Posts tagged CTD

Sampling: US to the Azores

I’m off again on an ocean sampling voyage but this time instead of being onboard the JCVI’s Sorcerer II, I am onboard the R/V Endeavor as part of a multi-institution, international scientific sampling team that is headed from the US to the Azores.

On Thursday August 22 we left Morehead City, North Carolina for Ponta Delgada on Sao Miguel Island in the Azores.  The research vessel will take multiple samples along the 23 day transect.  Here is a rundown of the teams and the science we are conducting.

Crew leaving Morehead City, NC.

Crew leaving Morehead City, NC. From the left: Sarah Fawcett, Amandine Sabadel, Malcolm Woodward, and Bess Ward.

R/V Endeavor

R/V Endeavor

I will be filtering large volumes of seawater on 293mm filters for DNA sequencing, as well as smaller volumes onto smaller Sterivex filters for RNA sequencing and associated studies of gene expression within various microbial communities. This research expedition is funded by a grant from the National Science Foundation program in Dimensions of Biodiversity to Bess Ward at Princeton University and Andrew Allen at JCVI. The goal of our JCVI group is to extend findings from the Sorcerer II Global Ocean Sampling program, which documented massive genomic diversity and unusual physiological and biochemical capabilities within and between many lineages of marine microorganism. With samples collected on this research cruise, we will have the opportunity to document large-scale patterns in gene expression, and generate key hypotheses related to the most biochemically-active microbes across a major section of the upper 1000m of the North Atlantic. Data obtained from this study will be combined with similar data we collected last February and August on cruises out of Bermuda to the Bermuda Atlantic Time Series (BATS) stations in the in the sub-tropical Atlantic.

North Atlantic Transect, north of Sorcerer II transect to the Azores in 2009.

North Atlantic Transect, north of Sorcerer II transect to the Azores in 2009.

The Princeton team headed up by Bess Ward includes Sarah Fawcett, Nicolas Van Oostende, Jess Lueders-Dumont, Dario Marconi, and Keiran Swart. Their primary research involves using flow cytometry to physically capture, size fractionate and identify microbes living in the sunlit layer of the ocean. These microbes are directly responsible for assimilation of dissolved nitrate, which accumulates in the dark interior of the ocean. Specific identification of these microbes is an important research goal for microbial oceanography because the regulation and magnitude of global oceanic CO2 assimilation is driven explicitly by nitrate assimilation by photosynthetic microbes. Such microorganisms also produce a large fraction of the oxygen in the atmosphere. The Princeton group will perform nitrification experiments and measure levels of dissolved nitrate, ammonia and carbon by using stable and natural isotope tracers. The team will investigate the origins of dissolved inorganic nitrogen by measuring the natural abundance of the nitrogen isotopes.  Net tows will also be performed to collect the “bigger” planktonic organisms, such as zooplankton, within the ocean food chain.

Real time nutrient data down to nanomolar levels will be determined by Malcolm Woodward of Plymouth Marine Laboratory (PML) and Amandine Sabadel from the University of Otago in New Zealand.

As we motor to our first station, which we should reach on Monday September 2nd, we stop every morning at 5 am to perform a CTD cast to 1000 meters.  Based on biological and physical features, observable in real time via CTD sensors cabled to the shipboard computer,12 bottles, each containing 30 liters of sea water, are sealed at varied depths and the 360 liters is brought to the boats deck.  Once the CTD is on the deck, the different scientists scurry to gather their allocated amount of water from the CTD rosette and hurry back to their labs to do the appropriate work.

CTD Controls

CTD Controls

CTD Controls

CTD Controls

CTD1

CTD1

As of Wednesday August 28, 2013, we have done 7 transect CTD casts, all but one to 1000 meters.  Today we sampled on the Grand Banks and the water column depth was only 57 meters. For every cast I have collected RNA samples at 1000 meters, 250 meters, within the Deep Chlorophyll Max (DCM) (if no DCM is apparent, then just below the Chlorophyll max), a sample from within the Chlorophyll max and in the mixed layer (normally at 20 meters).

The weather has been great except for one 24 hour period when the swells grew to about 7 feet and the boat was really rolling back and forth.  The crew is great, the food is awesome, good thing they have a small gym or I don’t think most of us would fit in our clothes after a few weeks out here! The scientists are working well as a team and this should be a very exciting and beneficial science expedition.

CTD Profile

CTD Profile

Dry Lab

Dry Lab

 

Once we get to the our first station we will stay there for two days………….it will be a very intense two days, then a day motor to the second station followed by another crazy two days of sampling………….more on that next blog!

In the Deep

After the brief stop in my hometown we continue our journey southward in the Baltic proper. Our first sampling site was the Landsort deep, the very deepest part of the Baltic Sea (459 meters!)  and a long-term monitoring and sampling site for various Swedish and international scientists and environmental agencies. We arrived late in the evening but were all curious about what out CTD cast would reveal about this key sampling station in the Baltic. We all took our positions for sampling, which by now has become a well-known routine: Captain Charlie at the helm, John holding the CTD , Jeremy dropping the CTD in the water and keeping the water pumping through our 100 m hose, Jeff at the CTD computer monitoring the data and of course me, the Swede, feeding the CTD cord.

Here, at Landsort deep, we did not have to worry about hitting the bottom with the CTD but rather wanted to go as deep as possible to try and find the oxygen minimum and get a sample from there. Just below 70 meters, oxygen levels were down to almost 0 and we decided to collect water for our deep sample right there.

CTD profile from Landsort deep.

CTD profile from Landsort deep.

Tomorrow we will hopefully run into some nice cyano blooms on our way to Kalmar, where we will meet up with our collaborator, Professor Åke Hagström.

Heading to the Mother Land — Sweden

After transiting through the Kiel Canal, the waterway that links the North Sea to the Baltic Sea, and welcoming Dr. Venter in a rainy Copenhagen, we embarked for Sweden, my home and one of the main destinations of our 2009 expedition. It was a proud and special moment for me when first mate, John, hoisted the Swedish courtesy flag.

Unfortunately, the weather has not been cooperating and was putting a damper on the excitement. My friends and family in Stockholm tell me it has been the worst June weather in 50 years! When we were about to collect our first sample in the Baltic in winds up to 30 knots, rain and cold, Jeff Hoffman felt the need to pull out his thermal underwear that he uses in Antarctica. For some reason he didn’t seem overjoyed when I screamed through the wind “Welcome to the Baltic!” In fact the rest of the crew appeared very skeptical and were probably wondering what they had gotten themselves into for the summer.

With Dr. Venter at the helm, and in spite of the weather, we made our way north along the Swedish coast and after a brief overnight stop in the island of Öland, we reached our first Swedish sampling site. Because of the cold weather I didn’t expect to find much of my beloved cyanobacteria, but the CTD cast revealed a chlorophyll max around 15 meters and just by looking at the 3.0 µm filters we could see the spiky colonies of Aphanizomenon sp., one of the common bloom-forming cyanobacteria in the Baltic Sea. We also saw some of the toxic dinoflagellates Dinophysis, and it will certainly be interesting to see what kind of smaller bacteria and viruses that are associated with these phytoplankton communities are also present.

After sampling we headed for Visby on the island of Gotland for the night. Visby is a well preserved medieval city and a United Nations Educational, Scientific and Cultural Organization (UNESCO) world heritage site. We did not have much time for sightseeing, but the crew did enjoy a short walk in the historical center before a good night’s sleep.

We took off early this morning and are now sailing in good wind, heading for Sandhamn in the outer part of Stockholm archipelago. In two days I’ll be home!

Bundle with filaments of the cyanobacterium Aphanizomenon sp.

Bundle with filaments of the cyanobacterium Aphanizomenon sp.

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)

Bermuda: Back to Where We Started

Sorcerer II arrived in Bermuda around 7 p.m. on Saturday April 25th after a five day, 1,000 mile sail from Fort Lauderdale, Florida. During the crossing, the crew experienced some challenging weather to say the least.  Two samples were collected, and the CTD data confirmed what the J. Craig Venter Institute (JCVI) science team expected:  this deep, yet nutrient-poor stretch of open water was very mixed and observed no chlorophyll maximum within 50 meters depth. We are spending three nights in Bermuda before leaving for the Azores, a cluster of islands in the Atlantic Ocean off the coast of Portugal.

Bermuda is where I first started participating in the global ocean sampling work of the Institute. In January 2003, Dr. Venter asked me to fly to Bermuda and to work with a team of scientists at the Bermuda Biological Station for Research, now known as the Bermuda Institute of Ocean Sciences (BIOS) . BIOS, led by Anthony Knap, Ph.D., is an independent marine science organization founded to research and better understand Bermuda’s unique deep-ocean and coral reef environment. Dr. Knap and Rachel Parsons (presently the Microbial Observatory Lab Manager) welcomed me and the crew of Sorcerer II.

Back in 2003, I did a few sampling trips with Rachel on their research vessel the Weatherbird. In May 2003, Sorcerer II sailed into Bermuda and we did our first sampling in the Sargasso Sea off Bermuda’s coast. This work was our pilot study of ocean environmental sampling. The results from this work were published in 2004 and helped launch the official Sorcerer II Global Ocean Sampling Expedition later in 2004. Learn more about that pilot project and the results from our work in the Sargasso Sea here. Although we have enhanced our sampling gear, the basic idea of what we do and how we do it is still the same. It is almost surreal to be here approximately six years later, a circumnavigation under our belt, 400 samples collected and the Baltic, Black and Mediterranean Seas just ahead of us.

While in Bermuda I reconnected with friends and colleagues from BIOS, including the Dr. Knap, Rachel, James Marquez and Kristen Buck. They hosted an incredible tour of the station and the new research vessel the Atlantic Explorer. In an ongoing journey down memory lane, it turns out that the Atlantic Explorer was the first boat I did research on in graduate school at Louisiana State University in the 1990s. The Sorcerer crew was very impressed by the tour of the new ship and the new facilities. Rachel and Kristen provided extraordinary summaries of some of the research being done at BIOS. I recommend that you take time to visit their website and review their ongoing research projects.

While in Bermuda, Dr. Erling Norrby joined the crew. Erling, a virologist and former Secretary General of the Royal Swedish Academy of Sciences, is a good friend and colleague of Dr. Venter and serves on the Board of Trustees of the Venter Institute. Erling has completed multiple crossings on Sorcerer II, including Fiji to Vanuatu and South Africa to Ascension Island.  He is an experienced sailor, and over the years I have found him to be a knowledgeable source on a range of topics. His presence ensures that the next 2,000 miles will include good science, good conversation, and additional sailing skill for the Atlantic crossing.

We leave Bermuda tomorrow (April 28th) and will not likely have internet connection until we reach the Azores so stay tuned for more exciting tales from the sea.

The Search for Environmental “Gems” Continues

As an original crew member of the Sorcerer II circumnavigation that began in 2003, I had not been sailing/sampling on the boat since September 2007. I arrived in Florida with a mixture of emotions. Although life on board can be tedious, I was excited to return and embark on this next leg of discovery. Dr. Venter has created an incredible team that functions well at sea. Despite the close quarters and monotonous periods that can overshadow the journey, there is an easy and familiar feeling among the crew. These expeditions are serious and challenging, but they are also full of fun and adventurous moments.

The crew spent the week getting the boat ready to leave Florida; repairing sails, provisioning for food and organizing the science gear/supplies (I hope that everything was fixed!).  After a few days of reacquainting myself with boat life, I, too, was ready to go. At noon on Tuesday, April 21, we left the dock in Ft. Lauderdale enroute to Bermuda. Bermuda is the first of two brief stops (second are the Azores) on our way to Plymouth, England. We plan to arrive in England around mid-May. Once there we will spend a week performing intensive sampling with the Plymouth Marine Laboratory team.

Sample Crew

Kimberly Ulmer, a graduate student onboard from Panama to Bermuda; me (Jeff Hoffman), Karolina Ininbergs, Swedish collaborator, and John Henke, first mate.

We departed Florida in partly cloudy and calm conditions. Within an hour of leaving we had hooked three medium sized skip jack tunas. We made sushi and grilled the rest for dinner (this would count towards one of the “fun” moments I referenced). Since around eight a.m. this morning the wind has been a constant 25-30 knots, so the captain killed the engine. We have been sailing with an average speed of 11 knots. With strong winds and seas between 6-8 feet, we are unable to deploy the CTD or even stop for a sample.

As a sailing research expedition we are very dependent on the weather, and we are hopeful that the winds will die down later this afternoon or early tomorrow morning. We are all eager to collect the 24th sample of this leg of the expedition.

It will be very exciting to get metagenomic sequences from the conspicuous cyanobacterial blooms in the Baltic Sea. Hopefully it can help us understand more about what regulates toxin production in some of the species. – Karolina Ininbergs, Scientist and Crew Member of Sorcerer II

In Florida, the crew welcomed Swedish scientist Karolina Ininbergs. Ininbergs, a researcher at Stockholm University, is an expert on marine cyanobacteria and nitrogen fixation. The earliest life forms on this planet are thought to be early ancestors of cyanobacteria, and they are the first organisms capable of photosynthesis. Cyanobacteria play key roles in the carbon and nitrogen cycle of the biosphere. In part to genome sequencing, information on the genetic basis of nitrogen metabolism and its control in different cyanobacteria is available and providing invaluable to researchers. In addition to securing sequences from cyanobaterial blooms in the Baltic Sea this summer, Ininbergs hopes to spot colonies of the globally important nitrogen fixer Trichodesmium, a bacteria essential to understanding nutrient cycling in the ocean, and “whatever else maybe out there that might be fixing nitrogen.”

By increasing the collection of the largest fraction from 20 to 200 micrometers we hope to include more of the larger species of cyanobacteria in the samples then previously possible; therefore making our new friend Karolina happy and ensuring more sequencing treasures from these extraordinary environmental gems. Now if only we can get the weather to cooperate…

Through the Canal

We are now out in the warm and saline Caribbean Sea, and the waters are an intense blue. The waters are so blue, there is very little in them: we drop the CTD and barely get 0.25 micrograms of Chlorophyll per liter all the way to the 50 meter mark. The clear waters of the Caribbean are very low in nutrients, and the nutrients below the thermocline are deep, well beyond the reach of photosynthetic plankton. In fact, our CTD profile looks like a series of straight lines rather than the peaks and curves seen in the Pacific. Still, we take two samples for comparison and continue on to Florida.

Going Green to Blue

As we round the southern most point on our trip we notice that the water has gone from blue to green, and that there appear to be surface current and eddies in the water. We decide to stop and have a look with the CTD. As we lower the instrument from the aft cockpit, we encounter a layer of chlorophyll so thick that it actually coats the lines and hoses with a green layer of algae. At right is the CTD profile – the thermocline here is particularly sharp, and the temperature (red line) drops from 29ºC at the surface to 14.9ºC at 50 meters depth, indicating that cool, nutrient rich waters are relatively close to the surface. As expected, oxygen (blue) peaks at 110% saturated at the chlorophyll max, and drops to less than 10% saturated at 50 meters deep, indicating a switch from photosynthesis to respiration. Equally telling, the pH rises slightly at the Chlmax, indicating the consumption of CO2, and then plummets as carbon dioxide is produced from respiration. This represents an increase in acidity of over 50% in the space of 30 meters, which is quite amazing to see. This is by far the largest bloom we have encountered on our trip, and we take samples at 50 and 20 meters before continuing to the Panama Canal.

CTD Profile

Below are images of the three sets of filter racks, corresponding to the 3.0 micron filters (top pair), the 0.8 micron filters (middle pair), and the 0.1 micron filters (the bottom pair).  The filters on the left side all came from the layer of active respiration at 50 meters, where the primary processes of metabolism are bacterially driven.  The filters on the right are taken from the CHLmax layer, where much of the primary production is occurring.  All three of the CHLmax filters were heavily pigmented, with the top filter almost a millimeter thick in green algae.

3.0 micron filters (top), 0.8 micron filters (middle), and 0.1 micron filters (bottom)

Gulf of Tehuantepec

We spend the day transiting the famously capricious Gulf of Tehuantepec, but today winds were calm, and we were able to cut across the bay in good time. At the southern end of the gulf is an underwater seamount, so we maneuver the Sorcerer over the seamount in hopes of encountering an upwelling. An indeed there are numerous dolphins in the area feeding on fish. We take a CTD sample just as the sun is setting, and I spend the rest of the evening processing the filters.

Two dolphins caught in mid-leap by our captain Charlie Howard.

Two dolphins caught in mid-leap by our captain Charlie Howard.