Monthly Archive for May, 2009

The Final Plymouth Sample

I returned to Plymouth on Sunday, May 24th after attending a wedding in Venice. During my time away I missed a tour of the Plymouth Marine Laboratory (PML) and the Marine Biological Association. Fortunately, Dr. Jack Gilbert arranged a second round of tours for Sorcerer II crew members who had not been able to attend. Like Karolina I was very impressed with both institutions. (For more details on the tours, please refer to Karolina’s blog of May 20th). I also apparently missed many good times that the crew of Sorcerer II shared with the PML team including a great dinner with staff from the University of Exeter, and the University of Plymouth Medical School.

On Thursday, May 28th the Sorcerer II crew, accompanied by Dr. Jack Gilbert and two of his Ph.D. students, headed out for one final sampling trip. The destination was E-1, a long term research station for PML located about 25 miles off the coast of Plymouth in the English Channel. As we arrived on site PML’s research vessel Plymouth Quest was there collecting ancillary samples to be paired with our metagenomics data. Below is the CTD cast from station E-1. Based on the information collected from the CTD cast, the Sorcerer II crew, Dr. Gilbert and the scientific team on the Plymouth Quest decided on a four point water column profile. The profile consisted of a surface sample, a sample at the top of the thermocline (20 meters), a sample at the bottom of the thermocline (30 meters) and a benthic sample (72 meters). As you would imagine it was a long day of sampling, and we are very interested in pairing PML’s extensive data collection at E-1 with our samples.

CTD Cast from Station E-1

CTD Cast from Station E-1

First Sampling in Plymouth Reveals Interesting Blooms — BBC Cameras capture it all!

After a couple of days in Plymouth we were ready for the first of two intense sampling days together with the Plymouth Marine Laboratory (PML). We had heard rumours about blooms of Phaeocystis, a conspicuous bloom-former in the North Sea and English Channel. When it blooms, it turns the water reddish-brown in color, and the degradation of the gelatinous colonies may result in foaming. It was another beautiful sunny morning in Plymouth when we left Sutton Harbour and headed for one of PML’s long-term coastal sampling sites, L4 and L4 east. In addition to the permanent crew, Dr. Venter, Heather Kowalski (head of PR and communications) and Dr. Chris Dupont were onboard from JCVI.  They were joined by a sampling team from PML of Dr. Jack Gilbert and two students, Nicole Bale and Ben Temperton, who were going to sample for transcriptomics, i.e. analysis of RNA to look at the expression of the genome. We also invited Dr. Dawn Field and her student Paul, bioinformatics experts visiting from Oxford, to join us.

We followed PML’s research vessel Plymouth Quest out to the sampling stations.  This group, headed by Denise Cummings, conducted a suite of measurements to provide us with an incredibly detailed picture of what the sampled microbial community was actually doing.

R/V Plymouth Quest

R/V Plymouth Quest

We dropped our CTD down to just over 40 m and observed two interesting changes in temperature, oxygen and pH through the water column at 12 and 28 meters respectively and decided to take a sample at 35m and a surface sample.  The step-like form of the temperature profile suggested that several storms had passed through recently, mixing the water, with quiescent weather in the intermittent periods.  Potentially, the drops in oxygen and pH were the result of increases in community respiration, which consumes oxygen (just like when we humans breathe).  The gradual increase in chl a with depth was due to photoadaptation, that is the plankton deeper in the water produce more of the light absorbing pigments because there is less light.   Fortunately, each of these hypotheses can be directly addressed by the work being done by the group aboard the Plymouth Quest.  Through collaboration with PML, we will know more about these samples than we have for any sample previously.

CTD profile from L4 east.

CTD profile from L4 east.

We were delighted to find our filters full of microorganisms after filtering 200 L of seawater from the two depths.  Upon opening the filter casings, we were hit with a very tangy sulfidic aroma caused by dimethyl sulphide (DMS for short).  This gas, which is literally the “smell of the sea,” is the result of marine plankton degrading dimethylsulfoniopropionate (DMSP for sanity).  Most phytoplankton produce lots of DMSP and the tiny animals and crustaceans that eat them are sloppy, so you essentially have a steady supply of DMSP to bacteria.  Some bacteria actually want the sulphur so they metabolize the DMSP. Others degrade it to DMS, which gives you that peculiar smell.  A curious side effect of DMS is that when in the atmosphere it acts as cloud condensation nuclei.  In simpler terms, lots of DMS production means lots of clouds, which reflect the sun’s energy away from Earth.  Therefore, in direct contrast to the carbon dioxide, DMS is a “global cooling gas.”

Just in time for the second sampling station we were met by a BBC film crew who motored up in a RIB boat. The crew from London was onboard to film the important work of the Sorcerer II Expedition and the collaboration with PML for a new science TV series to air later this year. Onboard the Sorcerer II, Dr. Venter, Chris Dupont and Jack Gilbert did an excellent job explaining our mission and the science behind it to the interested and professional BBC reporter, who also turned out to be helpful during the sampling procedure. It’s never easy with so many people onboard the boat during these intensive samplings and having a film crew, some of whom don’t have the greatest sea legs, adds to the intensity.

Dr. Venter, Jack Gilbert and Chris Dupont being interviewed by BCC reporter.

Dr. Venter, Jack Gilbert and Chris Dupont being interviewed by BCC reporter.

Earlier in the week the JCVI and PML teams had conducted some joint interviews in Plymouth while on the dock. These included a local newspaper and a BBC radio interview.

Click here to listen to one of the radio interviews.

(post by By Karolina Ininbergs and Chris Dupont)

Days of Discovery: Plymouth, Sea Urchin Cell Division and More Plankton

After a few days of fairly rough weather and winds up to 50 knots we finally spotted land and made our way to Plymouth. With our social interactions having been restricted to a pod of pilot whales and a few tankers passing through the night, we were excited to see a welcoming committee, headed by Dr. Jack Gilbert and Dave Robins from Plymouth Marine Laboratory (PML), waiting on the dock in Sutton Harbour. We were also excited to meet up with our colleague from JCVI, Dr. Chris Dupont, who flew from La Jolla to help us coordinate and run the intense sampling sessions together with our collaborators and hosts at PML. Plymouth showed us its best side with nice, sunny weather and curious and friendly spectators down in the Barbican.

Sorcerer II arriving in Plymouth.

Sorcerer II arriving in Plymouth.

Sorcerer II arriving in Plymouth.

Sorcerer II arriving in Plymouth.

On Wednesday the 20th the Sorcerer II crew was invited for a tour of the Marine Biological Association in Plymouth. The MBA is one of the oldest marine biology research institutes in the world and has been carrying out research and education for 125 years. In conjunction with PML and number of other institutions they formed the Plymouth Marine Sciences Partnership, an initiative to bring together leading marine science and technology organizations in the region. The crew was hosted by Dr. Richard Pipe, an associate fellow at the institute and head of the Plymouth Culture Collection of Marine Algae. Richard showed us around their facilities, introducing us to some of the researchers, who were happy to talk to us about their projects, ranging form cell division in sea urchin embryos to pheromones. Another highlight of the tour was the algal culture collection, consisting of some 280 strains, the oldest one isolated 100 years ago.

We also had the pleasure of visiting the National Marine Biological Library (NMBL). Linda Noble, Head of Library and Information Services, showed us some extraordinarily beautiful historical drawings of marine plankton. We were all amazed by the exquisite drawings and how well preserved the books were. Crew member Jeremy Niles put it all in historical perspective when he said, “Some of these books are older than our country!”

As our tour was coming to an end we made a final stop at the Sir Alister Hardy Foundation for Ocean Science (SAHFOS), the foundation in charge of the continuous plankton recorder survey. This marine monitoring programme has been collecting data from the North Atlantic and the North Sea on the ecology and biogeography of plankton since 1931 and is the world’s longest running marine biological survey. The continuous plankton recorders are towed by commercial ships around 17 regular shipping routes around the world every month. The data collected is used, among other things, to track global climate change, harmful algae blooms and fisheries.

Dr. Richard Pipe showing an experimental tank at the MBA to the Sorcerer II crew: Captain Charlie Howard, Jeremy Niles (Back row), Karen McNish and John Henke (front row).

Dr. Richard Pipe showing an experimental tank at the MBA to the Sorcerer II crew: Captain Charlie Howard, Jeremy Niles (Back row), Karen McNish and John Henke (front row).

The Plymouth Culture Collection of Marine Algae.

The Plymouth Culture Collection of Marine Algae.

The Plymouth Culture Collection of Marine Algae.

Captain Charlie Howard, Dr. Richard Pipe, Librarian Linda Noble and Jeremy Niles at the National Marine Biological Library.

Dr. Richard Pipe and the CPR (Continuous Plankton Recorder) at SAHFOS.

Dr. Richard Pipe and the CPR (Continuous Plankton Recorder) at SAHFOS.

We’re looking forward to sampling here in Plymouth with our PML colleagues and to the arrival of Dr. Venter. More soon.

Karolina

England, Here We Come!

In calm and clear conditions on May 11 Sorcerer II set sail for Plymouth, England.  We enjoyed our brief stay in the Azores, but we were all excited to get to the U.K. and complete our North Atlantic crossing.  As I mentioned in previous entries, we took samples near areas studied by the Department of Oceanography and Fisheries IMAR-University of the Azores (DOP/UAç).  We sailed from Faial to the neighboring island of Pico to collect the first sample.  On our second day out we collected another sample about 100 miles offshore.

On the second day of our five day transit we received word of bad weather on our projected route to Plymouth. With Charlie and John monitoring the forecasts from onboard Sorcerer II, and Craig monitoring from the US, the collective decision was made to head east to avoid the stronger winds and seas north of us.  We spent the day securing the boat and storing the science gear.  We had to travel so far east to avoid the heart of the storm that we were only 250 miles off the coast of Spain.  During this time we experienced winds up to 50 knots and seas ranging from 15-20 feet.  As you could imagine the weather put a halt to the sampling and the crew focused on the weather and making it to England safe and sound.

We arrived in Plymouth on Monday, May 18th two days later than expected, but happily in one piece.  Plymouth is a significant location for us since Charles Darwin embarked aboard the HMS Beagle from this same site 178 years ago.  As we sailed into our slip, we were greeted on the dock by Dr. Jack Gilbert, head of the Plymouth Marine Laboratory (PML) team and our host in Plymouth, and Dr. Mark Brown from The University of New South Wales (UNSW).  Dr. Brown (aka, Brownie) is a colleague who works on the Antarctic Lakes Project, a joint research program between UNSW and the J. Craig Venter Institute.  The Sorcerer II is in good hands with our hosts from PML.  We are all looking forward to some intense sampling in the coming days as well as a few nights of local food and fun with our UK friends and scientists.

Land Horta! The Sorcerer II on Faial Island, the Azores

We sailed into Horta on the island of Failal Saturday, May 9th around 1pm.  The Sorcerer II crew was excited to visit the island but then again, we were just happy to walk on land and sleep in a bed that was not rolling from side to side! As usual when we arrive in a new port, we cleared customs, arranged dockage, hooked up power, cleaned the boat and organized gear. Afterwards we arranged a tour of the island.

City of Horta on the Island of Faial in the Azores.

City of Horta on the Island of Faial in the Azores.

While I took in the sites and sounds of Horta from the back of the van, Karen our chef, sat next to the driver so had a much more detailed discussion about what we saw. Here is her account of this interesting island.

The guide, Louis took us up the closest old volcanic plug — Monta du Guia.  So called because of the guiding light of Virgin Mary to all the seafarers (guia means guide in Portuguese). Every August, there is a procession to the top to bring the image down from the chapel and put her in an old whaling boat and circumnavigate the mount. As you look down from the top, much volcanic activity is evident. There are two beautiful calderas and Monta Quemada (burnt mountain). Next we drove 900 meters to the highest point of the island to see another caldera — this one created from the main volcano that formed the island. Unfortunately the fog obscured everything so we had to take Louis’ word for it although he showed us a picture of something that looked like it could have been this caldera.

As we drove down the mountain we noticed two types of plants — blue hydrangeas that bloom in profusion in June and July and the other a Japanese cedar imported in the 1750s to be grown as a source of timber for the island. This cedar was used in making the windmills that we saw at the north end of the island.

There is little agriculture done on the island anymore because Louis told us it was so much easier and cheaper to get everything from the mainland EU.  I witnessed the lack of local produce when going to the supermarket to provision the boat. Fresh milk was especially impossible to find. We saw farmers and milk cans in trucks but we learned the milk was sent to the creamery to be made into butter and cheese which is much more exportable.

As we passed through a valley first populated by the Flemish, we saw the results of the 1998 earthquake. Large areas of houses were destroyed and the principle church ruined. Continuing along the road there were many small, quaint towns. In one the men were playing a traditional game which is a cross between the French game of boules and the Italian bocce. Every town has its own chapel dedicated to the Espiritu Santu and every year one family provides a typical meal of soup and beef to all the villagers and anyone who is hungry.

Next stop was the Calderinhas volcano. From September 1958 to November 1959 the volcano spat out smoke, lava and ash inundating the village houses, with the whaling station and lighthouse being especially hard hit.  The lava flows also created a new spit of land. Luckily no lives were lost but many, many homes were destroyed. As a result of this loss of property, approximately 30% of the population of the island fled to America with most of the people settling in the coastal whaling cities of New England. Since it was the Americans that brought whaling in to the Azores, many of the people on the island already had ties to those American cities and so the immigration wasn’t perhaps as shocking as it could have been. With our tour ended we said goodbye to Louis and left with a better understanding of these wild and rugged islands in the middle of the Atlantic.

Next we headed to see Dr. Sergio Stefanni from the Department of Oceanography and Fisheries (DOP) IMAR-University of the Azores, our science contact in the Azores, who offered to give us a tour of the facilities and research vessel.

Dr. Stefannin and the captain of the University of Azores research vessel explain the sampling they do to Sorcerer II captain Charlie Howard.

Dr. Stefannin and the captain of the University of Azores research vessel explain the sampling they do to Sorcerer II captain Charlie Howard.

The Department of Oceanography and Fisheries of the University of the Azores is a reference research center on deep-sea ecology, fisheries and conservation with a special interest in seamounts and hydrothermal vents. I was very impressed with the scope of research conducted there, and the state of art research equipment in the molecular, chemistry, optical, fisheries and oceanography labs. After the tour we asked Dr. Stefanni, his colleagues and some of the University’s graduate students to come visit our floating lab. While this team was onboard Sorcerer II, Captain Charlie and I took the opportunity to discuss the sampling sites we’d applied for in our permits. Dr. Stefanni and team explained to us some of the unique conditions around these sites such as the unusually warmer waters and the in-depth and long term chemical and oceanographic data for the one site, and the hydrothermal sulfur vents near the other which has been extensively studied by the Department of Oceanography and Fisheries. After the tour of Sorcerer II was completed and local sampling plan in place, the crew was given a tour of the Research Vessel, Arquipelago by the boat’s captain Manuel Fernando Serpa.

University of Azores team touring Sorcerer II.

University of Azores team touring Sorcerer II.

If you would like to learn more about the University of the Azores or the R/V Arquipelago, please visit their website.

North Atlantic Transit

After four days in Bermuda reconnecting with colleagues at BIOS and preparing for sampling across the North Atlantic, Sorcerer II departed on April 29th enroute to the port of Horta located on the island of Faial in the Azores.  There are nine islands in the Azores archipelago which is governed by Portugal and is located 900 miles from the mainland.

Unfortunately, we had to leave Bermuda with no permits to sample in Bermudian waters. However, shortly after departure we received word from the Harbor Master via the VHF radio that our permits had been granted, and we could indeed collect samples. We located the BATS (Bermuda Atlantic Time Series) station, one of the sites that  we sampled for the original Sargasso Sea Science paper but Sorcerer II was already 20 miles past. Fortunately, by changing course, we were able to resample one of the sites from that first analysis.

As we traveled to the Azores, we gathered eight samples, collecting our deepest sample yet at 70 meters and doing our deepest open ocean water profile of 100 meters. The profiles revealed some interesting data, one being that the chlorophyll maximum was located at 70 meters.

On the North Atlantic transit weather played a key role on when and where we could sample. A few days out from Bermuda we were informed that a weather system was coming from the north, and we had to move south to avoid the brunt of it. I have experienced rough weather during my time aboard Sorcerer II, but the rough weather system we encountered was persistent. The crew had a few days of light wind and high seas; however, we did not have enough wind in the sails to keep us stable, and we just rolled from side to side. If you’ve ever experienced this kind of weather onboard a boat you know what it feels like and it’s tough to walk, work, eat, or sleep. The crew and I were not too happy during this period. Thankfully, the weather finally retreated, and the crew was rewarded with great winds the final days. Sorcerer II sailed into Horta comfortably with an average boat speed of 10 knots.

With this expedition, we’ve established a “mini” Science Series in which a visiting scientist presents his or her specific scope of interest. This was our chef, Karen McNish’s idea since as a former science teacher in the UK she has a keen interest in the science we do. Karolina Ininbergs one of our collaborators from Stockholm University talked about cyanobacteria, her favorite group of microbes. Virologist and JCVI board member, Dr. Erling Norrby joined the crew in Bermuda and hosted two nights of talks focusing on viruses and prions. Both of these scientists are impressive, and it was an honor for the crew to be exposed so intimately to their extensive research. On a personal level the series allowed me a deeper insight into Erling. He is an incredible man with a remarkable life’s work. It was a thrill to have him on this leg of the expedition, and he’ll be missed by the entire crew when he returns to Stockholm after docking in the Azores.

The transit from Bermuda to the Azores covered close to 2,000 miles and took 11 days. When we weren’t sampling, avoiding weather systems, on watch, or sleeping, the crew did enjoy a few hours of down time. We participated in some very competitive games of Hearts, the Sorcerer II game of choice. Despite the weather and work, we were also able to toast a milestone in the life of Captain Charlie Howard. We celebrated his birthday with a delicious roast dinner followed by cake and ice cream. Happy Birthday, Charlie!

All in all, the North Atlantic transit met my expectations of good sampling, good boating, good science, and good conversation. I am glad to have made the crossing safely, and we are all looking forward to our time in the Azores before heading to Plymouth, UK.

As they say in Faial, Até mais!