2018 Cruise - JC165

JC165 returns to Southampton!

As we head from the Porcupine Abyssal Plain to Southampton the seas turn from a crystal blue to ever increasing shades of green. The seas calm and our pace changes from going from station to station over to cleaning, organizing, packing and thinking of what we will do next time.

One of my main areas of interest is tracing the influence of climate through the upper ocean. This includes production of algae and plankton at the sun-lit surface and the sinking of some of this carbon-rich material (marine snow) through the water column and onto the seafloor. Because this sinking marine snow is a key food source for life on the seafloor, climate variation can have a close connection to abyssal marine life even though it’s separated from the atmosphere by three miles of cold dark water.

The PAP- Sustained Observatory systems have one of the most comprehensive sets of tools in the world to address this climate to seafloor connection. On this research cruise we have been able to take extensive sets of seafloor samples and photographs that will be used to make some of the most detailed estimates of the amount of life found on the abyssal seafloor. Accurate estimates of the sinking marine snow and the mass of seafloor life help track the stock and flow of carbon in the ocean. Estimates of how climate change might alter seafloor life in the Northeast Atlantic suggest that the mass of life at the PAP-SO could decrease by nearly 50% in a century (https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.13680). So making accurate estimates now is critical to understanding how this globally important change might occur.


The effort is only possible because of the efforts of the officers, crew, technical support and science teams working together and this trip had some unusual challenges. These included servicing one of the tallest moorings in the world as well as running one of the deepest trawl tows still done today. Thanks very much to them, only some of whom are pictured below.


So now it’s back to our labs, workshops and offices to look at what we have found and what the observatory will tell us as it reports data back to shore throughout the year (http://projects.noc.ac.uk/pap/data). And back to life ashore with family, friends and summer coming right along.


Written by Henry Ruhl.

2018 Cruise - JC165

Molecular ecology at PAP

This is my fourth PAP cruise, and it has been a great trip. During this cruise, I have been collecting samples from the amphipod trap, the CTD, the megacore, and the trawl. I am a molecular ecologist, which means that I use molecules like DNA to make inferences about ecology. Every living organism, from microbes to humans has DNA, which is the molecule that encodes the information that the organism uses to grow from an egg to an adult and that the organism eventually passes on to its own offspring. It is a combination of the transmission of this molecule between generations from parent to offspring and the fact that every time it is replicated, the copy contains small differences from the original molecule that allows us to use it to infer properties of the ecology of a species.

For example, we can use DNA to track the movement of individuals between populations, to identify new species, or to reconstruct the evolutionary history of groups of animals. We can determine the DNA sequence of whole genomes, like those of bacteria, that tell us what types of compounds the bacteria might be able to consume. We can use the bits of DNA shed into the environment, like a forensic detective, to detect the presence of animals even if we haven’t observed them directly. We will be using all of these approaches on the samples that we collected this trip.

We collect water samples with the CTD throughout the water column, from the surface to just a few meters off of the seafloor, and we filter those samples to collect any material as small as 0.2 microns (about 1/200th the width of a human hair). The filter traps most bacteria and any larger material, from which we extract DNA and find out its sequence. From this information, we can tell what species are in the water that we collected and how those species change by depth, by the time of year, or over many years. We can tell what types of microbes are responsible for breaking down various compounds to help us understanding how photosynthetically produced carbon at the surface is turned back into carbon dioxide as it sinks through the water column.

Figure 1. Holothurians observed during the HyBIS dive.

We also extract DNA from the sediments samples that we collect with the megacore to find out which species are in the sediment and how diverse the sediment microbial communities are. We can determine how microbial communities are changing in the sediment in response to varying amounts of food arriving from the surface and what role they play in the energy budget for larger members of benthic communities. Even though microbes represent the vast majority of genetic diversity on our planet, we understand less about their ecological roles, because we cannot culture most microbes in the lab. Applying genetic and genomic tools to these environmental samples helps us to understand their roles in these ecosystems, even though we can’t culture them in the lab.

Every year we sort and preserve animals from the trawl and the amphipod traps for DNA analysis. We look for new species among the samples that we collect. This past year, using a combination of morphological analysis and DNA methods on samples that we collected on previous cruises, Tammy Horton (who curates the Discovery Collection at NOC) and I have found a new species of amphipod at PAP, even though researchers have been visiting the site for over 30 years. We will continue to search for new species in the samples that we collected this year.

Our target species from the trawl this year were the holothurians (sea cucumbers). Holothurians are some of the most numerous animals that we find at PAP. But we were not just interested in the sea cucumbers themselves. We were specifically going after the microbes in their guts. We dissected the gut contents out of individuals belonging to the 8 species that we came across this year, building up our collection from the previous two cruises. Our objective is to describe the microbial communities that live in the guts of these holothurians and to determine what roles the microbes play in helping the host species digest the material that they come across in the different ecological niches that they occupy. We want to know if there are any microbes that only occur in specific holothurian species and if these microbes help the host by specializing on specific types of compounds. By comparing the microbes in the water column, the sediment, and the dominant grazers in this environment, we will have a better understanding of how carbon and other nutrients flow through these ecological systems.

diversity of holothurians
Figure 2. Diversity of holothurians collected from the trawls.

The association of holothurians and their microbiomes begs the question: Are the holothurians cleverly taking advantage of the microbes’ diverse genetic metabolic repertoire to extract more energy from the environment, or have the microbes co-opted the holothurians as convenient vehicles to transport them efficiently to their preferred resources?


Written by Rob Young

2018 Cruise - JC165

Manoeuvring the RRS James Cook

My name is Adrian and I am a Deck Officer Cadet on board the ship. I am training to be an Officer of the Watch and spend a lot of my time on the ship’s bridge. The bridge is where all the key aspects of navigation take place such as manoeuvring and keeping a look-out for other vessels and navigational hazards. We also monitor all the deck and science operations.

View From the Bridge

During science cruises one of the most important things we are required to do is to manoeuvre the ship in a way that ensures the best results. Some operations, such as those that use the Megacore or CTD, require the ship to be stationary above the ground. Others, such as using the HYBIS to observe the sea-bed, may need us to maintain a constant speed and course along a track with many waypoints. We also require accurate manoeuvring to provide the best results during picking up of science equipment in the sea as well as triangulation. These things can be very difficult to do manually as you have to constantly provide thrust to account for wind and current.

DP Console

To help us achieve accurate positioning and manoeuvring we use a Dynamic Positioning (DP) system on board. This is a complex system, which uses an array of sensors to determine the vessel’s current position, vector and how much it’s being offset by other forces such as wind and current. It uses the data gathered to build a model of the various forces acting on the ship and determines what amount of thrust is required to maintain the position or manoeuvre. This allows us to position the ship exactly where it is needed with an accuracy of less than half a metre.


To provide the thrust required the ship has several methods to provide propulsion. There are two main shaft propellers, two rudders, three tunnel thrusters and a retractable azimuth propeller. The main propellers provide forwards and astern propulsion whilst working with the rudder to control the heading of the ship. The tunnel thrusters provide athwartships propulsion and can be used to help turn the ship and maintain a heading, or to ‘crab’ which is to move the vessel sideways, furthermore they can be used to do both of these things at the same time. The retractable azimuth thruster is a propeller which can be turned on the vertical axis to point in any direction with an arc of 360° and can be retracted back into the hull of the ship when not in use. This allows for greater amounts of thrust to be provided where it is needed.

Approaching PAP3 ODAS Buoy

As you can imagine, manually controlling all of the thrusters at the same time would require a great amount of skill and effort. By having a DP system to control all of them according to the instructions given by the Officer we can achieve the accuracy needed to provide the best results for our science operations. It also makes it a lot easier to manoeuvre the ship whilst still being in control. The system can be configured to our needs, such as automatically maintaining sway (sideways movement) and yaw, whilst giving control of surge (forwards and astern movement) to the Officer.


Sunset departing Southampton_2



Written by Adrian Reid



2018 Cruise - JC165

Searching for larvae in the deep sea!

So here I am again, about one year later, on the exact same site in the North Atlantic Ocean, the Porcupine Abyssal Plain Sustained Observatory (PAP-SO). This is among the oldest time-series stations in the world, which has been collecting data all the way from the surface of the ocean, across the water column to the seafloor, nearly 5 km deep. During just over three weeks, scientists, engineers and crew are working together to recover old instruments and deploy new ones in the ocean. The data collected with these instruments is transferred to the computers and laboratories onboard the ship, where they can look at the information and compare it with previous years.The kind of data collected are varied and include many chemical and physical parameters of the water, like oxygen, nutrients and temperature. During the cruise several other gear types (e.g. plankton nets, megacore, trawl and towed cameras) are used to collect biological information about small animals swimming around in the water (zooplankton) or buried in the sediment (benthic macrofauna and meiofauna), and larger organisms (megafauna) that live on the seafloor.

From such a comprehensive sampling program, scientists have been able to study patterns in diversity and abundance of the species and relate these patterns with changing ocean characteristics over the years. These long-term studies are very important to understand how natural changes, for example climate and food supply, and human activities (e.g. pollution, and overfishing) can impact the marine environment and its biodiversity. One critical aspect to know how marine animals survive and adapt to changing oceans is called population connectivity. In the same way that people travel around the world and move to new places, marine populations also exchange individuals among different geographic sites. While some of these movements are made by actively swimming between locations, others result from passive transport by oceans’ currents. But, how do species living on the seafloor disperse, and maintain populations across wide geographical areas? Most benthic animals have very limited movement, slowly crawling around (e.g. sea cucumbers and sea stars), or even staying at the same place for most of their life (e.g. mussels, anemones and sponges). However, many benthic species have a larval stage that can live in the water column and be transported hundreds or thousands of kilometres away from their parents.

Studying larvae from deep-sea species is extremely difficult because larvae are minute (a couple tenths of a millimetre) and very hard to collect in deep waters. Ocean observatories provide a great opportunity to test new sampling methods and standardize approaches, which may then be used simultaneously across the world to give us a global view of ocean’s health in space and time. With the goal to know more about larval diversity and distribution in the deep sea, I’ve started to deploy a series of larval traps in several deep-ocean moorings in the North East Atlantic and Mediterranean Sea. I also attached the traps to experimental substrates that larvae could use to settle and grow (see DY077 RRS Discovery cruise 2017), thus giving us a better understanding of population connectivity. Last Sunday, I collected the second set of samples from the sediment trap mooring at PAP-SO and preserved the samples onboard to observe them under the microscope when I return to my land-based laboratory at the University of Aveiro in Portugal.

recovery of larval traps
Figure 1.  Recovery of larval traps and colonization frames from PAP3 mooring

Last year, I also deployed traps attached to the Bathysnap mooring – a metal frame that hosts the time-lapse camera, but yesterday we couldn’t retrieve it. A malfunction of some kind has so far prevented the mooring from coming to the surface, so it is very likely still sitting on the seafloor. Next year, we may be able to bring an additional sonar to aid in locating and recovering the camera and also the larval traps and substrates. This misfortune may in turn reveal exciting new data since a longer time on the bottom will potentially allow more animals to fall in the larval traps and colonize the substrates. A new Bathysnap is now being prepared for deployment and I can’t wait to see what will come back next year.

larval trap recovery
Figure 2. Larval trap sample recovered from PAP3 mooring. 



Written by Luciana Génio.

2018 Cruise - JC165

Studying Ocean Acidification at PAP

Written by Sue Hartman.

The amount of biologically active dissolved gases in the surface ocean, such as oxygen and carbon dioxide, changes throughout the year. This seasonal change is influenced by temperature and the growth of plankton. The sensors that we have deployed track changes in all of these variables along with changes in the nutrients that influence the plankton growth.

CO2 team
Figure 1.  ‘Team CO2’ – setting up the new equipment to measure seawater and atmospheric carbon dioxide.

We now have a long time series of measurements and can see both the seasonal and year to year variations. Examples of the data are on the PAP website www.noc.ac.uk/pap/data. The cold, productive waters of the North Atlantic are especially interesting to study changes in carbon dioxide; this area is a sink for this important greenhouse gas. Whilst this oceanic sink may reduce the atmospheric carbon dioxide the water acidity is increasing and this can have harmful effects on some species. A process very similar to adding dissolved carbon dioxide to water to make soda water. We can track the increase in ocean acidification (a decrease in pH) through direct measurements of pH as well as measuring carbon dioxide.



Figure 2.  The box for atmospheric carbon dioxide measurements high up on the buoy mast.


The data will be calibrated using the bottle samples – once they have been measured back at NOC. Each year we collect bottle samples to full ocean depth to give us profiles of oxygen, nutrients, carbon dioxide and pH. All of these measurements are used to monitor the influence of ocean acidification at depth and to consider changes in relation to the longer time series.  Currently we are also setting up an underway system to measure carbon dioxide, temperature, salinity and oxygen with the sensors that we have on board to compare with the ships underway systems.




Figure 3. The pelagic team sampling from the CTD rosette for oxygen, nutrients, dissolved inorganic carbon, chlorophyll and temperature.
2018 Cruise - JC165

Deployment of the PAP1 mooring



The PAP 1 mooring is a collaboration between four organisations, NMF, OBE, The Met Office and OTEG. Overall design, development and deployment of the physical system is the responsibility of the Sensors and Moorings (S&M) team within the National Marine Facilities (NMF). The surface buoy (a Balmoral ODAS buoy) complete with meteorological sensors is supplied by the Met Office. Ocean Technology and Engineering Group (OTEG) with extensive support from Campbell Ocean Data, look after the electronics communications and power hub and real-time data stream as well as occasional trial sensor deployments. The specifications and scientific data are provided by and for thecustomer; the Ocean  Biogeochemistry and Ecosystems Group.


The mooring is over 6.5 kilometres in length and sits in 4850 metres (m) of water giving it a 4 kilometre plus watch circle. The majority of the scientific instruments are house in the Autonomous Sensor Platform (ASP) suspended 30 m below the surface buoy.


Most years the top end of the mooring including the ODAS buoy and the ASP and chain are all that is replaced. This year for the first time in four years, the entire mooring has been serviced, which unusually included stripping down and rebuilding the ODAS buoy at sea to replace the keel and many of the meteorological sensors.


Written by Nick Rundle

Senior Technical Officer

2018 Cruise - JC165

Gaining experience on the high seas!

If someone had told me in May of 2016 that in two years time I’d be on a research cruise to the PAP-SO, I would not have had a clue what they were talking about. At that time I’d been working for 4 years on commercial fishing boats as a fisheries biologist in Alaska and only just starting to look for other opportunities, particularly in higher education.

I hadn’t even heard of NOC, the James Cook, or the University of Southampton. Yet here I stand, an inexperienced masters student with the deep seas benthic group taking full advantage of every opportunity; slicing megacore samples, cutting through fish for amphipods, putting together traps, sieving zooplankton, labeling everything, asking questions, and peering over other people’s shoulders.


Blessed with inexperience, every moment is a learning opportunity. Even at the birthday celebration onboard I had a discussion that pertained to my masters thesis and European conservation efforts. The easiest way to start a conversation is asking someone about their day, and in doing so learn the many aspects of studies being conducted onboard. Lunch topics have included individual projects (who knew there was deep sea fungus?), HyBIS, how courses work in different countries, funding, the CTD sensors, amphipods, holothurians, tardigrades, abyssal fishes, writing proposals, the prospective trawls, and how everyone has gotten to being a part of the cruise. Just walking down the hall yesterday I peered into a bucket containing a portion of a deep zooplankton tow and saw a chaetognath and a very active amphipod. I helped with a zooplankton night tow and saw a couple hundred active amphipods, copepods, glowing blue flashes, and even a few pteropods!


Going through the cores every night could become monotonous, but the benthic gang turns up some tunes and most nights there is something to investigate at the top of a core. The excitement of seeing something, really anything from those depths, instantly has all of us crowd a core. Is it a foram? A polychaete? More green fluff? In the past day we’ve added pteropod test, large xenophyophore, and unknown ascidean to the list! Just this morning the group collected two unknown items from the top of the sediment, including the unknown ascidean, which looks like a beautiful, nearly blooming flower under the microscope.JC165

Surrounded by interesting equipment, samples, and people aboard the RRS James Cook, I’m soaking it all in and enjoying.


Written by Virginia Biede.



2018 Cruise - JC165

Baited beasties, or the scavengers of the deep.

Our first amphipod trap was deployed on Sunday morning and left to ‘soak’ on the PAP seafloor for about 40 hours before recovery. Amphipods are small crustaceans, shrimp-like in form but without a carapace, bearing different kinds of appendages on their thorax and abdomen, with impressive claw-like structures that can grip almost anything. The amphipods we collect at PAP are bentho-pelagic; they live on or close to the seabed and they are particularly ferocious! In fact, like piranha in the Amazon River, they can devour any ‘attractive’ prey, whether alive or dead. To attract these little deep-sea beasts, we use four dead mackerel as bait placed in funnels inside large cylindrical tubes mounted on a sampler that we simply call the “Amphipod Trap”. Deep seas are usually food-limited environments; benthic fauna relies mostly on the particulate organic matter that originates in surface waters and degrades through the water column before reaching the seafloor. We use the mackerel to simulate a natural food-fall that will appeal to scavengers.

Figure 1. Scientists waiting for the Amphipod Trap to come up to surface (left), and crew members trying to catch the trap with a hooked rope (right).

The trap is deployed from the afterdeck and sinks down to the Porcupine Abyssal Plain. A pair of bottom tubes containing the mackerel sits about 50 cm above the seafloor, and a top pair sits about 1 m above. When they smell the dead fish, the amphipods, many of the genus Eurythenes, swim into the funnels where they end up sampled. Depending on how many amphipods are trapped in the funnels and how long we leave the trap in the water, we sometimes only recover the bones of the fish (see DY077 Discovery 2017-cruise), and observe the largest specimens already eating the smallest ones. As if a whole mackerel was not enough!

Figure 2. Amphipod trap recovery on the after deck. A mackerel was placed as bait inside each of the four funnels to attract the deep-sea amphipods.

To recover the trap scientists release a trigger that ‘calls’ the sampler to come up to the surface. Crew members then catch the trap using a hooked rope before it can be brought back on the afterdeck. It is then our turn, were we process the samples; we collect all individuals caught in the trap and preserve them in ethanol. This will allow morphological and genetic analysis once back at NOC in Southampton.

Figure 3. Scientists part of the ‘Benthic Team’ picking out all amphipods trapped in the funnels before preservation with ethanol (top).
Example of deep-sea amphipods (bottom), many of the genus Eurythenes, collected on the PAP seafloor. Note the broad body-size range and morphologies of these little, necrophagous, creatures.

During this first deployment, the fish were not completely eaten, yet we collected a few hundreds of individuals. We aim at deploying at least two sets of samples during the cruise. NOC scientists have been collecting these deep-sea amphipods at PAP for over 30 years in order to assess any change in species abundance, diversity, and composition over time. These biological data are then related to local environmental factors such as food supply to the seabed and temperature that may explain the observed patterns of the baited beasties.


Written by Noëlie Benoist.

2018 Cruise - JC165

RRS James Cook Ship Systems

I am regularly asked “How did you go from oceanography research to becoming an IT technician?” … well. Let me explain. As one of the Scientific Ship Systems tech’s on the James Cook I don’t just look after computers. We support all of the scientific instrumentation that is physically fitted to the ship, and all the infrastructure to enable data acquisition, storage and transmission.

Each deployment to the sea bed is reliant on instruments that we support. I can tell you that the current depth is 4728 metres (m). This is provided by two echo sounders which are built into the hull; one is a single beam, and the other is a multibeam which we use for sea floor mapping. The surface water temperature is 12.8 °C and salinity is 35.54, as measured by instruments in the underway sampling system. The air temperature is 11.4 °C and the wind speed is 19.8 knots. These measurements come from the meteorological instruments that we look after on the bow of the ship.

Figure 1. The screen bank of RRS James Cook

At the moment the megacore is on its way to the sea bed and is currently at a depth of 1755 m and is descending at a rate of 50 m per min. On the core frame is a USBL beacon so we can provide high accuracy positioning of the instrument, knowing exactly where the sediment samples came from.

We record all these data and transmit this information all over the ship which means that although I’m in my cabin, I know what’s going on by checking the intranet live data feed. Some of the data is transmitted off the ship, feeding into weather and ocean forecasting models. Our data feeds support so many other operations onboard, such as the CTD and HyBIS.

All the data is synchronised into a file storage system and made accessible through the internal network for the scientists to work with. The network brings us back to IT because computers are a central part in data acquisition and processing. In between the computers and the instruments are several kilometres of wiring that we have to navigate; if an instrument isn’t getting the data feed it needs, we work out how to fix it. So yes, there is a lot of IT, but it is mainly understanding numerous scientific systems which are central in supporting oceanographic research.

I will end this post here by placing it in the public drive for the blog master to pick up over the network, and then upload via the satellite internet (yes, another system we look after!). If you want to know more about the RRS James Cook, read on here: http://noc.ac.uk/facilities/ships/rrs-james-cook

Date: 31/05/18 J151 20:48:42 << From a precision network clock

Position: 48° 58.94′ N 016° 33.03′ W << From one of scientific GPS’s. Copy into google to see in a map for yourself.


Written by Eleanor Darlington

2018 Cruise - JC165

Zooplankton sampling in the flAtlantic

At noon today we deployed our zooplankton nets into the flattest water I have ever experienced at the PAP-SO. We recovered an amazingly large number of zooplankton (microscopic animals).

zoopOur moorings at the PAP-SO provide year round data on primary production (growth of microscopic algae), nutrient cycling and carbon export (see sediment trap post), but do not yet give a full picture of secondary production – the feeding and growth of zooplankton. We use zooplankton nets to evaluate secondary production and fill in some of the missing pieces of our open ocean jigsaw puzzle. On land such animals are called herbivores (plant eaters) but in the ocean the food web is incredibly complex and our nets capture zooplankton that feed on microscopic  algae and on each other.

We lower our net to 200 metres and bring it back to the surface collecting an amazing zoo of animals along the way. Some of the samples are sub-divided into different sizes. Back at NOC we will run sub-samples through a FlowCam system to count and measure the animals and build up a picture library.

Below are two samples collected using exactly the same methods and at similar times, but on different days. It is really important for us to make sure that every time we take a sample, we follow exactly the same methods- we even make sure that the net is brought up at the same speed each time. This is because when we find differences we need to know that it is real variation that we are seeing and not experimental error. There is great example below.

Thank you to Chris Cardwell for the pictures!

The two samples are different in space and time and illustrate patchiness, the huge variation of zooplankton abundance on quite small scales, that makes it really difficult to quantify how much zooplankton are where and what sorts are present. We know that we treated these two sampling events in exactly the same way so what we are seeing is real. Perhaps the windy days at the beginning of the week mixed nutrients and phytoplankton together. Then with the calm we now see, that allowed the phytoplankton to stay in the warm water near the surface and grow super-fast.

We care about such changes because the types of zooplankton have an important impact on the sinking marine snow (see the Sediment Trap blog for marine snow). Zooplankton influence the carbon cycle. So although this is really difficult to investigate, we must try to measure it so that we can more fully understand the carbon cycle and ocean carbon sequestration (storage at depth).

This is something that is also being investigated by other scientists from the NOC who are now on board the RRS Discovery, sampling off Namibia as part of the COMICS program. Here is a link to that project: http://comics.ac.uk. We look forward to building up such perspectives for the Global Ocean.


Written by Corinne Pebody