Monthly Archive for August, 2010

Straits of Messina Transect

Friday July 16th

Today we woke up early and left our anchorage at Vulcano Island and headed to the Straits of Messina 20 miles away.  The plan was to collect a sample at the north entrance, anchor for 5 hours to process the sample.  Once the sample was completed then head to the middle of the straits collect another sample, anchor again process that sample, and pick up another sample on the south side of the straits and keep sailing towards the Adriatic Sea.

Map of the Straits of Messina (Red X )

Satellite Image of Straits of Messina

The Strait of Messina is 20 miles (32 km) long and from 2 to 10 miles (3.2-16 km) wide, separating the Italian peninsula from Sicily and connecting the Ionian and Tyrrhenian seas. The massive amounts of water being funneled into a relatively small space creates strong currents and whirlpools.  Since this is the area where two big bodies of water meet, we wanted to make sure we collected samples along a north/south transect.

John helping collect the sample in the middle of the Straits of Messina

Swordfish Boat

Swordfish Boat

As we collected our samples we saw a lot of these swordfish fishing boats.  The boat is actually driven by one of the guys on the top of the mast, also up there are a couple spotters.  They are looking for swordfish that sleep during the day near the surface.  Once they find one they can slowly approach it and a harpoonist launches a harpoon from the extremely long bowsprit!

Another Swordfish Fishing Boat

Sunset as we left the straits and headed into the Ionian Sea

Advance Access JCVI Metagenomics Reports Application Note

A significant JCVI informatics development is JCVI Metagenomics Reports, an open source Web 2.0 application designed to help scientists analyze and compare annotated metagenomics data sets. Users can download the application to upload and analyze their own metagenomics datasets.

METAREP has just been published in Bioinformatics (08/26/2010) as an open access article. The publication is currently accessible under the Bioinformatics Advance Access model. The PDF version can be downloaded at

http://bioinformatics.oxfordjournals.org/cgi/reprint/btq455v1.pdf

Supplementary information includes the METAREP data model and an overview about its search performance accessible at

http://bioinformatics.oxfordjournals.org/cgi/content/full/btq455/DC1

One of METAREP’s  key features that distinguishes it from other metagenomics tools is that it utilizes a high-performance scalable search engine that allows users to analyze and compare extremely large metagenomics datasets, e.g. datasets produced by the Human Microbiome Project.

If you like to learn more about METAREP and talk to the developers,  join us  at  Human Microbiome Research Conference in St. Louis in Missouri (August 31 – September 2, 2010). We will present METAREP  the first day of the conference at 10:35am (see agenda).

Contact Us:

We would like to hear from you. If you have questions or feedback or if you wish to contribute to the METAREP open source project please send an email to metarep-support@jcvi.org

Links:

JCVI’s METAREP Instance

METAREP Flyer

METAREP Manual

METAREP Source Code

Naples Harbor Sampling

Thursday July 15th

After getting some sleep at anchorage in Ischia island we sailed for a few hours to the main harbor in Naples.  Over the years the Sorcerer II Expedition has collected samples in major ports around the world (Sydney, Halifax, Boston,  Panama, Cape Town, just to name a few).  Naples harbor is not only a big industrial harbor but also a research site that has been monitored by Italian scientist for may year.

Naples Harbor With The USS Dwight D. Eisenhower Aircraft Carrier Anchored

Water Profile from Naples Harbor

As you would imagine from such a busy port the water was not clear blue like open ocean!  We could only filter 200 liters from the surface (normally we can easily do 400 liters) and 75 from the Chlorophyll max (we can normally do 200 liters).

After we collected our Naples sample we sailed overnight to the Southern Tyrrhenian Sea and collected samples from above a  thermal vent off of Lipari Island.  Once we had the samples collected we sailed to Vulcano Island to anchor for the night and prepare for the 3 samples we would collect the next day as part of our Straits of Messina transect.

Vulcano Island

Italian Sampling Continues-Unique Animal in Italian Waters!

Wednesday July 14th

Monday July 12th we woke up early and left the anchorage in Capraia Island.  We arrived at Ischia island at 5:00 a.m. on Wednesday the 14th.  In those  48 hours we collected 6 samples.  Two samples were collected in the Northern Tyrrhenian Sea, two samples were collected over a seamount in the Tyrrhenian Sea and two other samples were collected at a long term research station in the Tyrrhenian Sea.  It was a pretty intense 48 hours of sampling.

Night Sampling

Deepest Profile Ever Collected on Sorcerer II

I have been on Sorcerer II since  2003 and I have seen a lot of things at sea, whales breaching, sharks swimming around, dolphins, flying rays, I even saw a shark eating a dead whale near Nantucket (nobody believes me, but I swear it happened!), but what we saw the other day 30 miles offshore wins the prize for the strangest thing I have ever seen at sea!  John spotted something in the water so we changed course to see what it was!

The Cow-Pig Ahead!

Cow-Pig Close Up

Another View Of The Cow-Pig

As we passed this giant dead animal, there were two things it could be, a cow or a pig!  People disagreed so that night we decided to just call it a cow-pig.  As pictures were downloaded of the famous cow-pig we all took a look at the tail and feet, we all agree now it is a big bloated pig, but feel free to let us know your thoughts!  Either way it was strange to see this so far from land!

Mediterranean Sampling Season Starts

Sunday July 11th 2010

On Thursday July 8th Sorcerer II set sail from Valencia Spain to start the Mediterranean season.  Permits vary from country to country, Italy gave us 10 days to collect our samples, so we had to time our departure from Spain to fit our 10 day sampling window in Italy.  As we sailed to Italy we collected a sample in French waters from a long term research site important to French scientist.

Italian Sample Sites

Our planned route is to sail along the north coast of Italy into  the Ligurian Sea and Gulf of Genoa, head down the  the west coast, through the Strait of Messina around the boot and into the Adriatic Sea.  The sample sites in Italy include, shallow thermal vents, seamounts, long term research sites and sites where large bodies of water collide and mix.Today we collected our first Italian sample between the Ligurian Sea and Gulf of Genoa then headed to anchor in a bay off  Capraia Island for the night.

CTD Cast Profile In Northern Italian Waters

Karolina and Jeremy Collecting Samples

It has been only 3 nights at sea, but being anchored or docked is always better for a good nights sleep!  Tonight we hope to watch the World Cup Final, which should be fun except we are not in Spain any longer!!  Then it is an early rise to set sail down the west coast of Italy.

The Sorcerer II Sampling Process

July 6th

 In the blog about the media event I posted a few days back I put a link to the JCVI media page.  On this page you can learn about our research goals, funders and past expeditions (more links on the right side of the page).  Before we set out for this sampling season I wanted to explain how we actually collect our samples on Sorcerer II.

One question I get asked a lot is “How do you pick your sample sites?”  Well a team at the JCVI that includes Bob Friedman, Sarah Dyste, Andy Allen and Chris Dupont work with collaborators from the countries we will be collecting samples.  The collaborators give us the coordinates of research sites that they are interested in.  In most cases these sites have years of data associated with them.  It is our goal to pair metagenomic data with the ongoing in country research to establish a fruitful scientific collaboration.

Once all the proper permits are in place,  Karolina, Captain Charlie and myself chart out the best sample route that will allow us to collect the most unique samples and avoid rough weather and seas.  Once we arrive at a sample site the first thing we do is lower the CTD (which stands for Conductivity, Temperature and Depth).  As the name implies it measures temperature, depth, salinity as well as fluorescence, pH, and dissolved oxygen.  As the CTD is lowered it gives real time data that is graphed on a computer in the cockpit.

 

CTD

Jeremy and Karolina lowering the CTD off the back of Sorcerer II

CTD graph as the CTD moves down the water column

Once a profile is complete we decide where to collect our sample, from Sorcerer II we can collect water from 120 meters (393 feet).  Most of the time the sample is collected in the  chlorophyll max, but not always, we also are interested in low oxygen zones, salinity gradients and thermoclines.  Once an area in the water column is chosen, 200 liters of water is pumped up from depth.  At the same time 400 liters is collected from the surface waters, both depths are pre-filtered  through a 200um nytex net.  

The water is pumped via a small compressed air driven pump through a series of decreasing filters (3.0um, 0.8um and 0.1um).  Based on the CTD profile of the water column 200 liters of the filtered seawater  from the surface or deep sample is recollected and run through a Millipore tangential flow filtration device (TFF) with a 50 Kda cartridge.  The TFF removes excess seawater but retains all the viruses in the sample. 

Graphic on how the samples are processed (note the net should be 200um)

Filter racks and TFF system

0.8um filters. Left is from the surface sample. Right is from the deep sample

The filters are removed from the rack, stored in buffers and placed in the -80 degree Celsius freezer we have in the engine room.  2 liters of the viral concentrate in 10% glycerol  are stored at -20 degrees Celsius.  Other subsamples for nutrient analysis, flow cytometry, pigment, and microscopy work are stored in the appropriate buffer/temperature.   The entire sampling process takes about 7-9 hours.  The samples are shipped back to the laboratories in La Jolla and Rockville on dry ice when we get to a major port.

We also have a fluorescent microscope which displays on the HD television.

Microscope on Sorcerer II