints here. We also went through the more common man over board drill and other emergency procedures. After the drills the res-techs (two Scripps people whose job it is to help the science team get their work done, and keep us from breaking the ship or ourselves in the process) went through all the rules with us about how to behave on the ship (i.e., don’t piss off the cook!), where we are allowed to be, how to get help if we need it, how to deal with trash (new rules mean that we will be bringing ALL of our trash back with us to San Diego), and more.
Now we steam for about 90 hours before we get to our site. During this time people will be organizing and setting up (although that seems to be mostly done by now), and as a group we will be thinking about how best to use our now even more limited time at our study sites. Due to currents and the additional moves further south moving from site to site, it will take even longer to make the return trip which means we are limited to only about 5 days of science. I hadn’t through of it that way when I was planning so, so I’m now realizing how jam packed that few days will be. I’m looking forward to (hopefully) well organized chaos!
Unfortunately the Internet connection is very slow on board (think 1 dial up connection split among 30 people), so I don’t know how many photos I’ll be able to post. Hopefully the text only posts won’t be a problem though.
We sail early tomorrow morning. I haven’t met everyone yet, but those who I have met seem great. Everyone has the friendly excitement that comes with knowing you are about to share an intense experience that you are eager to get started with.
We leave from San Diego and it will probably take 4-5. Days to get to out first site. I haven’t had that long of a steam out before. It will provide lots of time for organization, planning, and getting to know people. The trip back will be the same length, which means that we really only have about 5 days out thee to collect and process all our samples – yeesh, no pressure! I’ve got lots planned: two different experiments measuring how fast the microbial community is fixing carbon and nitrogen, and collecting lots of different types of samples for DNA and RNA extractions as well as for different types of microscopy, I’m also trying to bring back water (and the microbes living in it) for more experiments back in lab. If I get all this work done it will provide samples to 5 different people, which will make me feel pretty efficient!
After spending the morning at the Mexican consulate getting visas to be in mexican waters, I’m about to check out of the hotel and head to the ship to unpack and start figuring out where everyone is going to get all their work done. It’s going to be cozy – lots of people doing different types of work in a spall space, but I’m sure we’ll make it work. Luckily all 15 of my boxes arrived safely. I have two more coming today, so fingers crossed about that. Seem other groups were not so lucky with items broken, stuck in customs, or just not showing up.
These are the CTDs (conductivity, temperature, and depth) that we will be using to collect the water that is the main object of my research on this trip.
It is strange to be on a research cruise and get 10 hours of sleep… 2 nights in a row! Since the last 3 dives of this cruise belonged to the geologists we have been able to work on other things for the last day or so. I spent most of yesterday talking working on my thesis proposal for my qualifying exam. Te good thing about being at sea with your advisor is that he is a captive audience with minimal distractions. We talked about my project for a few hours yesterday, which was really helpful. After that meeting I spent the rest of the day at my computer. Rocking back and forth (we had a couple of rough days) I tried to turn my proposal into s compelling story. I’m not sure how well I did with that, however.
Today Charles and I started packing up. We get into port tomorrow evening, and our flight is just about 24 hours later, so we won’t have much time. I think we got a good head start though. The sub is in the water scoping out lava flows and collecting rocks. Kinda makes me nostalgic for my geology days. In about an hour the sub will come up, and we will start the steam back into shore. It has all gone very quickly. It’s hard to believe that my qualifying exam is only 6 weeks away!
It’s hard to believe that our science on this cruise is almost over. This morning The sub picked up the last three iSmacs (my mineral samplers) that we had deployed and set out the three that we are going to leave out there. We are hoping that a colleague who will be working in the area in a month or so can pick them up or that we can get back out here next summer to collect them. I hesitate to write this because I don’t want to jinx things before the last 3 are in hand and sampled, but it’s pretty exciting how well things have gone with these samplers so far. Who knows if I will be able to extract DNA from them, but the deployment and collection has been pretty smooth. A couple have gotten broken by the sub arm during deployment, but nothing that I couldn’t fix.
This afternoon we take the final sample with the big instrument (the ESP) and tomorrow the instrument gets pulled, and the remaining couple of dives are not ours, so we will begin packing things and making sure we have all the necessary data files etc.
We have been able to collect lots of different types of samples at the same time or at least in the same area. Between ESP, iSmacs, niskin water samples that get preserved in a variety of ways, sulfide rocks, and tube worm collections we will be able to put together a nice picture of the microbiology of the area with good geochemical data to go alongside. Hopefully this will form a compelling story and translate into a nice paper or two.
It has also been fun to peek over the geologists shoulders. There is a group out here studying lava flows, so I have enjoyed talking with them and seeing how they do their science. The portions of the dives that they have controlled have been fun t watch too, because they go away from the vents and look at the area surrounding the vents that I would probably never see otherwise. Believe it or not, those lava flows are beautiful and very diverse in terms of shape and size of features and general texture.
I have to say that I am feeling scientifically rejuvenated. It’s easy to get discouraged after a year of lab work with out any great successes, but being out here watching the video feed from the sea floor every day gets me excited, once again, about the work I am doing. This is probably a good mindset to be in right before my qualifying exam (scheduled for September 6th).
No dive today. Something happened with the cable getting caught this morning and they had to pull back Doc Rikits. Hopefully they will be able t make the repairs, and we qcan dive tomorrow.
Yesterday was a great tive. We deployed all 9 iSmacs: 6 in one location near the ESP, and 6 right near a chimney called Marshmallow. S nice the dive today was cancelled, there will not be a 42 hour deployment, but that is probably fine. The question is when to collect and which ones to leave out there. As soon as I get the first few back I can start to prepare the last 3.
Yesterday was an exciting dive even though we spent more than 6 hours sitting in one place charging the big instrument that this cruise is focused on. The instrument is called the Environmental Sample Processor (ESP), and is really cool because it does molecular biology that we normally do in lab on the sea floor. The downside is that it takes hours each day to charge, which is a bit boring from the control room side of things.
Anyhow, the dive was exciting because we brought up 3 of my iSmacs.
One of my samplers ready (almost) to go.
Nice clean “ship-shape” lab space, we’ll see how long it stays that way.
We set sail tomorrow, and despite frustrations 24 hours ago, I feel pretty good about things. Charles (aka Dr. C) spent most of the day helping me repair and prepare my samplers for deployment, and I think we are just about good to go. I even had a couple of pictures to show you, but of course I am having Internet issues. I am thankful that I had today to get things organized, and didn’t have to do it while traveling and seasick!