PHYVIR expedition

In the weeks prior, sightings of marine macrofauna were few and far between. During lunch on our first day of sailing, Liam stood up and pointed at dolphins outside the window swimming alongside the ship. Dedmer posted himself at the front of the ship over the next few days and witnessed more dolphins playfully riding the bow wave. Through the nutrient-limited regions between Cape Verde and the Azores, our main nature sighting was beautiful, small Portuguese man o’ war. Sadly, we also saw pieces of plastic drift by. 

Of course, being microbiologists, we also enjoy glimpses of the organisms we are studying – phytoplankton! Corina or Hisham concentrates seawater samples each day so we can have a peek under the microscope. The concentrated water samples differ daily in species composition, offering exciting surprises each time. Recently seen: Dinophysis, a phytoplankton species responsible for harmful algal blooms (potentially toxic), and the diatom (with glass-like frustule) species Pseudo-nitzschia, and a surprising coccolithophore bloom (phytoplankton with calcium carbonate scales on the outside). And any time a copepod (adult or juvenile) zooms past is cause for excitement, “Copepod!!”. These adorable zooplankton were even inspiration for a story written by Eva during the Talent Event night.

Written by Hisham Shaikh (Post-doc NIOZ)

To kick off the final week of the PHYVIR I cruise, we retrieved the fourth - and last - drifting trap of the expedition. We were able to borrow this device from our NIOZ colleague Jan-Berend Stuut and it is an interesting addition to our research cruise across the North Atlantic. While Dorien Hoexum and I enjoyed working with these traps, we were not the only ones as the trap recoveries typically attracted some audience: people taking a break and interested in the occasional small animals in the traps. This final recovery came with very special visitors. A pod of long-finned pilot whales, including at least two calves, approached the ship with obvious curiosity. It was the closest these whales have come to our floating home for the past few weeks, the research vessel Anna Weber-van Bosse. A pretty incredible send-off as we lifted the final traps from the ocean.

So, what exactly are drifting traps and why did we deploy them? 

Drifting traps are a set of tubes at different depths that collect sinking particles from the sunlit surface waters. We deployed four drifting traps during this cruise, each carrying tubes positioned at 100, 200, and 400 m depth. As particles sink through the ocean, they are captured in these tubes. Our goal is to understand how viruses may influence the sinking of phytoplankton, that form the base of marine food webs and play a major role in removing carbon dioxide from the atmosphere. Sinking or sedimentation transports this carbon to the depths of the ocean. On its way down these particles are also degraded so finally there is only a very small percentage reaching the seafloor. We determine the sinking potential of the different phytoplankton populations (see earlier blog by Li Zhao) and the drifting traps is a natural extension of that. As there are indications that some phytoplankton groups are prone to aggregating upon viral infection, we specifically like to study which phytoplankton can be found in these sinking aggregates. 

Some tubes preserve the fragile aggregates in a gel on the bottom of the tube so we can study their shape and abundance. Others are used to do so-called bulk measurements on; the abundance and genetic composition of phytoplankton, bacteria and viruses; the total concentration of chlorophyll, and the transparent exopolymeric particles (TEP) that forms  sticky precursor of aggregates and make them sink faster. By sequencing DNA and RNA from the traps, we aim to uncover which viruses are infecting these sinking phytoplankton communities, and how these microscopic interactions may influence the ocean’s ability to store carbon in the deep sea. 

21 May – Are the cells feeling alright?

Written by Xiaonan Cai (PhD student at NIOO)

Tiny cells, big clues

The ocean is full of phytoplankton. These tiny organisms form the base of marine food webs and help take up CO₂ from the atmosphere. But phytoplankton are not all the same: different species have different sizes, shapes, and ways of using light and nutrients.

Because of this, phytoplankton communities can change strongly from one place to another. A community in warm, nutrient-poor subtropical waters may look very different from one in colder, nutrient-rich sub-polar waters. During our transect across the North Atlantic Ocean from south to north, one of the questions we are interested in is: how healthy are these phytoplankton cells, and does their photosynthetic capacity and cellular composition change along the way and is that related to external causes such as changes in environmental conditions or viral infection?

Phytoplankton cells carry chemical clues that help us decipher this. One important clue is elemental stoichiometry: the balance of carbon, nitrogen, and phosphorus inside the cells, often written as the ratio of C:N:P. These elements are essential for growth, metabolism, and energy transfer. When the C:N:P balance shifts, it may suggest that cells are adjusting to their environment, experiencing nutrient stress, or changing how they grow. 

This is also important for understanding phytoplankton–virus interactions. Being parasites, viruses depend on their hosts to reproduce, so the condition of the host may influence how successful the production of new virus particles will be. A nutrient-stressed cell may not provide the same resources as a healthy cell. 

Health across different size groups

Phytoplankton are often grouped into different size classes: microphytoplankton are about 20–200 µm, nanophytoplankton about 3–20 µm, and picophytoplankton 0.3-3 µm. These size classes do not always respond to environmental stressors in the same way. Smaller-sized cells often do well even in nutrient-poor waters because they are efficient at taking up nutrients, while larger cells may become more abundant when nutrients are more available. 

During the cruise, we collect seawater and filter it step by step through filters with different pore sizes. This allows us to separate the phytoplankton community into these different size fractions. Sometimes, the filtration itself already gives us a first impression of the water: if the filters clog quickly and the water passes through very slowly, there is probably more particulate material, including phytoplankton biomass. Later, back in the laboratory, we will analyse the filters for elemental composition and the main pigment that phytoplankton contain, i.e., chlorophyll-a. Together, these measurements help us see not only how much phytoplankton material is present, but also how their chemical compositions differ.

Written by Melle Versluis (PhD cndidate UvA), Xiaonan Cai (PhD candidate NIOO) and Amelie Wittig (masterstudent UvA)

We started our expedition in tropical waters, where everyone could get used to the daily routines on a research ship in calm and sunny weather. But since we are heading towards Iceland, we were all aware that we cannot count on such calm and flat conditions throughout our entire journey. Yesterday we finally got to experience rougher seas for the first time and the whole experience changed immediately. 

Having seen the predicted wave height in advance, we adjusted the scientific program accordingly. For our team this meant sampling our experiment earlier in the day. The sampling involves carrying 20L cubitainers, in which we incubate water for our experiments, from the incubators in the front of the ship to the ultraclean container (where we sample under clean conditions to avoid contamination) in the back, with two flights of stairs in between. We brought special backpacks to be able to do this safely, and it is a team effort to carry 18 cubitainers back and forth. But in rough seas walking straight becomes close to impossible even without 20kg of extra weight. Thus we rushed to sample earlier in the day and with extra support from the crew we managed to do it faster than ever before. Luckily so, because once the heavy lifting was done and we could focus on processing our samples in the lab containers, keeping the balance became more difficult. Before we knew it, we found ourselves clinging to a lab table or leaning to a wall in order to stay on our legs. Luckily, we had strapped down every single item in our lab container well in advance and sample processing proceeded smoothly. 

However, when sitting down for dinner after a long day of work, coordination became even more difficult. On the long dinner tables plates with food were sliding from one person to the next and soon after, even people started sliding sideways while sitting on their chairs. Holding on to the table while also keeping plates and glasses in place did not allow for comfortable eating, and most of us  quickly gobbled down some food, to seek a more stable place as soon as possible. Yet such places were not to be found on the ship anymore, instead we had to rush back to the lab to secure the last pieces that could still move: lab chairs, computer screens and fridge and freezer doors all needed some extra straps, before we could call it a day. And even then, rest is hard to find when moving sideways with each wave while trying to fall asleep…

18 May - Following the flow: studying phytoplankton at sea

Written by Emma Hynes (UvA MSc student 2026 at UvA) 

As we get closer to our half-way mark on board, my group is beginning the second set-up of our experiments. These experiments consist of so-called microcosms and in my case flow cytometry, a method used to detect and count the different populations of phytoplankton. We take water from the upper water column and incubate them in containers on board to be able to look at live interactions and changes in the populations of phytoplankton in response to us adding nutrients (nitrogen, phosphorus, iron) that potentially limit that growth of the algae.

Counting fresh samples is a very exciting opportunity as many earlier phytoplankton studies used ‘fixed’ samples. Fixing meaning adding a fixative (e.g., formaldehyde or glutaraldehyde) followed by freezing the samples and stored them at -80°C for analysis when back home. This is nice as it gives us the ability to take also samples when we do not have the flow cytometer at hand, but it also has a downside. Fixing samples can lead to reduced pigment (chlorophyll) fluorescence, making it harder to discriminate all phytoplankton groups that we see when counting fresh. Especially a specific group of algae found in the warmer waters and where some of my experiment focuses on. When using live samples on board we can see the entire composition with no degradation.

As mentioned in a previous blog post, iron is ‘micro’ nutrient that is important for all life, including phytoplankton. It is generally found in very low concentrations (hence micro- or trace-nutrient) and can be particularly limiting in certain areas in the global ocean. If we think of how much iron is found in the nutrient poor waters we are in now, it’s the same as a paperclip in an Olympic sized swimming pool.

We incubate 1L and 20L incubations and in these experiments, we’re focusing on which nutrients limitations affect the population composition over a 4-day period. After all, like how plants need fertiliser to grow, algae need nutrients too.

16 May - Life inside container #21

Written by Naomi Bakken (UvA) and Lea Simon (RUG)

Hello… Who is there?

Phytoplankton may be tiny, but they are some of the most important organisms in the ocean. These microbes form the foundation of almost every marine food web and even help regulate Earth’s climate by absorbing carbon dioxide. Understanding what helps them thrive, and what threatens them, is therefore incredibly important.

One major threat comes from viruses. When a phytoplankton cell becomes infected, it usually dies. Across the oceans, countless invisible battles between phytoplankton and viruses are constantly taking place, shaping marine ecosystems in ways we are only beginning to understand. This interaction is exactly what the PHYVIR project aims to explore.

The challenge is that these organisms are far too small to see easily, even with standard microscopes. So instead of identifying them by sight or pigment composition, we use something we – the writers of this blog - think is way cooler… their DNA. This is the genetic information that most microbes have which can be used to identify them, think of it as a molecular fingerprint. We filter a lot of seawater onto a filter which we store and take back to the laboratory. There, we can extract the DNA from the sample, sequence it and puzzle it back together to identify which phytoplankton, and using another filter type also which viruses, were present at our sampling stations.

But what are they doing?

But it does not stop there. Knowing who is present is useful, but we also want to know what they are doing. We can investigate this by looking at another molecule called RNA. Why is that? RNA gives us information about which parts of the DNA are being used at a given time. Responses to changing conditions may for example result in reduced photosynthesis, also to focus their energy towards responding to the stress induced.

Viral infection can also be considered a stressor. Viruses are obligate parasites, meaning they depend on their phytoplankton hosts’ cellular machinery to reproduce. Some of this reproductive activity is reflected in the RNA during infection. Using these signals, we can identify active viral infections.

We are also interested in phytoplankton RNA during viral infection because viruses can sometimes alter how their hosts function beyond basic replication. For example, a virus might require different nutrients than its host normally uses and can influence the host’s RNA to activate pathways that increase uptake of those nutrients.

Finally, some viruses have RNA as their only genetic material, which is relatively uncommon in biology. Because of this, DNA-based methods are not sufficient to detect all viruses present, but we can still gain insight into their presence by studying RNA. The analysis of viral genes expression (including RNA viruses) will be done in collaboration with others in the PHYVIR project.

Where do we work?

We work together in Lab Container 21, which is exactly what it sounds like: a converted shipping container set up as a laboratory. Having separate containers for different types of research is useful because conditions inside can be carefully controlled. For example, we adjust the temperature every day to match the seawater, so that the microbes experience as little stress as possible when we bring them inside.

We need to work clean to avoid contamination. This can be challenging, especially when equipment such as filtering systems can leak, but there are strategies to manage this. The main sources of contamination we worry about are enzymes called RNases and DNases, which break down the RNA and DNA we collect. These enzymes are widespread in our environment: in seawater, on our skin, and on lab benches. As a result, we spend a lot of time cleaning.

Wearing gloves is a must. The goal is to avoid contaminating our samples with genetic material from our surroundings, including our own.

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.

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.

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!

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!

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.

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.

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) 

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