Not the ending we wanted

I’ve been quiet on the blog for a few days, mainly because we’ve been busy and because I was feeling like I was running out of things to write about.  I’ve started two blog posts but haven’t completed them, but suddenly there seems to be something to say.  At the end of most cruises this summer I’ve returned home and sat on my couch to write a quick sum up of what we’ve done. Right now I’m at home digesting the last 24 hours, because you see, we were scheduled to be doing net tows right now, with our MOCNESS, Tucker Trawl, and Mid-Water trawl to sample for zooplankton, jellyfish, and fish. Unfortunately the ship lost one of it’s drives, and we were forced to return to the dock for safety reasons. It happened when we were about to weigh anchor and begin the trawling and towing, but the drive would not come on.  The captain and chief engineer spend about 3-4 hours finding, diagnosing, and trying to repair the down system, but alas you can’t carry a spare for everything and it appeared that a transformer deep in the belly of the ship blew out – very unexpected and completely unpredictable. Coming home, though painful from a science perspective was prudent and wise. The most unsettling part is that we just kind of packed up with no sense of completion; people were standing by, literally ready to deploy the nets as soon as they got the go-ahead.  Oh well, these things happen, and there is really nothing to do about it. Plus it’s been a long, data-rich summer so it is not like we don’t have plenty to do. In my newly found day at home I’ll be finishing up a few more blog posts that will go up later this week, just to finish off this summer of cruising. And of course, it’s never too early to get ready for next year’s field season – 3 trips on the RV Sharp in May, July, and September to sort out the story of plankton, hypoxia, and the rest of the food web.  Stay tuned!

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The littlest of the little plankton animals

One of the goals of this project in the Chesapeake is to identify the links the in the foodweb out here, and how those links are affected by the presence of low oxygen water, otherwise known as hypoxia. In previous posts I’ve written a bit about jellyfish and my favorite plankton, the copepods (though I could go on and on and on about copepods). But there are some zooplankton that are even smaller – the microzooplankton. This is a group primarily defined by size – smaller than .2 mm in length. Since they are zooplankton we know they eat other organisms (in contrast to phytoplankton, which are plant plankton and use the sun’s energy and nutrients in the sea for food). Some microzooplankton are multicellular while others are single-celled. The microzooplankton are an incredibly diverse and important part of the aquatic ecosystem, and they are fed on by tiny fish, other microzooplankton, and larger zooplankton (including the ubiquitous copepods). One of our collaborators on the ship is a world expert in microzooplankton and had a lot of fun taking pictures through the microscope the last few days to see what was there. I’ve selected a few of my favorites and put them in the slideshow below, with limited commentary by me. Hopefully later I’ll have time to update this or post some more commentary on the microzooplankton, but for now enjoy the pictures, they are certainly striking.  Oh, and I’ve mixed a few phytoplankton shots in as well, since they’re pretty photogenic too.

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The retreat (of hypoxia, not science).

We’ve been in the Chesapeake Bay for 36 hours now, and sampling for about 30 of those hours, so it’s probably time to check in. So far we’ve completed a Scanfish survey, 6 CTD casts and a few net tows. The weather yesterday was spectacular – flat calm and sunny with fish jumping all around the boat during the transit from the Bay Bridge to Rappahannock Shoals. Right around the time the night watch came on the wind picked up a bit and reached 25 knot gusts.  Not unworkable conditions, but not great, and we had to shut down some of our Z-traps this morning because the instruments don’t work well in high wind and current conditions. Not to fear, we’ve been keeping busy with CTD casts. In many parts of the ocean there are too few zooplankton to catch them in the bottles on the CTD (called Niskin bottles), but here in the Chesapeake there are so many animals in the water we can capture them quantitatively using the CTD.  It’s not ideal, the CTD samples a smaller volume of water than the nets, but it is also less prone to weather related problems like the Z-traps.

But I digress. Here I am talking about the weather problems when  I have data to show, and a comparison to discuss.

The two plots above show the Scanfish data, processed and averaged on the left, and the raw data on the right. I put these up to show how our processing routines can affect how the data is visualized.  It’s important to note here that we’re not changing the data – it’s all there, but when we process it we reduce the total number of data points to make it easier to understand and simpler for the programs to plot. The raw data plots use 57874 individual points of data, for each variable we plot.  The processed ones compress that to 6357 data points. That’s 11% of the previous data, which makes it much easier to deal with. In the grand schemed of things we don’t take nearly as much data as in some disciplines, but it still is easier for the computer to deal with fewer data points, when every data point has a number of values associated with it: Latitude, Longitude, Depth, and the variable value (dissolved oxygen, fluorescence, temperature, salinity, etc.). The other thing to note is that the overall patterns show up in both plots: hypoxic bottom water at the northern end of the transect, high salinity in the southern end, and temperature inversions (higher temps) down deep on all transects.

Now, the title is retreat.  If you were to compare this to the previous transects we did in August and May, you will see this is more similar to May, with oxic water in the southern end of the transect all the way to the bottom.  This is what we might expect, as the bay starts to mix up with the onset of autumn storms that churn the bay. I’m not entirely sure about the timing of this mixing event compared to other years, but it’s worth looking at. I’ll have more to say about the data later, but now I’m due on deck to try some Z-Traps. The wind is laying down and I think we can get some in before lunch (which is teriyaki/orange chicken salad).

Speaking of lunch, I’m trying to convince the cook to contribute a guest blog post. Help me out by commenting that you think that’s a good idea so I can print out the comments and post them in the galley. It could be interesting to get the perspective of the ships cook, and I can vouch for him being a good guy with fun stories and dry wit. You don’t want to hear only from the planktoneer for the next few days?

Update: I uploaded new graphics. It’s the same data but I cleaned them up slightly and have the transects in the same orientation now.  Other than that, they are exactly the same but it should be easier to compare them.
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An episode in which a word cloud is created, for no good reason. word cloud from RSS word cloud generated from our blog RSS feed.

I was turned on to when a colleague used it as  the opening slide of a presentation. Since then I’ve used it to create word clouds from various documents and papers I’ve written, mostly for fun, but it does give you an idea of the frequency of words used in a given document. There is a feature to create a cloud from a blog feed, and that’s what you see on the right. Again, this is just for fun, and I really should be doing something else, but I was curious what we were writing about, and it’s mildly surprising.  Enjoy, and stay tuned for more tales from the mighty Choptank. We sail at midnight and should have gear in the water by dawn.

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Once more for good measure

It’s been almost two weeks since we were last out on a boat so it must be time again!  On Monday we’ll be loading the RV Hugh R. Sharp for our last trip into the Chesapeake Bay to look at hypoxia this year. With the two Gulf of Mexico cruises this year on top of our two cruises earlier, not to mention the LiDZ cruise in July, it’s been an awfully busy summer, so we haven’t really had a chance to process, let alone digest, the data from earlier this summer. That’s what we’ll do this winter.

The idea behind having 3 cruises is to bracket the hypoxic period in the bay. That is, we are trying to sample the bay during the set-up, maintenance, and break-up of the bottom-water hypoxia. It turns out that so far I think we hit the timing pretty well.  In May we saw some hypoixa in the northern portions of our samples area, but much less at the south. In July and August (during the LiDZ and DeZoZoo cruises, respectively) we saw well established hypoxia and anoxia, as well as lots of jellyfish. This month we are expecting to see less hypoxia and anoxia throughout the region, particularly in the south where the breakdown in hypoxia generally begins.

Stay tuned for more posts from the Bay!

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Another one for the books

We’re all at the airport now, awaiting our flights back to Oregon, Maryland, and Florida. There is a van on its way back to Michigan with a freezer full of fish samples from the trawl. The shipping company will be picking up our stuff from the LUMCON docks today or tomorrow and we should have it back in our respective labs sometime early next week.

2010 RAPID Scanfish data

All preliminary Scanfish data from the 2010 RAPID NGOMEX project.

Despite some setbacks, we had an overwhelmingly successful cruise.  Early on it was unclear if we would be able to get all of our transects in, due to the weather and the simple fact that we had an ambitious plan, but in the end, we dropped one at the far eastern end. On the right is the final plot of our preliminary data showing all of our transects.

In some ways we had a dual purpose on this cruise. We have done quite a bit of work on the hypoxic “Dead Zone” in the Gulf, and its impacts on fish and zooplankton, so we continued that work, which was originally funded by NOAA (CSCOR office). But our intent was really to examine that region with respect to the oil spill. We did not see any overt visible oil anywhere, but there were some interesting patterns in the CDOM sensor that we will have to tease out to see if there is a hint of oil anywhere. We have some samples for chemical analysis that will be run in the coming weeks and months too, which will give a more definitive answer to the question of whether or not there was oil in our sampling area.

Oil definitely made it into the bays and marshes near where we were sampling, and in Cocodrie, LA we saw some of the impacts of the spill. Marinas where fishing boats were docked had controlled access, and restaurants were closed to the public because they were feeding BP workers and contractors. There were shrimp boats bedecked with oil booms where there were likely nets just a few months ago. But that’s all anecdotal, and the full story will continue to emerge as our data is processed and the data from other researchers in the Gulf region work up their samples.

One thing I always try to impart to grad students is that science is really about stories. What we do means nothing unless it gets out for people to understand and advance it. These stories take various forms, through science writing, peer-reviewed articles, blogs, and presentations. I hope this blog provided a little insight into what we do, and how and why we do it. If it was enjoyable too, well that’s just grand. I’ll be slowing down on the entries in the coming days and weeks, until our next trip to the Chesapeake, but I’m having fun doing this and I hope those who are reading it are having fun too.

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Revised TS Plot

Whoops, the TS plot I put up the other day (here) was completely wrong, but I’ve fixed it in the previous post and put it again here. Enjoy!

TS plot

Revised temperature salinity plot, with correct pressure contours.

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The home stretch

It’s about 5 am central time, we’re on our last transect of this cruise, Neil Young is ‘Rockin’ in the Free World’, and the Late-Night watch is feeling contemplative. As we turned the corner and deployed the CTD for our last transect, the seas laid down to a gentle roll for the final push. The data are still coming in, and we’re continuing to see some interesting patterns in the oxygen and CDOM – multiple layers of low oxygen that correspond to the fluorescence signals. The Mini-OPC is cranking along, churning out plankton patterns that also seem to have some correspondence with the physical features, but the details will have to wait for the post-cruise processing on dry land. Our water-catchers, who have been sampling the smallest organisms, including bacteria and micro-plankton, have almost exhausted their supply of sample vials, just in the nick of time. Upper trophic level sampling – meaning fish – has taken a break due to bad weather that interfered with the acoustic signals used to identify fish targets in the water column. The companion vessel that was shadowing us and trawling for fish had headed for home after filling their freezer and suffering through a long night of rough seas.

That’s where we’re at, but the work is not done yet. We’ll finish up the transect after day break, secure the gear on deck and begin our transit home. On the way back to Cocodrie, LA, we’ll start to pack up the labs and prepare our stuff for shipment back to Corvallis, OR, Cambridge, MD, Akron, OH, Dauphin Island, AL, Baton Rouge, LA, and Ann Arbor, MI. Once we hit the protection of Terrebonne Bay, we’ll have to calibrate the fish acoustics gear. This entails dangling two different tungsten carbide spheres from a fishing rod as standard targets for the acoustics instruments. In other words, the metal balls act as fake fish with known size and weight. After running the instrument with the simulated fish hanging below it, the operator can go back through the collected data and determine the density of fish at any given time and depth.

All in all it has been quite an eventful cruise. The OPC has been rebuilt twice and replaced once. The TAPS (a high frequency acoustic instrument used to measure zooplankton abundance) was fixed on day one as well. The 15 year old Scanfish tow cable, tired and frayed after so many years of service, had to be mended. The fisheries acoustics on the other hand, was brand-spanking new at the beginning of the cruise and had a successful shakedown after working out some kinks on the first couple of days. One other casualty, besides the OPC which is still here, is the ship’s gaff, which was lost at sea while retrieving the Scanfish in rough weather. ‘Twas a good gaff too, and will be sorely missed.

Much of our success would not have been possible without the experience and expertise of the RV Pelican crew. They have had a very busy summer, thanks in large part to the flurry of activity around the oil spill, but were nonetheless always ready to make sure the science happened. And we were well fed. Very well fed. Some highlights included sushi (!), carrot cake, tiramisu, eggs benedict, egg rolls, gumbo, and various baked goods, all homemade. Oscar Wilde once said something like, ‘The only difference between going to sea and prison is the added risk of drowning’, but I think the food probably elevates research cruising even more.

Speaking of food, it’s almost breakfast time. I wonder what we’ll have this morning?


Some content in this post provided by a ghost writer who shall remain nameless.
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Bottom and midwater hypoxia shows up

Scanfish data from transects Q, W, K, J, I, H, G, F, E, and D

Scanfish data from ten different transects.

Here’s the most recent plot of our Scanfish transects, showing 1) how far east we’ve come on the cruise, and 2) the presence of both bottom and mid-water hypoxia.

The second plot shows a blow up of only the last two transects we did with the Scanfish, in which you can see the structure in the oxygen signal. Note the ‘blob’ of red water on the eastern transect that looks like it is coming up off the bottom.  It very wall may be doing that – upwelling and moving offshore. I’m not sure about the mechanism, but I can imagine the impacts that might have on the animal swimming around. Now, the ones above that blob may have a false bottom, concentrating them in the surface layers, while ones below the blob and above the bottom water hypoxia have a false ceiling. Of course the actual implications are not known yet, but it is one of those questions I’m particularly interested in – how do the animals respond with complicated water column properties like this?

Scanfish E & D transects

Scanfish data from transects E & D

Of course you also have to know how they respond when the water column looks boring – meaning very little structure, and so the interesting part comes from comparing all these different transects, and years of data to see where the differences are.


Update on our progress: We are now sailing southwest along the “C” line. This line has been sampled for a long time and has quite a history of oceanographic data collection. In fact, our group has published data from this line in at least 3 publications. There is actually a mooring at station C6 on this line, and if the internet connection were a bit better I’d put a link up, but right now it’s not terribly strong and I’m just trying to get this off. But things are going well, considering the setbacks and the frantic set-up for this “RAPID” grant. We have not seen oil visibly anywhere, but we are taking samples and will be analyzing some of the electronic data to determine if there is a signal from it anywhere in our sampling area.  I should be able to get a couple more posts up in the coming days before returning to life on shore.

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Still here, still collecting data.

I’ve been quiet for a few days, mainly because of equipment problems that have kept me busy, but we also encountered some inclement weather last night that was not conducive to sitting at a computer. The equipment problems have been continuing with the Scanfish OPC, so we took a very drastic move of trying to rig up a different instrument onto the Scanfish – a mini-OPC. This is exactly the same technology, but in a smaller package. It’s a newer piece of gear – 10 vs. 15 years old, and has usually been mounted on a different towing package called an Acrobat.  The Acrobat is smaller and has fewer bells and whistles than the Scanfish, namely meaning it doesn’t ‘fly’ itself like the Scanfish does. We bring the Acrobat out just incase we have problems with the Scanfish – as my advisor used to say, when you go to sea you bring one of everything for you, and one for Davy Jones.

In this instance, we were able to take the mini-OPC off the Acrobat, and with the help of the ship’s engineers and technicians, we got it mounted onto the Scanfish.  The engineers and tech actually scoured the ships nooks and crannies to fine a piece of aluminum that could be drilled out to accommodate mounting on the Scanfish and attachment to the mini-OPC. Then we had to make a cable to plug the mini-OPC into the Scanfish. Fortunately, this was foreseen before we lit out for the bayou, and one of the Scanfish technicians ordered some spare ‘pig tails’, which are just pieces of wire with the proper moulded fittings on them. We took an old cable that had the proper fitting on the other end, cut it, and made an underwater splice with the pigtail and the old cable. This of course required us to make sure we had the correct wires connected. Probably the most nerve-wracking part for the planktoneer, who actually made the splice. I learned how to do this watching some of my mentors who resurrected failing equipment on some of my earliest cruises. There are a lot of different ideas about how to do this, and having only done it once before on my own, I was a bit anxious, and probably went overkill with the splicing tape, ScotchKote, and heat-shrink tubing, but so far so good.  It’s not a particularly ‘supple’ splice, meaning it’s pretty rigid because I layered so much material, but it’s watertight so far and fits in the Scanfish body, which is all that really matters. Here’s a picture of our newly mounted mini-OPC on the Scanfish, and stay tuned for a data update, once I get the stuff analyzed.

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