Posts by Jeff Hoffman

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!

What Happened to Sorcerer II?!?!

The last time I wrote a Sorcerer II blog was in November when we set sail from Spain to cross the Atlantic Ocean.  For all of you that have been worried that we have been at sea for 8 months, relax we made it!!  Over the next few days I will update everyone on what has happened and the upcoming plans for Sorcerer II.

First off, the Atlantic Crossing……….On November 13th we left Gibraltar and on November 17th arrived in the Canary Islands.

Canary Islands

Lanzarote Island

After a day on Lanzarote Island we sailed overnight to Las Palmas on Gran Canary, collecting two samples on the way.  We stayed in Las Palmas waiting for a good weather window for the big crossing.  During that time we traded out crew members, fully stocked the boat with food, supplies and fuel.  We also had time to meet our collaborators from the University of Las Palmas.  I gave a group from the University a tour of the boat and showed them the sampling equipment.

Giving a demo of the sample gear

Folks from University of Las Palmas

On November 22nd we took off for the USA USA USA!  There was one problem, a huge storm in the Northern Atlantic.  To avoid the storm we had to go much more south then originally planned, also this storm sucked all the wind up north, so we had very little wind to sail with.  With no wind and a much longer sail than planned, we couldn’t make it directly to Florida…………well we could have but we would have run out of fuel and food!  So on December 8th we arrived in St. Thomas USVI.  For two and a half weeks we motored our way from the Canary Islands to the USVI sampling and fishing.  Total fish count was 8 Mahi Mahi, 3 Wahoo and 2 Yellow Fin Tuna.

Route, Canary Islands to USVI

Les and Me with the catch of the day

Atlantic Ocean Sunset

John BBQ'ing dinner at sea

Crew Sampling

One more thing, during this crossing the following things all happened, the strange part is they all happened within 24 hours of each other!

1.  Little generator broke (not a big deal we have 2 generators), both were up and running in a few hours

2.  Auto-pilot went out……….could have been  a real pain  because we would have  had to hand steer 24 hours a day for the rest of the trip, this was on day 8, but it got fixed in a few hours as well.

3.  Water maker went down………no water for showers, dishes and oh yeah no drinking water……once again got fixed in a few hours

4.  Mainsail ripped, this was fixed a few days later, but for  those days we were pretty rolly out there with no mainsail to keep us steady.

5.  Busted pipe in my head (bathroom)………funny thing is I woke up around 4 am dreaming about waves then I woke up and still heard the waves; it was the water going back and forth in my bathroom floor!

6.  And the big daddy of them all…….. a full out engine room fire!!  Not just smoke or steam…….we are talking flames and extinguishers!  It was taken care of and the engine was up and running about 4 hours later.

On December 20th 2010 Sorcerer II arrived in Florida.  This wrapped up the 2009/2010 Europe Expedition.  During this time we collected 213 samples, filtered over 51,000 liters of water from 13 countries.  DNA from all 3 size fractions from the 213 samples have been extracted, although not all will be sequenced right away, a majority have been sequenced or are schedule to be sequenced this year.  I will write a future blog on the sequencing status of these 213 samples and how we are working with many collaborators from Europe to work up this data set.  I will also write about what has been going on with Sorcerer II since December 2010 and future plans for her.

Starting the Atlantic Crossing

Wednesday November 17th 2010

On November 10th Sorcerer II set sail from Valencia Spain to start the sail back to America.  The first leg was a 3 day sail down the Spanish coast to Gibraltar

Coastline to Gibraltar

Valencia Coastline

John showing the delivery crew around Sorcerer II

We spent one night in Gibraltar to get fuel and supplies.   The next day we took a very important sample on the Mediterranean Sea side of the Straits of Gibraltar.  We collected a surface sample, which should be the lower salinity Atlantic water coming into the Mediterranean Sea.  At the  same location we collected a deeper sample, this is the saltier Mediterranean water flowing on the bottom into the Atlantic Ocean. 

CTD cast from Med. Sea side of the Straits of Gibraltar. Salinity increased from 36 to 38 PSU

After we collected our last Mediterranean Sea sample, we sailed through the Straits of Gibraltar into the Atlantic Ocean and started our way to the Canary Islands.



Sailing through the Straits of Gibraltar at sunset

Moroccan Coast

Boat traffic on Med. Sea Side of the Straits

French Road Sampling Trip Saves Sorcerer II From More Rough Weather!

September 28th 2010

With one last sample to collect and the weather still rough in the Mediterranean, we made the decision to make the Banyuls sample a road sampling trip.  So Jeremy and I loaded up a rental car with carboys and headed out at 5 am to drive the 125 miles (200km) to Banyuls France from Barcelona Spain.

Driving to Banyuls

After being on the boat for a few months straight, the 2 hour drive was a welcome adventure, even with the 5 am departure!  We were greeted at the Observatory of Banyuls by Dr. Ian Salter.  Ian showed us around the laboratory and down to the dock to their research vessel. 

View of Harbor from Lab

Old facilities

Ian and I on the research boat

They have a station less than ¼ of a mile offshore, which they have been monitoring for many years.  We motored out to the site, they did a water column profile with a CTD that was very similar to the CTD we have on Sorcerer II, and then we collected our water from a few meters deep with a niskin bottle .  Once we got back to the dock we loaded the carboys into the car and drove back to Sorcerer II to process the sample.  It is always good to collect samples with collaborators that have long term monitoring sites and are interested in working with the Venter Institute to analyze the data!

Filling our carboys

Ian and me as we motor to sample site

Jeremy, Me and Ian

A Week Long Beat Down At Sea, All In The Name Of Science!

September 27th 2010

We just arrived in Barcelona after 7 very rough days at sea!  Lots and lots of rolling around, very little sleep, high seas and strong winds!  We have seen worse weather in the past, but normally it only last a day or two………..this lasted 7 days straight.  The constant beating by wind and seas also took its toll on the boat, satellite and radar went down, engine and generator problems as well as random things flying across the boat hitting people as they slept! Captain Charlie and the crew did a great job monitoring the weather (especially with no satellite for internet or communications).  Our course was plotted to avoid big weather systems moving through the Mediterranean.

Weather systems we tried to avoid, I stress the word tried!

John reading as we surf down waves


It was a rough sail and we are all happy to be back on land here in Spain.  Arriving back in Spain brings to an end the summer sampling season of the Mediterranean and Black Sea.  We have sailed over 7,200 miles since May and collected 60 samples from 6 countries.  The samples are some of the most interesting we have collected and come from a wide range of unique environments.   I have one more sample to pick up in France tomorrow (the weather was too rough to take Sorcerer II up there, so I am going by car and collecting the sample on our collaborator’s boat).  The crew is going to take some vacation and start preparing for the Atlantic crossing that will begin early November.

The summer route, over 7,200 miles

Rolling seas top view

Go To Greece!

September 20th 2010

We arrived in Crete today, bringing our Greek sampling leg to an end.  We were very lucky to be able to sail in Greek waters, this place is truly beautiful.    Not only did we get to see the natural beauty of Greece, but our hosts introduced us to the rich culture and extensive history of Greece.  Our hosts, The Captain (AKA Mr Panayotis Tsakos ) and his family have been good friends with Dr. Venter for years.   Being in the shipping business for decades, it isn’t surprising that they know the best places in Greek waters!   We learned a lot about their shipping business, Tsakos Group ,  as well as the Maria Tsakos Foundation .  The foundation is very interesting so please click on the link and read about it.  The Sorcerer II crew was given a once in a lifetime experience from the Tsakos family, one we will never forget and are very thankful for!

The Captain, Craig and Heather

Sub in Skiathos Island




Sunset in Santorini

Ios Island

Safety first Darwin!

Jeremy looking at dinner!

John on the Captain's wave runner

Poseidon's Temple

The Captain's Island

Beach BBQ

Crew in the Corinth Canal

Click here to read about the Corinth Canal

Corinth Canal

Mykonos Island

Everyone should go visit Greece, it is amazing!

Second Leg of Greek Sampling

September 19th 2010

Greek Sample Site Map

After we picked up our samples in Maliakos Gulf and changed Greek collaborators we sailed overnight to Psara Island to collect sample #30 on the sample map.  Weather became an issue as we tried to collect samples site #26.  The winds were blowing over 30 knots and seas were building over 10 feet, in these conditions we can’t deploy the CTD and it is unsafe to work outside.  We ducked into Tinos Island and Ios Island to avoid weather as we made our way to Santorini.

Satellite Image of Aegean Sea

 Santorini is an amazing place. It is a volcanic Island that is the site of the largest volcanic eruptions in recorded history, which occurred some 3,600 years ago.  The caldera is filled with water from the Aegean Sea………as you sail in, you are looking up 1000 feet cliffs, then you realize you are really in the middle of an active volcano!


There were a couple samples we wanted to take in Santorini.  The first was a deep sample in the middle of the caldera (Greek Sample #24 on the sample map).  The second sample was in an area called Iron Bay .  Iron Bay is called Iron Bay……….you guessed it, because of all the iron in the water!  As you go into the bay the water turns a brownish orange color, the rocks on the shores are the same color.  Iron Bay is a thermal vent so you can see the bubbles coming up the water column, you can smell the sulfur and the water temperature goes from 24 -32 C (75-90F).  This is going to be a very interesting sample!

Entrance to Iron Bay

Shoreline of Iron Bay

3.0um from Iron Bay

 In Santorini we dropped off Dora and picked up our last Greek observer, Paraskevi Polymenakou (Voula) from The Hellenic Centre for Marine Research.  Voula would do the leg from Santorini to Crete.


The Start of Greek Sampling and Rough Sampling Conditions!

September 15th 2010

Aegean Sea Map

On September 10th we arrived in the northeastern Aegean Sea and docked in the city of Alexandroupolis.  We spent a few hours dealing with customs which was not normal for the Mediterranean countries.  Turns out that this area is well known for being an entry point for illegal immigrants from Bulgaria and Asia via Turkey.  Lucky for us we had our Greek observer Alexandra Meziti from the University of Thessaly.  Alexandra helped get all our paperwork in order and got us all checked in with the local custom officials.

Alexandra Meziti

Greek Sample Site Map

 So the next afternoon we took off to start our Greek sampling leg………and to be totally honest it couldn’t have started any worse!  We arrived to the sample site (#44 on the sample site map) at sunset, after we collected the samples the seas and winds picked up, plus a big lighting storm could be seen to the north of us and moving our way!  For the record you don’t want to be in the middle of the sea with a 130 foot mast in a lighting storm!  I was out sampling in high winds, rolling seas as we outran the lighting storm………all worked out and we didn’t get caught by the storm. 
We sailed overnight and collected our Thermaikos Gulf (Site # 34) and then headed to an island called Skiathos to anchor for the night.  The next morning we sailed to Maliakos Gulf (# 28 on sample map), unlike the previous two Greek samples the water was dead calm and no wind………it was nice and relaxing! For this sample our Greek collaborator Dr. Amalia Karagouni from the University of Athens was onboard.

Dr. Amalia Karagouni helping lower the CTD in Maliakos Gulf

Typical CTD Profile from The Aegean Sea

 After our samples were collected we dropped off Amalia and Alexandra and picked up Theodora Nikolakopoulou from the University of Athens (AKA Dora the explorer).  Dora would be our Greek observer for the next leg to Santorini.

Theodora Nikolakopoulou

Tourist in Turkey

September 11th 2010

Our time in Turkey was relatively short, but we saw and learned a lot in that time.  Our first stop was in Canakkale, it would have been an uneventful 1 night stop if it wasn’t for this…..Byron Hellespont Bicentenary Swim.  This yearly race allows you to swim the 3 miles from Europe to Asia across the Dardanelles.  I would like to say that it was a great day for a swim, but that would be a lie…….the winds were blowing between 20-30 knots , very choppy seas and a 4 knot current.  The 4 knot current was the biggest problem, it pushed a majority of the participants way past the finish line, including myself, Sarah, Tea and John (with a snorkel no less).  We made it to Asia, but about a quarter of a mile downstream of the finish line!

The actual finish line of the swim race. The white town in the top right corner is where we started!

We were also lucky enough to be in Istanbul for some of the FIBA World Basketball Championship. The crew got tickets and went to watch the USA play Tunisia.  The USA won that game and all the rest to win the gold a few weeks later.

USA vs. Tunisia

We also had a private tour guide for one day in Istanbul.  One day isn’t enough time to see everything in Istanbul, but we did as much as we could, including a tour of the Blue Mosque, Hagia Sophia and the Basilica Cistern.  I highly recommend you click the links for the Blue Mosque, Hagia Sophia and the Basilica Cistern, as well as these;Ottoman Empire and the Byzantine Empire.  Of all the cities I have traveled to in the world, Istanbul was the one with the most extensive history, I learned a lot!  I suggest you read up on it from the above links and go check it out!  My only travel advice while in Istanbul, watch out ………..the cab drivers will try to rip you off! And the city is full of street cats!

Blue Mosque and Hagia Sophia as we sailed by

Blue Mosque

Everyone with Blue Mosque in the background

Basilica Cistern information

Inside the Basilica Cistern

City street in Istanbul

Turkish sub in the Black Sea

Air show as we sailed into Istanbul

Turkish Transect

September 10th 2010

Tonight we arrived in the Greek town of Alexandroupolis, which is located in northeast Aegean Sea. In the last 3 days we have collected 10 samples from 5 sites; it has been a long couple days!  In the last blog I talked about the 2 sample sites in the Black Sea, since then we have collected samples on the north entrance of the Bosphorus (in the Black Sea), the South entrance of the Bosphorus (in the Sea of Marmara) and in the Dardanelles

This transect is very important because you have huge amounts of water moving back and forth from the Black Sea and Aegean Sea.  There are also big salinity gradients, not only in the surface waters from each body of water, but also in the water column due to the movement of water from each area.  The salinity of the Sea of Marmara is slightly greater than that of the Black Sea but only about two-thirds that of most oceans.  However, the water is much more saline as you go down the water column in the Sea of Marmara; it is actually similar to that of the Mediterranean Sea.  This high-density saline water, like that of the Black Sea itself, does not migrate to the surface.

CTD profile of the Sea of Marmara, notice the salinity change

Our Turkish observer, Merve Karakus