Posts tagged photosynthesis

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!

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…

Back on Land

We arrive in Ft. Lauderdale and are all glad to be back on land for a few days. But we were also elated by the success of the first part of the expedition. This first journey was difficult because we had to deploy and test new equipment, to sample a diverse array of environments and oceanographic features, from large surface and subsurface blooms of photosynthetic organisms to nutrient-depleted areas of the Caribbean, and it was the first time in a year that the Sorcerer II had really been tested in open water and long distances. Data on both photosynthesis and respiration were captured, much of which will be novel and highly useful in explaining the metabolic pathways and biological participants involved in carbon and nutrient cycling in the ocean.

This week we prepare to depart for Bermuda and the Azores and will continue on to Plymouth Marine Laboratory in England. Based on the sampling success of the first leg of our journey, it is difficult to contain our enthusiasm over the microbial discoveries that lay ahead. Stay tuned as we share more scientific adventures with you.

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.