PHYVIR expedition
Team of the PHYVIR cruise aboard of research vessel Anna Weber - van Bosse.
Phytoplankton, microscopic ocean plants, produce around half of the Earth’s oxygen and play a key role in global carbon cycles. Yet their interactions with viruses, and the impact on ocean health and climate, remain largely unknown. The PHYVIR project aims to change this through a combination of lab research, ocean expeditions and advanced modelling.
In this blog series, we follow the research at sea aboard the RV Anna Weber-van Bosse. From the preparations in the harbour to the first measurements in the Atlantic Ocean, we take you behind the scenes of the life and science on board.
13 May - Eavesdropping to the chemical language of marine microorganisms
Written by Guy Schleyer, NIOZ
One great advantage of having a (new) big boat is the ability to bring on board a diverse group of scientists with complementary expertise and interests. Together, we study both the phytoplankton in the water and the environment in which they live and die. Each team of scientists is responsible for different measurements and analyses – some of them are performed live using dedicated instruments on board, however, many require instrumentation only available in our home institutes. We all collect samples. A lot of samples.
Chemical communication at sea
Seawater contains not only microorganisms in high abundances, but also many chemicals that they produce, consume and process throughout their existence. Together, marine microorganisms are responsible for cycling huge amounts of carbon and other nutrients (like nitrogen and phosphorus). These chemicals, also called ‘metabolites’, are furthermore used by microorganisms to interact with each other. Eavesdropping to this mostly unknown ‘chemical language’ of marine microorganisms helps us understand their physiological status as well as the intricate relations they have with each other.
Filtering seawater to collect microorganisms and microorganism-free water (photo: NIOZ)
Studying metabolites of microorganisms at sea is, however, challenging: their amounts can be minute and some of them are processed so fast that it is hard to capture them. In addition, the salts from the seawater can harm the instruments used for analysis. So how do we collect and study these metabolites then? First, we remove all microorganisms from the seawater using different filters. Then, we load this microorganism-free seawater to special cartridges that capture metabolites while letting the salt go through. This allows us to collect metabolites from large volumes of seawater and concentrate them. Once the cartridges are loaded with metabolites, we can release them using chemical solvents, dry them and store them until they are analyzed back in the home lab. And of course, all of this is done in a secure way – we do not want any glass to break while the ship is moving.
Our team starts the day with two containers of 20-liter seawater and ends the day with 50 different samples that are stored frozen until they can be analyzed in the lab. With more than 20 stations, this sums up a lot of samples that for sure will keep us busy in the months after the ship returns to Texel to unload.
Capturing seawater metabolites using dedicated cartridges and a secure setup. Water pass from the glass bottles through the cartridges (photo: NIOZ)
10 May - Creating perfect conditions
Written by Jitske Luttikholt (HBO student) & Amelie Wittig (MSc student University of Amsterdam)
By now we have gotten into our daily routines on board. Getting up early, grumpy or not, after putting on our safety shoes and helmet, we are sometimes treated with a beautiful sunrise above the sea. Once we receive the first water samples of the day, we start our assays (incubations to measure growth and mortality rates). We have by now adapted to our routines related to the organisms we work with. During the experiments we are working with live algae, bacteria, and viruses on the ship, so we want them to be as happy as possible. The light conditions at the different depths we sample varies, logically decreasing when deeper in the water column. To get enough nutrients (nitrogen and phosphorus) in the current low-nutrient ocean surface waters, the algae hang out a little deeper where they still have access to the higher nutrient concentrations from the deeper water. But algae need light (for photosynthesis) and therefore cannot go too deep. Therefore, one can find an increased concentration in chlorophyl (important pigment for algae) between 50 and 100 m, the so-called deep chlorophyll maximum (DCM). There the algae have very little light, but they are adapted to it. To avoid exposing them to bright daylight when brought up to the surface will cause stress and impact our experiments- just like we protect ourselves from the sun with sunscreen and hats- we also protect these unicellular algae from “frying” at too high light.
This begins when we get the water: it is tapped from the CTD sampling bottles into containers that are wrapped in several layers of dark bags (renewed regularly). Secondly, the light in our laboratory container is dimmed, with the windows and lights covered as much as possible. We then prepare what is needed: we filter out viruses and grazers (predators), to be used to dilute the phytoplankton to see how reduced mortality pressure affects algal growth. We prepare bottles that are placed in an incubator on deck. To bring the bottles there, we use backpacks that shield the light as much as possible. Doing this makes us feel like mountaineers, climbing across the deck and up several flights of stairs to reach the other side of the ship. There, we use a cover while we place the bottles on a wheel in the incubator that has screens to mimic the natural (at the depth they were sampled from) light condition. After doing this routine, the algae can survive happily during our experiments, and hopefully we’ll have some fascinating results!
Cleaning equipment (photo left by Dorien Hoeksum) Putting our samples into the incubator requires shading (photo right by Dorien Hoeksum)
10 May - Funnels at 5 kilometres deep
Written by Dorien Hoexum, PhD candidate NIOZ and UU
Letting go isn’t easy
Last year, I deployed three large funnels attached to a mooring in the Atlantic Ocean for my PhD project. Now it is time to haul them up and see which nutrients sink down in the ocean. The funnels are located along the route of the PHYVIR-expedition, which makes it possible for me as the sole geologist to join this algae adventure!
Collecting the funnels starts with tracking them down. All three are connected to a long cable, attached to a block of iron on the sea bottom weighing 800 kilograms. First, the deck crew sends a signal to the cable, so it releases itself from the block. We are supposed to be at the exact spot of the funnels, but the return signal comes from over 12 kilometres away! If you leave equipment on the sea floor for over a year, there is of course a lot that can go wrong. Are the funnels still attached to the anchoring block? Have they been moved by the current? Luckily, the crew from the RV Anna Weber-van Bosse is very experienced with these kinds of jobs!
Crew collects the beacon attached to the funnel (photo: Dorien Hoexum/NIOZ)
The funnel coming up above water (photo: Dorien Hoexum/NIOZ)
A well-oiled machine
Once we arrive at the spot from the signal, I receive an e-mail from the beacon. This only works when it’s above water, which means the release has worked! Looking out from the bridge, after some time we spot the orange buoy so the crew can start on hauling the funnels in. Immediately it becomes clear that I am the only who is nervous about this: the crew handles it like a well-oiled machine. Getting the funnels on board takes all morning: they were located 1500, 3500 and 5000 kilometres below sea level which means there is a lot of cable to reel in.
The crew hauls one of the funnels on deck (photo: Dorien Hoexum/NIOZ)
Roll up your sleeves (or maybe not)
With the funnels on deck, it’s time for me to get to work. The ship remains at it’s position for a while longer to allow the biologist to carry out their work, which is rather convenient for me. Working in the full sun in a rain suit might seem strange, but it is the safest. Every funnel has 12 bottles, one for each month, in which they collect everything that sinks down in the water. Each bottle contains a bit of mercury, to kill everything that lives in these samples. I am a geologist after all: I am only interested in the chemical composition of the material. Once I’ve closed and cleaned all the bottles, they are stored in the refrigerator for me to analyse them once I’m back at the lab.
Dorien Hoexum collecting the sampling bottles from the funnel (photo: Dorien Hoexum/NIOZ)
8 May - Into the ocean, before breakfast!
Written by Jasmin Stimpfle (marine biologist Alfred Wegener Institute), Thomas Cupido (master student RUG), Melle Versluis (Phyvir PhD candidate UvA) and Yael Artzy-Randrup (assistant professor UvA)
Now that we’ve waved our goodbyes to the last view of land we will see for the next month and have officially entered international waters, the real adventure can begin: collecting water samples from the depths of the ocean.
Every morning at 5 AM, the ship’s thrusters gently rumble us awake. They keep the ship perfectly steady so we can begin sampling with the Ultra-Clean CTD (UCC) system, which allows us to collect seawater from different depths (down to the deep sea!). We, the UCC team (Jasmin, Thomas, Melle, and Yael), go to the changing room, pull on our safety boots and helmets, and gather on deck. There are the deck crew members already.
For a brief moment, everything is calm. The ocean is still dark and endless, while the sky slowly turns pink and orange around us. We get a spectacular view before it all begins. The crew lowers the UCC into the water, a heavy frame weighing over half a ton.
Early morning Ultra clean CTD PHYVIR (photo: NIOZ)
Exploring the deep
Once the UCC disappears beneath the waves, its sensors begin recording temperature, salinity, water density, chlorophyll fluorescence (indicator of the algae in the seawater), oxygen concentration, and more, creating a vertical profile of the ocean below us. Our chief scientist, Corina, watches the incoming data closely as the profile appears on her screen in real time.
As the instrument ascends through the water column, Corina pinpoints the depths at which seawater samples will be collected. Meanwhile, two of us scrub down the clean room where the samples will later be processed. Once the UCC returns to the surface, things move quickly. The instrument is transferred into our clean-room laboratory container, equipped with an air filtration system designed to keep contamination out. Here we are waiting already in full clean-room gear: coveralls, hair nets, and rubber boots, somewhere between a hospital ER and a low-budget space mission.
Watching the incoming data closely as the profile appears on screen in real time (Photo: NIOZ)
Heavy metal in the clean room
One contaminant we work especially hard to avoid is iron. The microorganisms we study here come from extremely iron-poor environments, so even tiny traces of iron contamination could affect the experiments. That means everything has to stay meticulously clean: no shortcuts, no stray dust, and no rusty equipment anywhere near the samples. Even the UCC frame is made of titanium to minimize trace-metal contamination during seawater collection. Nonetheless, while seawater samples are being processed, upbeat rock and light metal music fill the container walls. Between the sterile suits, filtered air, and heavy guitar riffs, the clean room has developed a very particular atmosphere.
As soon as each sampling bottle is filled, the UCC team distributes it to the small hallway in the UCC container where it is brought out by another dedicated member of the scientific party on board. They distribute the water samples to different research groups waiting patiently in line outside the container. Everyone is eager to begin measuring different parameters or setting up incubation experiments (more on those in future posts). It is a carefully coordinated operation, and every team depends on these samples for their work. By the time the last bottles are handed off, we are just in time for breakfast (the program is carefully planned to make sure all can have their meals in time).
The cleanroom UCC team (photo: NIOZ)
An orange a day keeps the scurvy away
Breakfast always comes with eggs (e.g., fresh omelet), oatmeal porridge and then there can be pancakes, cut fruit – all that in the middle of the ocean. And while we try not to finish all the fresh oranges too early in the voyage, morale remains high and scurvy remains low.
Right after breakfast, the UCC heads back down for a second round of sampling so all teams can collect everything they need. By the time we finish processing the second deployment and finally step out of the lab container, one of us checks the clock. It is only 10 a.m…
The UCC is being led to the cleanroom lab (photo: NIOZ)
3 May - Get your sea legs ready for a safety drill!
Written by Eva Hekma
Flying fish and wobbly sea legs
Yesterday, we left the harbor. As the coastline slowly disappeared from sight and the waves grew higher, we all stood on deck watching flying fish shooting out of the water right alongside the ship. Not everyone was simply enjoying the view, though. Many of the researchers still had to find their sea legs. Fortunately, by this morning things already looked very different.
All equipment has been secured for the first wave
Fortunately, by this morning things already looked very different. By morning, most people found their balance, and the real work could begin. Working at sea comes with just a few more safety measures than working on land. Before we departed, we had already secured all of our lab equipment and crates to prevent our lab from suddenly deciding to conduct its own research at the first decent wave.
Seven short ones and one long one
After almost a day at sea, it was time for our first safety drill. Everyone was busy preparing for our first water samples when we paused our work. The ship’s horn sounded seven short blasts followed by one long blast, while the alarm systems inside joined in with loud, unmistakable beeping. That signal means only one thing: report to the muster station, the designated assembly point on deck. At first, that did not go entirely smoothly. A large part of the group was standing enthusiastically, but in the wrong place. Luckily, that is exactly why you practice.
Sea survival in practice
Once everyone had finally found the correct spot, the crew explained what to do if we ever had to abandon ship for real. Fortunately, much of this was already familiar thanks to the sea survival training we had completed beforehand. The specific procedures for this vessel were reviewed once more, but it was all a refresher. With safety once again fresh in our minds and our sea legs finally found, we were ready to get back to work with confidence.
Practice for abandoning ship: survival suit on, and head straight for the life raft. The lifebuoy is just for fun.
2 May - Ready to set sail, but we’ll have to wait a little longer
Written by Dedmer van de Waal
Arrival
There she was, the RV Anna Weber-van Bosse, the newest research vessel in the Dutch scientific fleet. After a seven-hour flight from Amsterdam, we arrived on Thursday 30 April in tropical Mindelo, the capital of the island of São Vicente in Cape Verde, off the African coast. After going through customs at the international port (well, we’re leaving the country again straight after arrival), we were able to board the ship. There we were introduced to our brand-new home for the next four weeks.
Who’s on board?
We are a diverse group comprising senior researchers, research assistants, post-docs, PhD students and undergraduates from various universities and colleges. In total, our scientific team is a colourful mix of 22 people from 7 countries. We are joined by the ship’s 15-strong crew, whose capable hands ensure that we can sail, eat and carry out our research.
Laboratory at sea
For our research, we need laboratories where we can process water samples. There are three permanent laboratory spaces on board, but that's not enough. Which is why we also have containers that are fitted out according to the researchers’ requirements. For example, there are labs equipped for filtering water samples. The suspended material (such as plankton) is retained on the filters, which we can then analyse. We use these to measure, for example, the total amount of algae in the water. We also use filters to analyse the DNA so that we can see which algae and viruses are present in the water.
Oh no, a delay…
Whilst we were busy setting up the laboratories, we received word that we couldn’t leave just yet. A number of formalities had caused a delay, whilst 1 May is a public holiday in Cape Verde. The advantage for our research team, however, was that we were able to set everything up and secure it properly in the calm waters of the harbour. Because the laboratories at sea… they’ll soon be moving with the waves!
…but we’ve set off!
The time has come; we can set sail! On Saturday 2 May, we received word that we were cleared to sail. After casting off from the jetty, we sailed towards the harbour mouth, out into the Atlantic Ocean and the real start of our adventure.
Project team
Corina Brussaard
Senior Research Leader
