Posts tagged chlorophyll

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



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!

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!

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.

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)

Costa Rican Dome

In Nicaraguan waters is a regular spring upwelling event sometimes referred to as the Costa Rican dome. Winds blow across the Central American Isthmus near Lake Nicaragua and contribute to an upwelling of nutrient rich waters. These nutrients enable phytoplankton to grow, and as we approach the southern end of Nicaragua, the water takes on a greenish hue, and we note large amounts of sea turtles on the surface of the water.  The turtles don’t seem to pay us much attention as we stop and take a sample. At 11 meters is a thick band of chlorophyll, and the oxygen saturation at the surface of the ocean is 117%, indicating very active photosynthesis (and production of oxygen). As before, we take samples from the oxygen minimum layer and the chlorophyll max. From what I understand, this bloom has only been detected by satellite, and we are the first research group to take genomic samples from this important phytoplankton bloom.

Sampling Blooms in Cabo Corrientes

Just south of Puerto Vallarta is Cabo Corrientes, and our satellite data indicate a large bloom extending 25 miles off the coast. As we enter the bloom the water turns an intense green, and there are numerous fish feeding in the area. Sampling conditions are ideal: bright sunshine, light winds, moderate swell. We deploy a large plankton net which rapidly fills with algae and zooplankton. Karen McNish looks at the larger diatoms and zooplankton under the scope while the rest of the crew prepares our instrumentation for deployment.

Satellite image of phytoplankton blooms along the Mexican coastline, March 2009.  The Ilsa Cedros bloom is halfway down the Baja peninsula on the west side, the Cabo Corrientes bloom is the red area in the lower right corner of the image.

Satellite image of phytoplankton blooms along the Mexican coastline, March 2009. The Ilsa Cedros bloom is halfway down the Baja peninsula on the west side, the Cabo Corrientes bloom is the red area in the lower right corner of the image.

The CTD profile of the water column at Cabo Corrientes showing a surface phytoplankton bloom.

The CTD profile of the water column at Cabo Corrientes showing a surface phytoplankton bloom.

From the aft cockpit we deploy a CTD equipped with a sampling hose. A standard CTD measures conductivity, temperature and depth: our unit also contained a pH probe and a fluorometer for measuring chlorophyll concentration. As we lower the CTD through the water column, we generate a profile of the ocean at Cabo Corrientes down to 40 meters in depth. At left you can see the CTD plot: depth is plotted on the y-axis as a change in pressure, and pH (black) and temperature (red) are plotted on the top two x-axes, with oxygen (blue) and fluorescence (green) plotted on the bottom two x-axes. In this case, the peak fluorescence (green trace) is at 8 meters in depth, and after that, the concentration of oxygen (blue trace) falls from 90% saturated to 5% saturated. The peak fluorescence indicates the location of the chlorophyll max (or Chlmax), where most of the photosynthetic plankton are located, and the oxygen minimum (or O2 min) indicates an area of intense respiration immediately under the Chlmax. Both of these areas contain a wealth of undescribed microorganisms, and understanding the relationship between photosynthesis and respiration in the ocean is one of the keys to understanding the global carbon cycle. We took samples at 8 meters and at 35 meters before continuing our southward trip.

Blooms and Clear Skies

We left under clear skies and light winds, and within hours of heading out, we were sampling the waters off of the Coronado Islands near the US/Mexican border and plotting our sampling schedule for the next few days. The team passed around the latest satellite data from SeaWiFS, NASA’s global orbiter for monitoring levels of chlorophyll in the ocean. We noted the locations of several large phytoplankton blooms along the Mexican coastline, and we made plans to sample the large bloom near Cedros Island, about halfway to Cabo San Lucas near the ‘spur’ of the Baja Peninsula.