Feb
15

In the run up to the Ocean Sciences meeting next week, I have been exploring the Chilean Seaglider data from the March 2009 deployment in more detail. As far as I know, our Seagliders are the only ones currently in use that have PAR (photosynthetically active radiation) sensors on them, so I wanted to highlight some of those data on my poster. One process that I wanted to look for was daytime fluorescence quenching (DFQ) in the surface waters. Before I get into DFQ, let me back up a bit…

Chlorophyll-a is a pigment used by plants (and algae) during photosynthesis. It is what gives plants their green color. When a chlorophyll molecule has more incoming light than it can effectively shuttle into the process of photosynthesis, it has two ways to get rid of the excess radiation: it can release it as heat, or re-emit the light as fluorescence. Fluorescence by Chlorophyll-a is one thing that we measure with the Seagliders, and is often used as a proxy for plant biomass in the ocean. The first order assumption is: more fluorescence = more chlorophyll pigment = more biomass. However, biology being what it is (inherently complex, and therefore, FUN), there are many factors that can add significant variability in the relationship between fluorescence and pigment concentration (let alone biomass). Some of these may be community composition, light history of the cells (changes in mixed layer depth or stratification, e.g.), nutrient limitation and other stressors.

Now, back to DFQ. When the sun is high during the midday, the amount of incoming solar radiation is often much higher than the amount that phytoplankton cells in the surface waters can effectively process. When this happens, the cells basically throw up their hands (if they had hands), cry uncle (if they had uncles), and start to dissipate the excess energy as heat rather than fluorescence. So, what we would observe in this scenario would be decreased fluorescence during noon hours relative to the amount of chlorophyll pigment that is present, or daytime fluorescence quenching. Profiles of chlorophyll concentration or chlorophyll absorption during this same time period would not show a decrease in the amount of chlorophyll present in the water column, so interpretations of surface fluorescence data have to be carefully considered. This is where the PAR sensor on the Seaglider makes it’s contribution.

Below is a plot that shows the effect of DFQ on the fluorescence signal. I took the Seaglider data from each dive or climb, and median binned the data in ten meter surface bins from 0-10m, 10-20m, 20-30m, and 30-40m. I plotted PAR in black, and Chl-a in green, and plotted both vs. time (day of year) on the x-axis. This is one transect of data.

Section 3 Chl-a and PAR bins

Section 3 Chl-a and PAR bins

You can see that DFQ is quite apparent in the 0-10m and 10-20m bins, but the effect starts to fade and is hardly visible deeper in the water column. Neat, eh?

The next step, which I probably won’t get to before the conference, is to look into where and when DFQ is more pronounced, and relate this variability to the physical environment of the cells. One place to start would be to look at the mixed layer depth in order to estimate the daily integrated PAR that the surface community is getting. It seems obvious, but can I relate a shallower mixed layer depth with higher DFQ using in situ data? That would be pretty exciting! There are caveats, of course. The existence of a mixed layer doesn’t establish that mixing is actually taking place, etc., but the effort is worth making with these unprecedented data…

Aug
26
Filed Under (Chile, gliders, Iquique, MOOMZ, OSU, seagliders, sg158) by shearmar on 26-08-2009
Track line for glider sg158 lauched at the beginning of August

Track line for glider sg158 lauched at the beginning of August

After performing a very nice “butterfly” pattern during the MOOMZ cruise, we sent sg158 offshore to start cross-shelf transects. Shortly after that, we started getting loads of roll retries and even a few roll errors – this means the internal motors were trying to shift the batteries and execute a roll to turn the glider and the motors either did not respond enough or did not respond at all. We panicked a bit a called Fritz at UW. He gently chided us for not digging a little deeper into the log files, and then suggested some glider magic:

Create a pdoscmds.bat file with these 3 lines and let the glider execute it during next phone call:

menu hw/pitch/read
menu hw/roll/read
menu hw/roll/rolls

This ran the glider through a series of tests on the roll mechanism. Things seemed ok, but the problem continued to worsen as we made more and more dives. Eventually, the glider was stuck rolled partially to the starboard side, meaning all dives now executed as a slow clockwise spiral on the way down and counterclockwise spiral on the way up with no real control of heading.

Last 1000 m dive from sg158 stuck rolled to starboard

Last 1000 m dive from sg158 stuck rolled to starboard

Now, this meant sg158 had to be recovered. It wasn’t in imminent danger, but it was way (30+ nautical miles) offshore. Once again, Gadiel Alarcon sprang into action (on a Saturday and Sunday no less), and late on Sunday August 23 sg158 was safely recovered and brought back to Iquique.
On Monday, Laura emailed with Ruben Moraga at UNAP and they got sg158 turned off and stowed away. Now we’ll need to get the gliders shipped back to the US to replace sg157’s batteries and figure out what went wrong with sg158.

Jul
21
Filed Under (Chile, gliders, Ha ha, Iquique, OMZ, seagliders, SG157) by Amanda Whitmire on 21-07-2009

We continued to have communication problems with SG157, so we decided to call on our Chilean colleagues to help with a rescue on July 10th. The Seaglider was close to the coast at the time, so the pilot worked to keep it as close as possible to the port of Iquique despite a current pushing it to the south.

The plan was to have a student, Nadin, fly from Concepcion to Iquique to help with the recovery, since he helped us with the deployments and recoveries back in March. We communicated with our Chilean colleagues mostly via Email, so sometimes things were happening there faster than we could follow. It turns out that before Nadin could get from Concepcion to Iquique, the Chilean Navy was already on sight and recovering our glider! Jack’s words were, “Chilean Navy to the rescue!” We were all surprised that they had gotten involved, but I guess it’s not every day that a misbehaving Seaglider needs to be rescued off of the Chilean coast. We were (are!) very grateful for their assistance, and they did a great job on the recovery. By the time they got the glider back to shore, Nadin was able to get there and shut the glider off with the magnet. All’s well that ends well in the world of Seagliders!

We received this clipping from a Chilean newspaper yesterday (click for bigger)…

Chilean newspaper article on the SG157 recovery

Chilean newspaper article on the SG157 recovery

We’re famous!

Jul
03
Filed Under (Chile, gliders, Iquique, MOOMZ) by shearmar on 03-07-2009

sg157 stopped communicating with the basestation sometime late last Friday (06/26/09). sg157 disappeared for 4 days, and then finally called in Tuesday evening. Anatoli and Justin handled it like pros, and figured out that the glider had happily continued to dive and receive GPS fixes, during it’s seclusion. This means there’s nothing wrong with the antenna and that the antenna is getting far enough out of the water. It also means that there’s nothing mechanically wrong with the glider.

The problem appears to be isolated to the Iridium satellite phone communications.

sg157 has been calling in more consistently since then, but misses a scheduled call in every now and then …

Out plan is to continue to fly sg157 onshore. If we get another big disappearance, then we’ll have to figure out an emergency recovery. If things continue to go OK, then we’ll send Laura out at the beginning of August to put sg158 in before the MOOMZ cruise, and we’ll send Justin out at the end of August to recover sg157.

Jun
11
Filed Under (Chile, gliders, Iquique, MOOMZ, OSU, power, seagliders, SG157) by shearmar on 11-06-2009
Energy usage plot for sg157 since the beginning of the deployment.

Energy usage plot for sg157 since the beginning of the deployment.

We’ve been experimenting with some power saving strategies on sg157 this week. In the plot of energy consumption, you can see that the blue 10V battery is draining a lot faster than the red 24V battery. The 10V battery powers the onboard computer and the scientific sensors. The 24V battery mainly powers the buoyancy pump. So, our energy consumption for science is rapidly outpacing our energy consumption for flying.

How to fix that? Shut off the science sensors! So we tried that starting MondayJun 08 by uploading a one-line science file:

// Science for OSU sg157 and/or sg158 with PAR sensor
/depth  time    sample  gcint
1000    600     0000    600

This file determines that from the surface to 1000 m the sampling interval is 600 seconds (10 minutes), none of the sensors are turned on (0000), and the guidance and control interval (time between steering) is also 600 seconds. This had an immediate affect:

10V battery energy usage by sensor, major consumers are optics and TT8 (computer)

10V battery energy usage by sensor, major consumers are optics and TT8 (computer)

Notice the major drop near dive 540. This is great, it extended our mission duration from end of August to end of October! Nevermind the fact we are no longer collecting data … and this had an added complication of suddenly erratic flying by the glider. With the glider checking in only every 10 minutes to steer and make flying decisions, sg157 would fly past 1000 m, go to deep and rocket up to the surface in what I’m assuming is an emergency manuever.

Anatoli did some experimentning, and now we are flying with shorter gcints and the CT sensor on, consuming only slightly more power than everything off, and having no more erratic dives.

May
21
Filed Under (CDOM, gliders, OMZ) by Amanda Whitmire on 21-05-2009

I spent some time today looking at patterns of CDOM along our glider sections. As an introduction, CDOM is colored dissolved organic matter, also known as “yellow substance,” “gilvin,” and “gelbstoff.” CDOM is a subset of the pool of dissolved organic material in the ocean (and lakes, streams, estuaries, etc.) that is optically active (i.e. has color). CDOM appears yellow or brown to the eye depending on it’s concentration, it absorbs light very strongly in the blue region of the spectrum, and fluoresces in the blue as well. CDOMs optical characteristics enable us to monitor it’s concentration and distribution with a fluorometer on the Seaglider (WET Labs ECO-Puck; CDOM fluorescence excitation/emission at 370/460 nm). CDOM is an important parameter to keep track of for many reasons (see excellent review by P. Coble, Chem. Rev., 2007, 107, 402-418), but for our purposes we are primarily interested in monitoring the variability of sources and sinks of carbon in the OMZ.

Here is a plot of all of the CDOM-depth profiles from our most recent complete section, Line 11, with oxygen concentration in color. The red line is a running average at each depth bin.

CDOM profiles from SG157, Line 11

CDOM profiles from SG157, Line 11

A couple of things pop out right away. CDOM is degraded by sunlight very quickly, which is evident here in the surface data. That’s just a good double-check that the fluorometer is working. Second, there appears to be (maybe?) two discrete pools of CDOM – one associted with phytoplankton production and degredation in the chlorophyll maximum (photic zone, high O2), and one associated with the microbial community in the OMZ (low light/aphotic & hypoxic). However, it is impossible to tell from these data alone if the source of the CDOM in the OMZ is local or if it was derived from far away sources and has been transported with the water mass. Collecting water samples for CDOM spectral absorption  measurements will tell us a great deal about the nature and origin of CDOM in this area. It’s also important to remeber that not all CDOM is fluorescent, so we are actually looking at a sub-pool (the fluorescent bits) of a sub-pool (the colored bits) of the pool of dissolved carbon. However, the CDOM data that we are able to collect autonomously could be very instructive when considered in conjuncion with other variables like chlorophyll, backscattering, and physical indecies of mixing and mass transport.

This is just a first-look at the data, and I’m still trying to get my head around it. Feedback in the comments is encouraged!

May
11
Filed Under (gliders, Iquique, seagliders, SG157) by Amanda Whitmire on 11-05-2009

Hey all – just realized that Seaglider 157 made it’s 400th dive off of Iquique on Saturday (9 May, 2009). Very exciting! The glider is now on it’s usual onshore-offshore route, about 2/3 the way through the seventh ~135 km, cross-shore transect. The eastern south Pacific oxygen minimum zone has never been sampled over these time and space scales, so I hope you all can share some of my enthusiasm for these unprecedented data. Now, if we could just find a research vessel so that we could get out there and do some discrete sampling…

Anyhow – thanks to everyone involved for your continued efforts.

Apr
22
Filed Under (Chile, gliders, Ha ha, SlocumGliders) by Amanda Whitmire on 22-04-2009

Courtesy of our fearless photographer David Reinert, here’s a Slocum glider being launched off of Concepcion, Chile a couple of weeks ago.

Launching a Slocum the Chilean way

Launching a Slocum the Chilean way

Now, that’s a small boat!

Apr
22
Filed Under (Chile, gliders, Iquique, MOOMZ, seagliders, Video) by Amanda Whitmire on 22-04-2009

In this post we share a short video documenting how we launched the gliders in Chile.

Before we get to the video, though, I’d like to extol one of the [major] benefits of using gliders as a tool in Oceanography: they are easy to launch and recover from small vessels. “Traditional” oceanography takes place on large research ships (well over 100 feet long), which is problematic in terms of the costs involved (very expensive) and their limited availability. Launching or retrieving a glider from a small boat is simple and inexpensive, and if we need to get out on the water for an unplanned emergency rescue, small boats are relatively easy to come by. Case in point: this was our small-yet-capable Chilean launch vessel, which belongs to the Universidad de Arturo Prat (UNAP):

R/V Antares

R/V Antares

We launched two gliders and recovered one from this nimble little vessel. While the rest of the research team was stranded on land after our larger research vessel blew an engine, the OSU Glider Research Group was still able to get out there and save the day with gliders (fist bump!).

Okay, on with the video:

Thanks to Laura for sharing her photos and video from the trip!

Apr
19
Filed Under (Chile, energy, gliders, power, seagliders, SG157) by shearmar on 19-04-2009

I’m trying a drastic change in the science file to see if I can make any impact on the energy consumption. Right now the power remaining should get us to end of July, and this may work well for the timing of a MOOMZ cruise, but if the cruise gets delayed further having sg157 last as long as possible will be a priority. Here’s the new science:
// Science for OSU sg157 and/or sg158 with PAR sensor
/depth time sample gcint
50 4 1111 60
150 4 1111 120
250 52 1110 180
600 104 1110 300
1000 104 1100 360