Wednesday, July 9, 2014

Glass squid video

This is a short video of a glass squid that was brought up in a MOCNESS tow from the deepest net, 800-1000 meters, on 2 September 2012 in the NE Pacific at station 7 (47.02172N  144.61145W).  It got a bit damaged during the slow ride to the surface but was still alive.  Notice the huge eyes, necessary for gathering light at great depths where it's pitch black.


Glass Squid in aquarium on board the RV/New Horizon

Wednesday, September 19, 2012

Cruise Complete!

Gareth here. We arrived today in Port Hueneme, California, just north of LA. The cruise was an enormous success. We managed to survey a total of 34 stations, out of a planned 31! The success of the cruise wouldn't have been possible without the outstanding efforts of Captain Ian Lawrence and the New Horizon's crew, as well as our Scripps Institution of Oceanography Resident Technicians Meghan Donohue and John Calderwood (and Dan Schuller for Leg I), and we are very appreciative of their efforts.

Wire and plastic cages in the van [Photo: P. Wiebe]
Installing the VPR into the van [Photo: P. Wiebe]

After a few days of packing while in transit, our gear will soon be en route for Woods Hole: a truck picked up our storage van, our ethanol-preserved samples are traveling via refrigerated truck, some frozen samples are headed via cryo-pack, and some seawater samples are being driven up to Santa Barbara for nutrient analysis. The science party will soon be dispersing, heading to their various homes.

From left to right: Gareth Lawson, Peter Wiebe, Taylor Crockford, Liza Roger, Amy Maas, Leo Blanco Bercial, Nancy Copley, Aleck Wang, Nick Tuttle, Katherine Hoering, Sophie Chu, Alex Bergan, Tom Bolmer, Elliott Roberts, Meghan Donohue, Kelly Knorr. [Photo: John Calderwood]

We all feel an enormous sense of accomplishment and I am very proud of our team. A few numbers to put the magnitude of this project in perspective:

Distance we traveled: 5269 nautical miles (6063 conventional miles)
Amount of fuel we burned: 40,476 gallons
Number of days we spent at sea: 34 days
Approximate cost of that shiptime: Somewhere around $800,000
Number of blog hits: 5,348

I'll sign off for now with a very nice movie Liza Roger made of a Cavolinia uncinata. This pteropod was about 1 1/2 cm long. You can see by how it moves why they're called sea butterflies, and hopefully can see why we find these animals so charismatic.

Tune in again soon for our next field effort!


Monday, September 17, 2012

SEA Alumni are Everywhere!

On a research vessel you are bound to get scientists, crew, engineers, and technicians from all over the world on a cruise.  There is this special subset of people who sometimes come out on our research vessels, SEA Alumni.  SEA, Sea Education Association, is a unique study abroad program operating since 1971 that combines oceanography and traditional tall ships sailing (think of square rig or pirate ships).  It is still rare to get more than one SEA alumnus on a single cruise.   Gareth and Peter, however, put together an impressive science party for this pteropod study.  We have not one…not two…not three, but FOUR SEA alumni on this cruise.   We comprise both the old and new alumni.  We represent the following classes Westward 28, Westward 178, and Corwith Cramer 223.

Left to Right: Meghan Donohue (W178), Tom (W28), Katherine Hoering (C223), and Nick Tuttle (C223) on the bow of R/V New Horizon owned by Scripps Institution of Oceanography. [Photo: P. Wiebe]
Once you've sailed with SEA you can never take the sea out of us. Katherine, Nick, and Tom all work for WHOI. Meghan works for SIO. The four of us share a very special bond allowing us to instantly trust each other's knowledge and capabilities both on deck and in the lab. For one we all know how to tie a bowline behind our back. Can you?

Thanks SEA for making us lifelong oceanographers and sailors.

- Meghan Donohue

Sunday, September 16, 2012

Pteropods and the Arts II

Gareth here. Dedicated followers of this blog will recall that last year during the first cruise of our Ocean Acidification and Pteropods Study we had just started a collaboration with sculptor Cornelia Kubler Kavanagh. Earlier this year Cornelia's show, The Pteropod Project: charismatic microfauna opened at the Blue Mountain Gallery in NYC. Cornelia carved some of our favorite shelled (thecosome) pteropods, Limacina helicina and Limacina retroversa, as well as the predatory naked (gymnosome) pteropod Clione limacina, which feeds exclusively on its shelled cousins. Cornelia's pieces show via her medium of sculpture how she imagines these animals might respond to the more acidic conditions of the future ocean. This is exactly what we're doing via our project, only through the 'medium' of science. For the show, our group contributed photographs, text, and some 'specimen boards' of actual pteropod shells, to complement the artwork and provide context.

Below are some photographs of the opening reception, the sculptures, and the animals that inspired them. Hopefully you find these animals as charismatic as Cornelia and we do!

Cornelia's Limacina helicina

Cornelia's Limacina retroversa
The Pteropod Project at Blue Mountain Gallery [Photo: D. Allison]
Cornelia's Limacina retroversa installed in Blue Mountain Gallery [Photo: D. Allison]
Opening reception. Left to right: Nicole Smith, Gareth Lawson, Nancy Copley, Cornelia Kavanagh, Unknown gallery visitor. [Photo: R. Schmitt]
Opening reception, Clione limacina in foreground [Photo: R. Schmitt]
One of the specimen boards (with magnifying glass) our group provided for the show [Photo: G. Lawson]
Limacina helicina sampled during our cruise [Photo: L. Roger
Clione limacina sampled during our cruise [Photo: L. Roger]

Saturday, September 15, 2012

Where Do the Data Go?

Oceanographers normally collect large amounts of data in the course of the work at sea. In the background on most academic research vessels are the sensors deployed to measure meteorological conditions (wind speed and direction, air temperature and barometric pressure, humidity and precipitation, and long and short wave solar radiation) and sea surface conditions (seawater temperature, salinity, and fluorescence) continuously as the ship moves along the trackline from the time it leaves port to when it returns.

The New Horizon's bridge and above it the meteorological sensors. Note the two anemometers on either side, presently measuring winds of 19 knots and out of a direction of 318 degrees relative to the vessel. After correcting for the ship's speed and heading, this corresponds to a true wind speed of 14 knots out of 21 degrees (i.e., just east of north) [Photo: G. Lawson]

On our cruise, additional data are collected continuously by acoustic transducers attached to the hull of the ship to measure backscattering at various frequencies (an indicator of plankton and nekton living in the water column). A hose mounted on the bow pulls in air to measure the partial pressure of CO2 (pCO2) and the water from the uncontaminated seawater line is used to measure pCO2, Dissolved Inorganic Carbon (DIC), and pH continuously. At stations, more data are collected by the instruments deployed over the side of the ship.  The CTD/rosette with the Video Plankton Recorder attached deployed to 1000 m, or the CTD/rosette deployed to 3000 m collects pressure, temperature, salinity, fluorescence, oxygen, and light transmission data, and hundreds of Gigabytes of video pictures of plankton. The MOCNESS towed to 1000 m, measures pressure, temperature, and salinity while collecting zooplankton in 8 depth strata between 1000 m and the surface on the up-portion of the tow, and the HammarHead towed body collects broad-band acoustics data as well as pressure, temperature, salinity, and fluorescence at selected depths. The Reeve Net, used to collect animals for live work and other experimental purposes, also has a time-depth recorder to provide a record of the tow.

In the lab on the ship more experimental data are generated in the analysis of the water samples from the Niskin bottles on the rosette that go to depth open and are closed at specific depths on the way back to the surface. These include pH, alkalinity, nutrients (phosphorus, nitrate, nitrite), pCO2, DIC, and Dissolved Organic Carbon (DOC).  Furthermore, on board, there are the data being generated from physiological, morphological, and genetic studies being conducted on the pteropods. In order to keep track of all of the data being collected, an electronic event log (E-Log) is kept that records the beginning and end of every over the side deployment of the instruments including the instrument name,  time, ship position, depth of the cast, water depth, station number, transect number, and person responsible. On this cruise we have an IPad that can be taken around the ship to where events are happening and used to log the event via a wireless connection to the main event log server. The total amount of data can be in the 100’s of megabytes to a few terabytes, by the time the cruise ends. So what happens to all of these data sets at the end of the cruise and some which are not produced until samples get back to the laboratory for further analyses?

The electronic event logger. This is a web browser-based application running from a server on the ship that can be accessed by any computer on the ship's network. We use it to keep track of when and where each event (e.g., instrument deployments, the ship arriving on station, etc) occurs. This is key to later data analysis.

Gareth Lawson using the IPad to enter a CTD recovery into the E-Log [Photo: P. Wiebe]

The answer is that the research funds come with a requirement for data sharing.  Since this cruise has been funded by the biological oceanography section at the National Science Foundation (NSF), the data must be submitted to an official data repository and made publically available within a two year time period or sooner if possible. The repository these data will be submitted to is the Biological and Chemical Oceanography Data Management Office ( located in Woods Hole, MA. The BCO-DMO has a mandate to serve principal investigators funded by the NSF Geosciences Directorate (GEO), Division of Ocean Sciences (OCE) Biological and Chemical Oceanography Programs, and Office of Polar Programs (OPP) Antarctic Sciences (ANT) Organisms & Ecosystems Program. The BCO-DMO manages a repository where marine biogeochemical and ecological data and information developed in the course of scientific research can easily be stored, protected, and disseminated on short and intermediate time-frames. Ultimately the data will be sent to permanent archives like the National Oceanographic Data Center.

The data (and metadata) in the BCO-DMO repository are readily available to anyone with a computer and web browser via the internet. They are available either in a text-based format or in a graphical map-server form.  Anyone reading this blog can go to the BCO-DMO web site and locate data from this cruise (once they are submitted) or other cruises.  It is important to remember that using other peoples data requires informing them if you intend to use them for some reason.

Researcher's End Game

When all is said and done
And we are long since gone
What will remain to be distributed
Are the data we contributed
With digital identifiers assigned
And our names clearly defined
Our work will be on-line
Until the end-of-time.
- PHW 16 June 2008

- Peter Wiebe

Pteropod Assemblages

In all ecosystems, whether terrestrial or marine, species combine to form assemblages. These assemblages are often specific to various environmental conditions at work in that ecosystem and so as you cross from one ecosystem to another the species assemblage changes. Although the ocean might seem like one big ecosystem made of water, this conception is wrong. The ocean is made of many different ecosystems, each characterized by different parameters such as seawater temperature, salinity, currents...even the exchanges with the atmosphere that occur at the surface can affect the species assemblages.

I described in a previous post how I am out here preserving pteropods for my dissertation work on the structure of pteropod shells. As a preliminary analysis, I decided to plot the number of shells of each species I have preserved so far to see if any assemblages are obvious along the geographical gradient of the first three survey lines (aka transects) we have sailed along. I quickly plotted the numbers of shells sampled at eight 'test stations' along our survey transect 0 (the first run from Newport to the study region) and transect 3 (the second transit out from Newport).
Map showing sea surface temperature (in color) and the location of our sampling stations. The regularly-spaced stations extending from 50N 150W to 35N 135W are our main study region. We also conducted a series of 'test' stations during our transit to the study region, which are the less regularly-spaced stations that together make a line from the survey start to Newport, Oregon, our port of departure.

At each of these stations we sampled with the Reeve net, and caught a few different pteropod species, including Limacina helicina helicina forma pacifica, Limacina helicina helicina forma acuta, Clio pyramidata and one more species labelled below 'AB'. To help you decode this, in Limacina helicina helicina forma pacifica, Limacina is the genus, helicina is the species, the second helicina indicates the sub-species, and pacifica denotes the forma. Formae describe sub-groups within a species where the individuals can be subdivided morphologically and geographically into several related groups that overlap and interbreed.

The morphological difference between pacifica and acuta are easily seen in the pictures below. Acuta is high-whorled, with distinct regular striations on each whorl; pacifica is low-whorled, without striations. These two formae have been found to cross-breed. In the graphs below I've grouped under the label 'AB' all the Limacina helicina helicina shells that do not fit in the forma pacifica or acuta. 'AB' individuals can be a combination of any of the features of acuta or pacifica: low-whorled with regular strations/with irregular striations, high-whorled without stration/with irregular strations.

Forma acuta
Forma pacifica

Clio pyramidata has a totally different shell morphology.

Clio pyramidata shell
So, here are the graphs...
Can you see a pattern? Here are a few hints:
-Compare test stations 05 and 02
-Compare test stations 06 and 03
-Compare test stations 07 and 04

If you look back at the map you can see the location of each station. Based on the changes in the composition (%) of the catch we can draw a range for each of the three species plotted here, along a geographical gradient going from southeast to northwest. Here is a new map to help you visualize where we crossed into the range of each species.

Map showing the relative abundance of the different pteropod species sampled.

We entered the range of Clio pyramidata near test stations 04 and 07. The pacifica forma of Limacina helicina helicina was present at test stations 02, 05, 03 and 06, with highest abundance at 06 and lowest at 03. This indicates that while we were deep inside its range at T06 we were only on the edge of it at T03. A very sharp change in the abundance could be explained by environmental parameters (seawater temperature, salinity etc).

Test station 08 was totally within the range of Limacina helicina helicina forma acuta but no other species or formae were seen there. With acuta being present at every test station we can presume its geographical range is much bigger than that of the other species or formae presented here. From the colors in the background of the map (representing the sea surface temperature) we can also see this forma prefers colder temperatures. 

Well, I hope this has given you a better idea of what we are seeing here. These analyses are very preliminary but already interesting. We hope the MOCNESS depth-stratified samples will help us further determine the species range with regards to geography, bathymetry, and seawater chemistry. Stay tuned!

That's all folks!

- Liza Roger

Friday, September 14, 2012

Arts and Crafts at Sea

Interspersed with deployments, sampling, and data processing, the scientists and crew have been decorating Styrofoam cups to be sent to great depths in the ocean. This is a common tradition among oceanographers and something that is well planned before we leave home -- we make sure to bring numerous cups, sharpies, and mesh bags. In addition, some people bring cups from home that have been colored weeks in advance by friends and family. Yes, we are that serious about this activity!
Sophie coloring
Colored cups ready for deployment

The cups are placed in a mesh bag that is then zip tied onto the CTD rosette frame and lowered to 3000m (that’s almost 2 miles below the surface!!!).

Cups in the bag before deployment
Shrunken cups attached to the CTD rosette frame

Pressure increases with depth and forces the air out of the Styrofoam and thus the cups shrink. Shapes and text are deformed and distorted as a once 4 inch tall cup becomes a mere 2 inches!

Shrunken cups that completed the journey
Shrunken cup

With good luck, the cups make the entire 3 hour journey down and back up again. Cups are generally decorated with cruise information and serve as a unique souvenir from our journey.

- Katherine Hoering