Blog Posts

2018 Cruise - JC165

Imaging the sea bed

Yesterday we completed the third successful deployment of the HyBIS system (Hydraulic Benthic Interactive Sampler). HyBIS is one of several underwater vehicles operated by the National Oceanography Centre to study deep-ocean seabed environments. It consists of a stain-less steel frame that carries several underwater cameras designed to observe the environment and to monitor the vehicle’s operating systems, which include a steering unit with two propellers and a complex array of telemetry, hydraulic, and electrical systems. This includes a special ultra-Short baseLine (USBL) beacon that helps map the HyBIS position as we survey. Additional ocean bottom sensors and sampling devices can be attached to the frame, depending on the aims of the mission.

Figure 1_HyBIS on deck
Figure 1. HyBIS on deck the RRS James Cook. The remotely controlled submersible system is deployed over the starboard side of the ship. Energy is supplied from a high-voltage power source on the vessel via an umbilical cable. The vehicle’s systems are designed to operate at depths of up to 6000 metres. Images of the seabed are captured with the downward facing camera.
Figure 2_Image display
Figure 2. Imaging the deep. Left: A large computer screen in the ship’s observation lab allows the scientists and crew to watch real-time video from the HyBIS Ultra-High Definition camera system. Right: Typical still image from the PAP abyssal plain showing the soft seabed. Video is recorded continuously and still images are typically taken every 5 seconds.  

During this year’s PAP cruise, HyBIS is deployed to collect seafloor images from the abyssal plain and, if possible, from abyssal hills. We use the image data to study the larger invertebrates that live on the seafloor such as sponges, anemones, worms and echinoderms. We call this group of organisms benthic megafauna. Back ashore, we will be counting the number and types of the organisms on the photographs to describe the diversity and the composition of the species assemblages.

We will also be measuring the body size of the organisms to estimate the mass of the living megafauna (biomass). We will be using the biomass data together with the physical and chemical data that we collect at PAP to assess the links between surface carbon production, sinking carbon fluxes (marine snow) to the seabed (food supply) and deep-ocean biomass distributions (food demand). We will also be comparing this year’s observations with image data collected in previous years to assess how the megafaunal communities at PAP are changing over time and to help answering questions about impacts of climate change on ocean carbon budgets and deep-ocean food webs.


Figure 3a
Figure 3. Examples of benthic sea cucumbers observed during the first two dives of HyBIS in water depths of about 4850 meters



Figure 3b
Figure 4. Examples of benthic megafauna observed during the first two dives of HyBIS.


Figure 3c
Figure 5. Examples of Lebensspuren (life traces) that can be seen on the seabed of the Porcupine Abyssal Plain. Left: Central mound surrounded by several small depressions possibly created by one or more acorn worms (Enteropneusta). Right: Central burrow hole with radial extending feeding tracks likely created by an annelid worm. 


Written by Simone Pfeifer

2018 Cruise - JC165

Sediment Trap Recovery

27 May, 2018.

Today we recovered the Sediment Trap Mooring that we deployed on our cruise last year on the RRS Discovery (DY077).

Figure 1. Recovery of a sediment trap on board JC165.

Sediment traps collect particles that sink through the water column from the surface to the seabed – which at the PAP-SO is 4850 metres down, just over three miles deep. The particles, sometimes referred to as marine snow, fall inside the yellow funnel into the bottle underneath. The trap is programmed to rotate the bottles so collects a sequence of bottle samples over the years’ deployment. We deploy traps at different depths from 100 metres above the bottom to 2000 metres above the bottom. This means that the top of the mooring is still 3000 metres deep so completely invisible from the surface. When we come back to collect the mooring, we send an acoustic signal, which then brings the whole mooring to the surface. It is so deep that it takes almost an hour for the top floats to reach the surface where we can see them. The bottom of the mooring takes even longer.



Figure 2. Control box sending the acoustic signal to the sediment traps.

We use four different traps so that we can measure the marine snow at different depths in the water column. When we bring the samples back to the National Oceanography Centre (NOC), we measure the collected material in many different ways (such as Volume, Dry weight and Organic Carbon) so we can understand what the marine snow is made up of and how it changes as it sinks through the open ocean waters.


Figure 3. Tubes collect the falling particles over the whole year.

The phytoplankton (microscopic plants) in the surface waters draw down carbon dioxide from the atmosphere so that they can grow. Zooplankton (microscopic animals) feed on the phytoplankton and in turn are fed upon by nekton (bigger animals such as fish). Together the phytoplankton, zooplankton and nekton create marine snow from their cells, moults, feeding and faeces, forming what scientist call the Biological Carbon Pump. It is called a pump because it moves the carbon from the atmosphere down into the deep ocean. If the oceans didn’t have a Biological Pump there would be much more carbon dioxide in the atmosphere.

sed data

Shown above is the Estimated Volume Flux (EVF) over the most recent deployment. In the coming weeks we will analyse the samples in more detail to include estimates of the amount of carbon being transferred down to the oceans depths.

When we measure marine snow each month and each year, we build up a picture of how much carbon the North East Atlantic is removing. This is important because although we want to measure climate change, the oceans have their own natural variation and we must understand this and be able to separate it from any human induced change.

Written by Corinne Pebody.

2018 Cruise - JC165

Water in, Data out

Ship life is well underway now and there is a huge wealth of knowledge and experience on board. I am working with the scientists and technicians to ensure that all data recovered are kept securely and has the correct accompanying metadata. Keeping records of times, dates, locations and methods of data collection are as important as the data itself. A wise woman once told me – ‘Data without metadata is like a tree without roots’. Data are only collected once, but it can be used many times and precise metadata combined with secure storage of data ensures reusability.

Figure 1. Sue taking water samples for oxygen analysis

In addition to data management on board, I am working with the pelagic team from the National Oceanography Centre (NOC) in the chemistry lab. The bottles on the CTD rosette collect water at different depths, as far as ~4840 metres, or about 10 m above the seafloor at PAP. The first water sample to come out of the CTD must be measured for oxygen – the water needs to be collected and preserved before the air intrudes when the niskin bottle is first opened. The temperature of the water in each bottle needs to be measured shortly after the CTD is back on deck. Next is the dissolved inorganic carbon and nutrient samples. These will be taken back to NOC and analysed later.

Figure 2. Left: Ship-based chemistry lab, Right: Filtering equipment for chlorophyll, PIC and POC.

Back in the ship-based lab, the seawater is filtered to investigate levels of chlorophyll, particulate organic carbon (POC) and particulate inorganic carbon (PIC). After filtering, chlorophyll is measured using a fluorometer, the POC and PIC is frozen at -20°C for analysis back at NOC Southampton.


Written by Charlotte Miskin-Hymas

2018 Cruise - JC165


It’s been a week already since our departure from Southampton, my name is Amine and this is my first time on board the RRS James Cook. I am one of the electronics engineers that are present on the PAP expedition from The Ocean Technology and Engineering Group (OTE).

My activities focus mainly on PAP1, a number of sensors are attached to the buoy keel and on the frame which is 30 metres under the buoy. The frame contains a hub which powers and processes the data measured by the sensors attached to it. The hub compresses and sends the data measured by the sensors to the telemetry unit positioned on the buoy which then forwards the information to a server based at the National Oceanography Centre (NOC) via the Iridium satellite system.

Figure 1. Printed circuit board of the Hub

The preparation for deploying PAP1 buoy and frame involves investigating the recovered sensors from last year’s cruise. This is a good opportunity to assess the data obtained by the sensors and to learn on how to improve the robustness of this year’s system as a whole.

So far, the testing of the hub that will be deployed this year and the sensors attached to it have been verified. This includes making/changing wiring harnesses and assigning individual battery housings to each sensor.

Figure 2. Telemetry unit used to communicate over satellite. 

In the next couple of days, the sensors on the buoy will be tested as well as communication over satellite. Once this has been conducted, PAP1 will be ready for deployment.

Written by Amine Gana.

2018 Cruise - JC165

Megacoring, Mud and Observing the Benthos

Making regular observations of the communities on and in the seabed is important in understanding how these systems respond to changes over longer periods of time. During the 2018 cruise, we are collecting sediment samples from the seabed as part of the continued long-term time-series observations at the PAP-SO site. As in previous years, the coring effort is focusing on small animals that live in the sediment such as worms and isopods (macrofauna), microscopic animals such as copepods and nematodes (meiofauna), microbes and microplastics. We will also look at trace chemical signals in the sediment that tell us about food supply to the deep. Together, this will help to give us a better understanding of the benthic communities at the PAP abyssal plain and how these communities may be changing over time.

The sediment is collected using a Megacore, which is a weighted device fitted with 10 Perspex tubes. This is deployed at night to enable teams who look at pelagic organisms and processes to work during the day. Once the Megacore is on the seabed, the tubes are triggered mechanically and fire into the sediment, creating a core of sediment inside each tube. Once the sediment cores have been collected, the Megacore is brought back up to the surface. From the time the Megacore is deployed into the water to when it is winched back on board the ship, can take around 4 hours. The seabed is about 4,850 m (3 miles) deep at PAP, so it takes a long time to get the Megacore down onto the seafloor and to winch it back up again.

The Megacorer on back on deck with core tubes full of sedimentFigure 1.  The Megacorer on deck with tubes full of sediment.

When the Megacore arrives on deck, the benthic team is ready to remove the tubes of sediment from the device. This requires some careful manoeuvring and a rubber bung is placed onto each end of the tube to hold the sediment and layer of bottom water in place. The team work in pairs and one person places the core tube on a stand whilst another takes slices of the sediment core using pre-measured cutting rings. It is possible to take different sized slices of sediment, such as 1 cm or 5 cm for further analysis. The sediment is carefully sieved for macrofauna and microplastics analysis. Intact slices are used for microbial and meiofauna analysis. The team must then store, label and preserve the samples immediately. Whilst the team are working, the Megacore is deployed again with new, clean tubes to take more samples from the seabed. Then the process starts again and the benthic team can process two Megacore deployments in one night.

Benthic team group photo
Figure 2. The benthic team on board RRS James Cook.

Then, the clean-up operation begins, which is no mean feat, as the sediment is usually a very sticky clay that coats everything it comes into contact with. The mud has to be washed from all of the equipment, then everything must be safely stowed away and the deck cleaned. This is done in time for the benthic team to have a much-appreciated breakfast and enables the teams who work during the day to start their experiments immediately. Working day and night means that work can continue 24 hours a day and make the most of the time aboard the James Cook.

Written by Anita Hollingsworth

2018 Cruise - JC165

Ocean Technology and Engineering at PAP

The National Oceanography Centre (NOC) employs not only scientists to understand the oceans, but also teams of engineers who develop new technology to increase the amount of data that scientists can access.

Figure 1. Deploying the CTD 

The Ocean Technology and Engineering Group (OTE) design new sensors, samplers and other devices based on the needs of scientists both at the NOC and other centres around the world. Some of the OTE team are present on the PAP Cruise for two reasons this year. Firstly, we design and implement the equipment that collects much of the data from the many sensors at the PAP Sustained Observatory and transmits that data back to base via satellite for the scientists to interpret (and that you can follow at ). Secondly, the PAP site is an ideal test bed for both long term and short term testing of other sensors and samplers that we design as the North Atlantic conditions are so tough throughout the year. Last year we deployed two of our in house technologies, a “Lab on a Chip” (LOC) wet chemical sensor to measure nitrate values and one of our miniature Conductivity and Temperature sensors. We will be taking these back to NOC for evaluation of how they have performed and to see what lessons we can learn after a year in the ocean.

Figure 2. NOC LOC before and after a year at sea. 

We have also brought with us two more of our latest designs of Lab on a Chip sensors, an improved version of our nitrate platform as well as a design for measuring phosphate concentrations. Both of these nutrient levels in the ocean are of interest to our scientists (the Global Ocean Observing System lists them as high priority Essential Ocean Variables). We hope that by developing a high accuracy sampler using the same techniques as would be used in the lab we will be able to increase the number of locations that samples can be taken from, the frequency that those samples can be taken and the precision and accuracy of the samples compared to current in-situ techniques.

Figure 3. New NOC LOC ready to go to 4800m!

Yesterday evening we fitted both of these sensors to the CTD frame in place of two of the standard bottles and had the sensors collecting data down to 4800 m depth and we hope to do this several more times over the coming weeks.

If this sounds interesting, we are currently recruiting! Keep an eye on where posts for both an Electronic and Software Engineer will be advertised shortly.

Written by Chris Cardwell.


2018 Cruise - JC165

The PAParazzi have arrived!

After the glassy sea and clear sky we had in Southampton, we encountered rough sea and grey sky till today when at about 0600 we reached the PAP-1 mooring and the sun tried to get out.

Figure 1. Sunrise at the PAP-1 site, 22/05/2018

My name is Giulio and I’m on board of the RRS James Cook for the first time, and for the first time here at PAP-SO. During this cruise my main activities will focus collecting samples to investigate sedimentary organic matter and extracellular enzymatic activities as well as abundance, biomass and diversity of benthic microbes and viruses. The rest of the benthic team has a wider objective that includes also environmental DNA, benthic metazoans and microplastic.

It has been a busy couple of days setting up the chemistry lab and preparing the sensors for deployment. The first main job is to tie down all the equipment in preparation for the high seas.

The first CTD was deployed today to 100m; mini CTDs were attached and water samples were collected for the oxygen, carbon, nutrients, salinity, temperature, chlorophyll and silica analysis. Some of these samples were measured, preserved or filtered and labelled appropriately in the lab in order to calibrate the instruments for deployment on PAP-SO for the next year.

Figure 2. The first CTD before deployment





2017 Cruise - DY077

The Boat That Rocked

On the 28th of April the last sampling at the PAP-SO finished with a zooplankton net and then the RRS Discovery set sail back towards the UK.

The cruise was a great success with all of the expedition aims met and 108 stations sampled in 13 days, an impressive amount! Stations are recorded every time a piece of equipment is deployed over the side of the ship with the general rule of ‘if it got wet, it’s a station’. This rule is used as not all deployments are successful but this cruise had a great success rate of more than 95 %. The PAP-1 and PAP-3 moorings were successfully deployed and recovered, the bathysnap frame was successfully deployed and a whole host of other scientific sampling and experiments were carried out as has been detailed on the blog these past few weeks.


The PAP-1 buoy being deployed. It floats on the ocean surface for a year recording data and sends it back to land via satellites

We had to leave the PAP-SO site by the evening of the 28th as the Captain had warned that the weather forecast predicted we were in for a bumpy transit back to land. This meant lashing down boxes and securing all lab equipment for the journey until it was time to start packing up. The transit to Portland took about two and a half days but luckily the large waves and rocky weather was mostly finished by Sunday!

At the end of a research expedition it is tradition that a ‘cruise party’ is organised to allow everyone to have some down-time after working for 2 and a half weeks without a day off and to celebrate a successful cruise. On Saturday evening everyone met in the bar to socialise, have our two drinks and we were treated to a surprise jamming session from Rob, Morten and Richard!


Rob Young (left), Morten Iversen (middle) and Richard Lampitt (right) played Hotel California and other classics, a mix of country songs and Richard sang Wonderful Tonight by Eric Clapton.

Another cruise tradition is to have a team photo at the end of the cruise up on the foredeck with the Captain.


First team photo with the Captain. From left to right: Rob Young, Chelsey Baker, Ken Buesseler, Meg Estapa, Luciana Genio, Corinne Pebody, Katsia Pabortsava, Noelie Benoist, Miguel Charcos Llorens, Sue Hartman, Richard Lampitt, Nick Rundle, Joe the Captain, Kev Saw, Brian Bett, Lenka Nealova, Claire Laguionie-Marchais, Christian Konrad, Morten Iversen and Andrew Gates


Team Photo Round 2 with the addition of Claire Evans, Jessica Song and Jennifer Kenyon

We are now back on dry land in Southampton with lots of unpacking to do, but on a more exciting note, we also have many samples to analyse, data to collate and explore, and many questions about the ocean, such as how processes work and how they are changing, to be answered! The research cruise was great fun, very productive and a resounding success due to hard work from the crew, the scientists, the technicians and engineers, as well as Richard the Principle Investigator, who organised the daily activities and made sure that everyone achieved their research aims during the cruise. A big thanks to everyone on board for making it a great experience and an enjoyable cruise.

That’s it for this year’s cruise blog but you can check out previous year’s blogs from 2015 (here) and 2016 (here) or go back check out the posts you missed from this year!

Want to have regular updates about the PAP-SO? Follow us on Twitter or Instagram.

Do you want to know more about this cruise, oceanography in general, or life at sea? Leave a comment or tweet us and we will answer your questions.

We hope you have enjoyed the blogs and we’ll be back next year. See you in 2018!

Author: Chelsey Baker

2017 Cruise - DY077

Connecting the oceans’ depths

One year ago, I started the project LO3CATed Larval Occurrences in Open Ocean: Connectivity studies in the East Atlantic and Mediterranean – in the frame of a Trans-National Access to Fixed Point Open Ocean Observatories (FixO3-TNA). This project aims to obtain observations of deep-sea larval distributions and settlement at bathyal and abyssal depths across the North Atlantic biogeographic region, encompassing the Mediterranean Sea. Obtaining direct observations of larval abundances and distributions in the deep sea is extremely challenging due to the small size of larvae coupled with haphazard sampling in space and time of a vast and complex fluid environment. Within FixO3, I am using a network of mooring arrays to obtain long-term samples using a modular sampling device that includes passive larval tube traps attached to a settlement frame containing experimental colonization substrates. We chose three biogenic substrates – wood, bones and shells – that mimic common habitats found in the deep-sea benthos, such as wood and whale falls, and also cold-water corals, which typically have fragmented distributions and potentially serve as steeping stones for species dispersal over wide geographical distances.


Figure 1. LO3CAted modular sampling device.

As I joined the Porcupine Abyssal Plain cruise DY077, I had great expectations because I was going to collect samples from the first year deployment. During the PAP cruise DY050 in 2016, the LO3CAted frames were clamped to the PAP3 mooring and placed at 2997m and 4777m depths, the latter being approximately 55m above the bottom, above the acoustic release. This release is placed at the bottom of the mooring and an acoustic signal is sent when we want to recover the mooring, detaching the cable from the anchor. Therefore, the traps and other sensors have to be placed within a safe distance above it. Because the PAP3 mooring is used as a continuous time-series study of particle flux into the ocean, a new mooring had to be assembled and deployed before the old one was recovered. So my first tasks onboard were to prepare the substrates to put inside the settlement frame, and the solution that is used as a DNA-fixative in the larval traps (salt-saturated Dimethyl sulfoxide, DMSO). Since I started this project I gained a wealth of other skills and experiences, some of them most people wouldn’t think are part of a marine biology job. This includes building PVC prototypes in a workshop and sewing net baskets with bones inside!


Figure 2. Sewing bone baskets

PAP3 mooring was successfully deployed with two sets of LO3CAted frames attached at 2960 m and 4730 m depth, similar to the mooring array deployed one year ago. A few days later, I finally recovered the frames from the old mooring. At a first glance the substrates looked very clean and intact, and I couldn’t see any signs of animals (metazoans) colonizing the substrates. But as in other fields of oceanographic research, we don’t get to see the data until were are back in land. The substrates were preserved in various different ways (ethanol, formalin and frozen at -80˚C), so when I go back to the lab I can analyze them under the light and scanning electron microscopes and use genetic tools to investigate the microbial community forming biofilms on the substrate surfaces. Also the DMSO-fixed larval samples will be sorted under a stereomicroscope to search for minute (less than 300 micrometers) invertebrate larvae and other zooplankton.


Figure 3. Recovering colonization substrates

Although these results felt slightly disappointing, it’s still premature to draw any conclusions from a single-point collection. We know that several benthic deep-sea species develop through an upper ocean larval stage, but we don’t know where in the water column most of these larvae live, for how long and at what depths. And we also suspect that many of them may stay closer to the sea bottom where they can more easily find their natural habitat. So during the PAP cruise this year, we also deployed larval traps and wood substrates attached to the Bathysnap camera frame that will stay at the seafloor for the same period as PAP3. With these experiments we’ll be able to compare samples from just a few meters above bottom (ab) to the ones in the water column (50-100m and 1890m ab). Also, PAP moorings are equipped with a series of other sensors that will provide us with data on various physical ocean parameters, such as salinity, temperature and current flows, which will help us understand the environmental conditions driving different microbial and metazoan communities.


Figure 4. Bathysnap with the larval trap attached

The results obtained from PAP Sustained Observatory will be compared with data collected from three other FixO3 sites (ESTOC, CVOO and PYLOS), and the Nazaré Canyon mooring (MONICAN01). LO3CAted results will provide new insights into spatial and temporal patterns of larval assemblages across geographic and depth gradients, advancing the existing knowledge of biogeographic distributions and connectivity of deep-sea metapopulations. This information will be useful to comprehend the resilience of marine organisms and habitats to natural and anthropogenic disturbances, and to inform stakeholders and decision-makers on science-based options for management and conservation.

I am extremely thankful for the opportunity to join the PAP DY077 cruise and work directly with such an experienced team of scientists and technicians that were so supportive and insightful throughout the whole trip. In addition to the work on my project, I had an amazing time with the benthic team processing megacore and trawl samples, and I also learned from many other activities onboard with various instruments for studying the water column. I couldn’t be more pleased to be part of this incredible research environment contributing to the global understanding of our oceans.


Author: Luciana Genio