Shelf Sea Biogeochemistry blog

Thursday, 23 April 2015

Snow catching across the Celtic Sea

Alex Poulton, National Oceanography Centre

Picture 1. Snow Catcher going over the side of the ship. Photo: Jose Lozano.
Of particular interest during this cruise is the fate of the material that is produced in the upper part of the water column - this material sinks down through the water column as large particles called marine snow. Marine snow is formed in many different ways. Some is formed from phytoplankton sticking together to form large aggregates when growth conditions are not optimal in the surface ocean, for example when nutrients are limiting growth. Others are produced by zooplankton eating phytoplankton and then producing faecal pellets. These marine snow particles can sink through the water column at various speeds, with their sinking speeds linked to their composition and size. As they sink they act as a food source for zooplankton and other organisms that live in the lower depths of the water column.

Picture 2. Snow Catcher being deployed to 70 m. Photo: Jose Lozano.
Collecting marine snow is a challenging business. During this cruise we are using Marine Snow Catchers - large volume (100 L) water bottles which we send down to the depth of interest and then close, enclosing the sinking particles which we then bring back up onto the ship and allow to settle for an hour or two (pictures 1-4). After this settling period we can then remove the water from the Snow Catchers and examine the particles in the bottom of the Snow Catcher. 

Picture 3. Snow Catchers taking a rest. Photo: Jose Lozano.
These Snow Catchers have been used on multiple cruises from the Arctic to the Caribbean individually, but unique to the Celtic Sea is the deployment of not one or two, but four Snow Catchers twice - once in the upper 10 m and then again at 70 m. This is quite some operation, taking a large amount of organisation, (patience), timing and around five hours. Over the entire length of the cruise we will carry out this large-scale water collection and snow catching exercise at five different sites, including our Central Celtic Sea site (Candyfloss). Our hope is that as well as seeing changes in the surface community we will also see changes in the composition of the material leaving the upper sun lit ocean and sinking down to the seafloor.    

Picture 4. Team Snow Catcher celebrating success. Photo: Callum Whyte.

Tuesday, 21 April 2015

Game of Filters: A Song of Filters and Water

Clare Davis and Calum Preece, University of Liverpool (Westeros)

The University of Liverpool team (picture 1) is responsible for determining the composition and relative concentrations of dissolved and particulate organic nutrients, namely carbon, nitrogen and phosphorus. This is a key part of understanding both nutrient cycling and the fate of carbon fixed by primary production in the shelf system.  

Picture 1. The Liverpool team with [Jon] Snow Catcher enjoying some afternoon sunshine. Photo: Jose Lozano.

In real terms, this equates to an awful lot of filtering during the SSB cruises. To achieve this we travel down from Filterfell in the North to Southampton where we join the ship. From then on, we employ all of the Seven Filtrations to collect a wide range of samples. But first of all, we trot our little legs over to whichever device we are using for sampling that day, be it Jon Snow Catcher, CTD or Ned SAPS, armed with Tygon Lannister tubing and fill our bottles with as much seawater as we can get our hands on. There is one exception however, when we are working alongside the Fe Island team we aren’t trusted in the clean lab so they sample their fancy CTD on our behalf and deliver the water to us.

During transects and at designated stations we collect water samples from the CTD which we analyse for dissolved organic nutrients, including dissolved organic phosphorus (DOP), dissolved organic nitrogen (DON), dissolved organic carbon (DOC), amino acids (AA) and coloured dissolved organic matter (CDOM). We define these nutrients as those which pass through what is arguably the king of filters; King GFFrey with a pore size of 0.7μm.

We collect a selfish amount of water from the CTD for sampling particulate nutrients, including particulate carbon, nitrogen, phosphorus, lipids, amino acids, stable nitrogen isotopes and pigments. We define the particulate fraction as anything stuck to King GFFrey after filtering a couple of litres of seawater (picture 2).  We also collect particulate samples from the now infamous Jon Snow Catcher. 

Picture 2. A [King] GFF[rey] filter covered with particulate material. Photo: Chata Seguro.

A personal favourite for sampling particulate nutrients is the honourable and reliable Ned SAPS. With the help of Lord Commander Jon Short (picture 3), his Men of the NMF Watch, and good old Ned SAPS we can filter hundreds of litres of seawater in situ, separating out large particles from smaller ones which can give us useful insight into the composition and variability of the different sized particles in the water column.

Picture 3. [Lord Commander] Jon Short of the NMF [Watch] and good old [Ned] SAPS. Photo: Chata Seguro.
After all the samples have been filtered most are frozen in the freezer room which lies beyond the great hangar, but the Cercei CDOM samples must be analysed on Hodor Horiba…Horiba before they degrade. This is helps us calibrate the CDOM sensors on Samuel ‘Tarly’ Ward’s sea gliders that roam the Celtic Sea.

While many are currently playing in the Game of Filters, there is no denying that the North is a force to be reckoned with as they rule over their Seven Filtration rigs across the not-so-narrow Celtic Sea.

The bloom is coming! And soon the seabed will be covered with marine snow…

Saturday, 18 April 2015

Ship's inbuilt equipment that science uses on the cruise

Jon Seddon, National Oceanography Centre, Southampton

I look after the science equipment that is permanently fitted to Discovery. I am also responsible for the storage of all the data that we record and the satellite system that we use for communicating with the shore.

On this cruise we’re using several of the instruments that are permanently fitted to the RRS Discovery. We have a weather station that every second records the air temperature, humidity, air pressure, the intensity of the light coming from the sun, and the wind speed and direction. Every second we also measure the properties of the sea 5 metres under the surface. We record the temperature, salinity, how much the phytoplankton in it fluoresce and also how clear the water is, from which we can work out how much is growing in the water (see picture with measurements below). The whole cruise is looking at how the phytoplankton start to grow in the Celtic Sea in spring. The data from the ship allows us to continuously observe how much phytoplankton there is at the surface throughout all of the sea that we pass through.

A screenshot of the underway data that is continuously logged aboard 24-7.  Since 7 am this morning temperatures have increased and fluorescence (chlorophyll) has decreased.
We’re using the echo sounders on the ship to make a profile of how deep the sea underneath us is. There’s more information about how echo sounders work here. We’re using two types of echo sounder on this cruise. The single beam system sends a single pulse of sound down from the bottom of the ship to measure the water depth directly under the ship. We’re also using the multibeam system, which sends out 400 beams of sound out in a triangular pattern to measure the water depth underneath and out to the side of us. We’re currently on the flat shelf and so the sea bed is uniform and 118 metres deep. When we dropped off the edge of the shelf during the iron transect the water went as deep as 2650 metres. There were lots of canyons flowing from the shelf into deeper water that showed up in the multibeam data. 

Multi-beam data from the iron transect showing increasing depth with colours going from red (shallow) to deep blue (deep). Below the ship is a deep canyon running east to west.

This is the unprocessed multibeam data from the deepest part of the iron transect.  The yellow line is the course that the ship took. The blues show the deepest areas of the sea and the reds are the shallower parts that are on the edge of the shelf. The navigation charts that we have for this part of the sea are not that detailed. The echo sounder data allows us to know how deep to lower the CTD to make sure that we measure all of the sea but that we don’t bump the CTD into the sea bed.

There’s a 2.4 metre wide satellite dish on top of the ship that connects us to the Internet and gives us four phone lines (see picture below). Satellite data is very expensive and so our system only works at 256 KBits per second. This is about one-eighth of the speed of the data on a mobile phone and we have to share this amongst the 50 scientists, crew and technicians onboard. There are nine computers around the ship that we can use to access the Internet. You have to be very patient though – the BBC Sport page takes 30 seconds to load and even longer if all nine computers are in use at once.

Picture of the bridge of the RRS Discovery with satellite dome and lots of other aerials and instruments. Photo: Chata Seguro.

Everyone has a phone in their cabin and the ship has four lines with Aberdeen phone numbers because that’s where our satellite ground station is. Friends and family can call us on these numbers or we can call them using phone cards that we’ve bought in advance. Because of the Aberdeen number it only costs the same as a UK phone call and so is very affordable but there is a bit of delay on the line, which can be confusing if you’re not used to it. 

Friday, 17 April 2015

All change: half time in the Celtic Sea

Alex Poulton, National Oceanography Centre

This morning marked a key placeholder in this cruise: a boat transfer and change of scientists. After half a day's steam we arrived in Falmouth bay, although the ever present sea fog meant that we could have been anywhere from the depths of the South Atlantic to the icy waters of the Arctic. Out of the fog came our three new recruits: Angie Milne, Matthew Fishwick and Elaine Mitchell. 

One of the new arrivals (Matthew Fishwick) climbing up the ladder from the launch. Photo: Chata Seguro.

Like half time in a football match, though without the orange quarters and deep heat, our three new recruits were soon on the pitch – after a brave climb up the ladder and onto the deck of the RRS Discovery. This was a straight like for like substitution for us: two new iron chemists to replace the two leaving and a new bacterial ecologist to replace the departing one. After a quick hello and bye from the new recruits to those getting off, the three leaving climbed down the ladder into the waiting launch and then disappeared off into the mist.

Farewell to those departing. Photo: Chata Seguro.

Before the new team members had a chance of relaxation they were informed that sampling would begin again in 12 hours - they had just half a day to orientate themselves on the ship (i.e. find their bed, their lab coat and the galley) before joining the rest of the team for a full night and day of sampling, firm in the knowledge that there was just over two more weeks to the final whistle.

Thursday, 16 April 2015

OMG - Glider glee!

Dr Charlotte Williams, Marine Physics and Ocean Climate, National Oceanography Centre

Today at our main sampling site (CANDYFLOSS) we are deploying our sixth and final ocean glider! Ocean gliders are robots which ‘glide’ up and down in the water whilst taking measurements of temperature, salinity, chlorophyll and oxygen (plus a few more things), and these are what I work with. They send their data back to us when they surface via satellite. The amazing thing about gliders is that we can see the data they are collecting from anywhere with an internet connection as soon as they surface (every 30 mins or so in 100m of water). In fact as I am writing this blog I am checking the data that is coming in from the 4 gliders we have out at the moment! This has been useful for our research cruise as we are trying to catch and sample the ‘spring bloom’. This is where light and nutrient requirements for phytoplankton in the surface become just right in spring, and so we see a bloom in phytoplankton growth. This can be observed by an increase in chlorophyll, which the gliders measure.  

The ‘OMG’ glider being ballasted in the tank. Photo: Jose Lozano.

Sam Ward, the glider engineer from National Marine Facilities, has been working very hard to ensure that the gliders are ready for the water. This includes ‘ballasting’ them in a big tank on the back deck. The gliders don’t have a propeller, they move up and down in the water by changing their buoyancy, which is much less power hungry. Sam has to check how buoyant the gliders are in the seawater that they are being deployed in, as the density of seawater changes according to its temperature and salinity. There will be more to come on how the gliders work in Sam’s future blog! The last glider being deployed today is particularly exciting as this is an Ocean Microstructure Glider (OMG). This glider measures all of the things listed above, but also measures the turbulent kinetic energy dissipation, which is a kind of fancy term for turbulence and mixing. Being able to estimate the mixing in the shelf seas is important because we can then estimate how nutrients and carbon move around.  We will have to see if the dolphins return to see the OMG glider!  

Another glider about to dive under the waves. Photo: Jose Lozano

Wednesday, 15 April 2015

Spring has sprung - here comes the bloom

Alex Poulton, National Oceanography Centre

After two weeks in the Celtic Sea we are seeing clear signs that the spring bloom has truly begun - nutrients are declining whilst levels of the pigment chlorophyll, used by phytoplankton for photosynthesis, are steadily rising. 

Just how green the water is at present (slightly cheating as this is a pigment extract rather than seawater). Photo: Chata Seguro.

The bloom appears to be patchy across the Celtic Sea; from the shelf edge where the bloom has not started to show strongly yet, to the central Celtic Sea (where our Candyfloss site is) where small phytoplankton are actively growing, to the northern Celtic Sea where we saw huge diatoms (images below) - a type of phytoplankton which often characterises blooms and productive waters - which were at least a hundred times larger than anything we have seen so far. 

Diatoms and zooplankton seen under the microscope. Photo: Chata Seguro.

A close up of one of the large diatoms we saw in the NE Celtic Sea. Photo: Chata Seguro. 

As the nutrient levels continue to decline we are keen to see what happens within the phytoplankton community: will there be a clear progression from large cells to smaller cells which needs less nutrients for growth, will the diatoms be succeeded by another phytoplankton group? How these changes are reflected in the rest of the ecosystem is a key question we will address over the next two weeks. For example, how will changes in which type of phytoplankton is present influence the different nutrients needed for their growth (nitrogen, phosphorus, silica), and will we see changes in the dominant types of zooplankton (tiny animals that eat the phytoplankton) across the Celtic Sea.

The ever present fog viewed from the bow of the RRS Discovery. Photo: Chata Seguro.

Though the bloom has arrived, we have lost the sun - a dense sea fog has descended on us over the last few days which means we can only see a hundred to two hundred metres in any direction (see image). The eerie silence that this has brought to the ship is broken up at regular intervals by the ear shattering sound of the ships horn announcing our presence. If the spring bloom didn’t know we were here before, you can be sure that it does now.

Tuesday, 14 April 2015

The Mysterious NMF Fellows on DY029

Jon Short, National Marine Facilities Sea Systems, National Oceanography Centre

In other blog posts, both from this cruise and from previous cruises in the SSB programme, there have been references to the National Marine Facilities technicians but few added details. So just who are these mysterious fellows and what do they do?

National Marine Facilities Sea Systems (NMFSS) is the organisation who manage the RRS James Cook and the RRS Discovery and the National Marine Equipment Pool as well as providing technicians and engineers providing specialist support to NERC research cruises on both the NMFSS ships and other vessels.

Jon Short preparing the trace metal rosette and Niskin sampling bottles. Photo: Callum Whyte.

There are seven technicians from NMFSS on board Discovery for DY029; Rob (who looks after the mooring deployments and instrumentation), Alan (our mechanical engineer who looks after equipment ranging from deck winches to the machine that produces liquid nitrogen at -300oC), Jon (our IT expert, who makes sure that all of the vital data, from numerous instruments, is logged and recorded), Sam (who prepares and deploys the autonomous gliders) Robin and Colin (who are learning how to operate and maintain the two CTD systems on board) and me, another Jon (also looking after the CTD systems and, very loosely, in charge of the team).

The NMF team preparing to deploy a mooring. Photo: Alex Poulton.

For each cruise supported by NMFSS the preparation starts at least six months before the sail date when we meet with the senior scientists involved and discuss with them what they want to achieve and which pieces of equipment from the pool are best suited to gather the data. This equipment is then prepared for use on the required research cruise. For DY029 this involved the design of moorings and the procurement of hardware for these moorings, payloads for the autonomous gliders to be identified and fitted, laboratory containers to be fitted out to the specification of the scientists involved and instruments, fitted to the CTD frame and on the moorings, to be calibrated to very precise standards.

The NMF team and deck crew recovering a glider. Photo: Callum Whyte.

Once this is all complete the technical team and the ship's crew "mobilise" the vessel. This involves loading all of the equipment required (including everything the scientists bring), installing it on board and commissioning it for use. After the ship sails we provide 24 hour support, operating, maintaining and deploying equipment and making sure the scientific team have everything they need for a successful cruise.

The NMF team preparing the anchor chains for the moorings. Photo: Callum Whyte.

Monday, 13 April 2015

The breath of the ocean

My name is Jose Lozano and I am a PhD student from the University of Vigo, Spain. In this cruise (DY029), I work with  Elena Garcia, post-doc at the University of East Anglia, taking samples and doing  measurements of oxygen (O2) respiration in the Celtic Sea (Candyfloss) by using different methods, Optodes (optical sensor devices, which is designed to measure absolute oxygen concentration and % saturation), Electron Transport System and Winkler (a test used to determine the concentration of dissolved oxygen in water samples).

Net community production (NCP) is a measure of the net amount of carbon removed from the atmosphere, which represents the difference between Gross Primary Production (carried out by phytoplankton through the photosynthesis) and Dark Community Respiration (from both phyto and zooplankton). Plankton found in the world’s oceans are crucial to much of life on Earth. They are the foundation of the bountiful marine food web, produce half the world’s oxygen and suck up harmful carbon dioxide.  It is therefore vital for scientists to closely observe the oceanographic and biological variables related with these little buoyant organisms, temperature, nutrient content, light extinction or partial pressure existing in the water column.

During the cruise we have very busy schedules, not only the scientists but also the crew and  the technicians. They all work constantly, making the practice of science much easier, by cleaning, cooking, creating tools, or fixing devices. We, the scientists, couldn't make it without their support.

Dolphins, Photo: Jose Lozano

When you spend 24 hours a day in an oceanographic vessel, even in hours of rest, you feel very tempted to go on deck to chill out and breathe the fresh air at the stern. In a good day you can feel the ocean breathing gently and musically through the waves, the cool wind blowing on your face, you can observe the wildlife, the terns and the gannets flying over your head and families of common dolphins jumping playful just few meters away from the vessel. You can even see some land animals, such as owls, garden birds or little spiders, which are travelling with us on the ship. All these organisms, from the smallest diatom to the biggest marine mammal, breathe oxygen (though in the case of archaea or bacteria, other molecules may be used) in order to obtain energy from organic matter, so to be able to keep going.

Sandwich tern. Photo: Jose Lozano

Friday, 10 April 2015

DY029 Fe transect trilogy: The return of the Team Iron

Metal contamination free science on a metal ship: trace metal saga

Main characters:  The Incredible Team Iron

Maeve Lohan (University of Plymouth)
Antony Birchill (University of Plymouth)
Dagmara Rusiecka (University of Southampton/Geomar, Kiel)
Amber Annett (University of Edinburgh)

Metal contamination (Everywhere)

 . / . 

 DY029 Fe transect trilogy by Dagmara Rusiecka (University of Southampton/Geomar, Kiel): The return of the Team Iron 

It’s been less than four months since DY018 and ‘Team Iron’ is back on board RRS Discovery waiting with excitement for the first cast of the first iron transect…

Encouraging message from the Team Iron fan club onboard. Photo by Chata

April the 7
, 11PM, kick off: Team Iron is all dressed up in clean white Tyvek suits and white mop hats rushing around in the clean sampling lab. 24 grey bottles designed specifically for the trace metal sampling returned from 2500m and with gloved taps were very quickly transferred from the deck to the clean lab to minimize the risk of metal contamination. Now, they’re racked on the wall, safe, secured and ready for a solid 4 hour sampling session. Team Iron wearing ‘dirty’ gloves is tackling through sample bottles for other scientists; DOM (dissolved organic matter), SPM (suspended particulate matter), alkalinity, flow cytometry, chlorophyll a, oxygen, salinity. Finally, it’s time for the ‘clean’ gloves and the ‘clean’ samples!

In meantime, outside of the clean lab, Amber Annett is already waiting for the stainless steel rosette to return on deck with 480L of seawater just for Ra (Radium) isotope measurements at only a few depths! In plastic cubic containers she’s carrying 20L of seawater one by one on her shoulder to her container. She’s not only strong but also a lucky girl. No need to worry about the metal contamination but hey, she needs liters of seawater to detect the short-lived Ra 224 isotope! Therefore, the rosette is deployed again for another round and more water for Amber.

Team Iron in the zone of discussing results from DY018. Photo by Jose Lorenzo

All geared up with clean sampling clothing. Team Iron is tackling through ‘clean’ sample bottles.  5 liters for chromium isotopes, 1 liter for iron isotopes, 500 ml for copper speciation ……. It’s time for their own samples. 250 ml for iron speciation, one 125ml bottle for trace metals and one 125ml bottle for iron.

3 AM: Team Iron is packing samples from the first cast whilst the ship is already at the next station and the crew is ready for the next cast. “Here we go again guys! 6 stations to go!” and the process is starting all over again.

Rare and short appearance of 'Rosie' the trace metal clean titanium rosette with bottles on deck. Still with gloved taps, almost ready for the deployment. Photo by Dagmara Rusiecka

Coming up soon:
Volume two: The Two transects
Volume three: The Fellowship of the Iron: Final transect

So why do we do what we do?

As some of you may know, iron is an essential micronutrient to marine organisms present at very low concentration. It influences phytoplankton productivity, community structure and ecosystems and is a limiting factor on primary production in some regions. Our aim is to capture the mechanisms of iron off-shore transport to the open ocean that currently are unknown.

Saturday, 4 April 2015

Three, two, one … go! .... Welcome to the Central Celtic Sea!

Chata Seguro, PhD student,  University of East Anglia

It is 4th of April, 10 am and we have just finished almost all of the work for the day. Many of the SSB (Shelf Sea Biochemistry) scientists had a very early morning, rising at 2:30am for the first pre-dawn CTD of the cruise. 

Why we are doing all the work so early in the morning? 

Because we need to catch the phytoplankton while they are not fully active, so that we can start our measurements and experiments early and follow their activity throughout the day. There was a bit  of confusion and “moving in slow motion" at the first CTD, but  the usual pre-dawn rhythm quickly set in, followed by two glider deployments, and then another CTD after that. 

The last rays of sunlight disappear behind the clouds the night before the first pre-dawn.

Sunset was quickly followed by many scientists disappearing as well to rest a few hours
 before the early CTD. Photo: Chata Seguro

The deployment of the sea-gliders later in the morning, appeared to act as a big colourful toy for the local dolphins as a large school of them, including baby dolphins, appeared on the horizon just after the glider deployment. They remained around during breakfast, but unfortunately, I did not manage to take any photos. Soon after breakfast, I decided to try a  trick that worked well one night during the cruise last November - to whistle to them! And .... they came! But once the large yellow toy disappeared under the waves, the dolphins  couldn't find anything interesting to play with, so they left as fast as they came. To my disappointment, no photos, but still great to see them coming after just a few whistles! It is thanks to Charlotte Williams, a physical oceanographer, that I am able to post a picture of dolphins playing around during the glider deployment (picture below)


Dophins playing around the Seaglider and ship.
Photo by: Charlotte Williams.

Dophins playing around the RRS Discovery.
Photo by: Charlotte Williams.

Apart from seeing the playful dolphins, it is always great to see scientists in action. James Fox and myself (both PhD students) enjoy comparing how our daily peaks of photosynthesis and oxygen production match on our instruments, which are set up next to one another in the main laboratory of the ship.

A few minutes ago, there was another call for another CTD and scientists were already queuing to sample the CTD. Suddenly, Robin (our NMF technician) shouted: "three, two, one … go!" It is the Central Celtic Sea and we were ready!