Shelf Sea Biogeochemistry blog

Wednesday, 3 December 2014


Ocean research cruise blog of Jonathan Sharples


We finished up all of the sampling during yesterday afternoon, and headed in past the Needles lighthouse on the west corner of the Isle of Wight. The pilot was picked up just before Calshot Spit, and we steamed up Southampton Water. It was bitterly cold! Probably the coldest weather we had experienced all cruise.

The ship docked in Empress Dock, in front of the Oceanography Centre, just after 1700. As soon as the gangway was in place, and we’d got the announcement that the ship had been cleared by customs, off we all went – the entire science group headed off through the docks to the Platform Tavern.

And that’s it. A very busy morning ahead as we unload the ship, but normally we are able to get away by noon. The end of a very productive cruise, with remarkable weather allowing us to do a lot more than we expected.

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The Needles

Tuesday, 2 December 2014

Land sighted

Ocean research cruise blog of Jonathan Sharples 


We steamed along the south coast overnight, and at breakfast this morning we passed Lulworth Cove and then Swanage. There’s just one last bit of science left to do. We are crawling slowly into Poole Bay and Christchurch Bay, taking surface samples of seawater. Clare Davis, from the University of Liverpool, is processing these water samples for a couple of the Liverpool University PhD students. The students are researching the dispersion of organic matter from estuaries out into the ocean, and also looking at the relative supplies of nutrients from rivers and from the deep ocean to the shelf seas. These samples are also tying our work into another research project focussed on land catchments and river nutrients. Anouska Panton, a researcher working at the University of Southampton, will be carrying out fieldwork in Christchurch harbour today so that later we can link the data together with what we are collecting to get a broader picture of river-supplied nutrients and their fate in the autumnal shelf sea.

One important job we managed to clear yesterday was the cruise photo. We picked the right time for it, sat 20 miles off Plymouth with nice, sunny weather. Today wouldn’t have been as good – it’s windy and grey outside. But at least we can now see land, for the first time in three and a half weeks.

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DY018 people

Monday, 1 December 2014

Visitng E1

Ocean research cruise blog of Jonathan Sharples


We arrived at position E1, south of the Eddystone, at about 0600. This is a site regularly sampled by the Plymouth Marine Laboratory (PML), generally about once per month but more frequently recently in collaboration with the project we are working on. Scientists and technical staff at PML maintain a data-gathering buoy out here. We carried out 6 seabed cores this morning, and were then met by the two PML boats. Coring the seabed from the PML boats is difficult, so they are very happy that we can stop here for a few hours to collect these samples for them, and transfer the samples to their boats to be taken back to PML and analysed.

pml explorer alonside

It was also our last CTD profile here at E1, at 0630. And it was fully mixed from the surface down to the seabed! Not too surprising as E1 is fairly close to the permanently-mixed water of the English Channel, and it’s only 75 metres deep. So we expect it to become mixed relatively early in autumn. We’ll do some more zooplankton nets this afternoon – Sari Giering is keen to have a lst go at collecting some more of the trichodesmium nitrogen-fixing bacteria, this time to get some samples for some DNA analysis.

Nick shows us the engine room

The clear-up of the labs has begun. The ship has a fast turn-around in Southampton, so we need to be ready when we arrive tomorrow evening to get some of the larger bits of equipment and container labs off. Some of the scientists took some time to go on a tour of the ship’s engines. Nick, the 2nd enginner, showed us around those normally hidden parts of the ship that power us through the water, provide fine-control of the ship’s position when we are working a station, as well as powering all our instruments, making our freshwater, ventilating the ship, and treating the sewerage. Remember there are about 50 people living on this 100m-long metal box for several weeks at a time: the ship is like a small, very independent village.

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Sunday, 30 November 2014

Last of the Snowcatchers

Ocean research cruise blog of Jonathan Sharples


The weather eased off very quickly during yesterday, ending up with winds less than 10 knots. We arrived back at the mooring site in the central Celtic Sea and began a last set of sample collection and experiments, mainly focused on the zooplankton and on the particles settling down through the water.

The Marine Snowcatcher worked well. We’re getting better at operating it, though we think that is mainly a result of calmer weather. We are still not completely convinced that the deeper samples collected with the Snowcatcher are always from the depth that we think we have triggered the catcher to shut – if the ship is pitching at all it’s possible for the catcher to shut while it is being lowered through the water to the sample depth. However, we can solve that by collecting nutrient and salt samples from the catcher and comparing those with what we see in the CTD data to tell us the depth that the Snowcatcher sample was really taken.

last snowcatcher
Elena Garcia-Martin, from the University of East Anglia, and Darren Clark, from the Plymouth Marine Laboratory, are working on last these samples. They are measuring how the different sizes of particles, and their different components (carbon, nitrogen phosphorus), and being recycled by bacteria. The deep bacteria are acclimatised to darkness, so they have to be collected after sunset, extracted from the Snowcatcher carefully so that they don’t get fried by the ship’s deck lights, and taken into a darkroom laboratory for analysis.

Elena and Clare sampling particles

One last set of measurements to do here this morning, then we head off towards Plymouth. Should arrive just south of the Eddystone lighthouse about 0600 tomorrow.

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Saturday, 29 November 2014

Glorious mud

Ocean research cruise blog of Jonathan Sharples


We reached the northern-most station by about 7 pm last night. There was great excitement watching the data from the CTD as it was lowered through the water. If any site was going to have reached the fully mixed winter state by now, it was going to be this one. About a dozen of the scientists were crowded around the CTD computer in the main lab, willing the temperature of the water to stay the same as the CTD went lower. But there was a collective groan as a thermocline appeared at 66 metres below the surface. It’s a bit disappointing that we are not going to be out here to see that final transition to the winter mixed water, but I’m pleased that I appear to have generated so much enthusiasm for shelf sea physics amongst the crowd of biogeochemists on board.

box corer

Matthew Bone, from the University of East Anglia, is interested in the muddy seabed at this site. We collected 4 cores from the seabed using a large “box corer”. This is a large steel cylinder that is lowered down onto the seabed, and then pushed into the seabed by the large weights above it. When it is pulled out, a core of the seabed mud is held within the cylinder and brought on board. Matt has been working on measuring how the mud releases nutrients back into the water. This muddy area of seabed, in an area called the Celtic Deep, is an important fishing ground for a scampi that lives on, and burrows into, the mud. At one point last night the radar was showing 12 fishing vessels around us, within a distance of about 10 miles. One of the cores caught a scampi. It seems happy enough in the lab, busily shifting mud around the top of the core and tending a burrow. The plan is to release it later today when we pass over another area where we have in the past seen scampi on the seabed.

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Friday, 28 November 2014

A windy morning

Ocean research cruise blog of Jonathan Sharples


A bit of weather more typical of November today and last night. We finished over-the-side work at about 7 pm yesterday, with winds of about 40 knots about to make use of the iron-free CTD unfeasible. The wind has dropped a little this morning, 30 knots of so, but the sea and wind are giving us a fairly good list to port as we steam between stations.

windy morning

We had to cancel the work planned for the first site this morning, as a fishing boat close by suddenly decided that the spot we had been sat on all night was exactly where he needed to drag his nets. Once we’d cleared away from where the fishing was, the winch that lowers the iron-free CTD suddenly threw us an error. The ship’s engineers are working on it now, and I decided that we’d lost enough time waiting around that site and should just head up to the next one. Timing is a bit tight today. Ideally we need to get up to our most northerly site by about 6 pm so that we can do some seabed sampling up to about midnight. That should give us time to head back for one last set of measurements back at the mooring site before we start to make our way into the English Channel.

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Thursday, 27 November 2014

Heading north

Ocean research cruise blog of Jonathan Sharples


Another successful day yesterday, with the wirewalker mooring and both of the gliders recovered very quickly. Jo Hopkins immediately removed all of the instruments from the wirewalker, and strapped them to the CTD ready for the next time we lowered it through the water. This allows Jo to calibrate the wirewalker data with the data collected by the CTD, with the CTD data all calibrated against analysis of samples we collect in the sample bottles. Every profile of data we collect through the water with the CTD involves samples being collected for salt concentration, dissolved oxygen and chlorophyll. These samples are analysed against known, internationally-recognised standards and lab techniques, so that we can calibrate the sensors on the CTD and estimate the error associated with their measurements. This is a vital part of any science: no other scientist would allow us to publish our results if we couldn’t demonstrate that our measurements achieved acceptable standards.

omg glider recovery

We can measure salt concentration to within about 2 thousandths of a gramme in 1 kg of seawater. We need to know salt to this level of accuracy because it has, along with temperature, a big influence on how dense the seawater is. The sea is always attempting to sort itself out so that less dense water floats above denser water, so knowing salt and temperature can tell us a lot about how the water will be moving. I’ve mentioned dissolved oxygen before in the context of Chata’s work – biology both produces oxygen (when the microbial plants are glowing) and consumes oxygen (when bacteria break down the organic matter), so accurate data on the oxygen in the water tells us a lot about how the biology is operating. Chlorophyll in the ocean is the same green stuff that you see in leaves and grass – the chemical that plants use to collect energy from sunlight. Chlorophyll is particularly good for plants that live in the ocean. Sunlight is absorbed very quickly as it passes downward from the sea surface. All of the red light from the sun is absorbed within the first 1 metre below the sea surface. Blue light travels the deepest in the sea, and chlorophyll is well suited to capturing energy from blue light. Clearly this is an advantage for the microbial plants in the sea, as they are mixed through the upper few 10s of metres and need to maximise their chances of collecting the sun’s energy. But why should land-based plants use chlorophyll when they don’t have the problem of metres of ocean absorbing the light? Photosynthesis first evolved in the ocean. Land-based plants haven’t bothered to evolve a form of photosynthesis more suited to life above the sea, instead they just highjacked the system that the ocean’s microbial plants had developed. Quite literally. At the heart of the photosynthesising biochemical machinery in every leaf lies a light-capturing system that can be genetically traced right back to photosynthesising marine bacteria.

Billy does the salts

We’ve started to head north through the Celtic Sea now, stopping every 25 km or so to lower the CTD through the water and collect more information. The wind has picked up, with about 25-30 knots now. The sea is looking rough, but it’ll take a few hours for the swell to pick up and start to move us about.

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Wednesday, 26 November 2014

November weather

Ocean research cruise blog of Jonathan Sharples


The remarkable weather continued yesterday as we continued a series of measurements and zooplankton nets next to the moorings. A couple of scientists were even spotted sunbathing between net hauls. The wind continued to drop, and the sea finally reached a glassy state by sunset. Pretty good for November in the Celtic Sea.

The winning picture of the salps in the process of releasing faecal material into the water is below: look at the streaks of back trailing from the curl of colonial salps in the lower left of the picture. Some of these salp groups are reaching lengths close to 2 metres.

chain of salps

salps cought pooing
 This morning just as the sun came up we carried out one vertical profile with the CTD just next to the wirewalker mooring. That will provide Jo Hopkins with vital data for her to calibrate the instruments on the mooring. We are now pulling up the wirewalker, and will then head off to collect the 2 gliders that neeed to come back with us. The glider “pilot” back at the Oceanography Centre has sent instructions to the gliders to meet as at a specific location, so the gliders will have dutifully reached that position this morning and will now be bobbing about on the surface waiting for us.
ctd at down

The weather is due to close in tomorrow, with 25-30 knots of wind expected from mid afternoon through to mid afternoon on Friday. But the longer term forecast is suggesting a return to these calm, sunny conditions. Feels strange for this time of year, but none of us are complaining.

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Tuesday, 25 November 2014

More jellies

Ocean research cruise blog of Jonathan Sharples


The children at Churchtown Primary School are I gather busy working on the questions we asked them about sinking salp poo. The zooplankton group on board are getting very excited about their results, and already planning the scientific papers that they want to write. We collected more of the zooplankton yesterday so that we can make better estimates of the rate at which they eat and the rate at which they release the faecal pellets. In an attempt to get an idea of what these delicate organisms look like in the ocean we attached a few waterproof cameras to the CTD, and lowered them into the sea surface to record pictures for half an hour or so. I set the challenge to get a picture of a jellyfish or salp in the process of releasing faecal pellets into the water. There was a clear winner (Clare Ostle, from the University of East Anglia), but she was working very early this morning and is currently in bed – so I’ll get the photo for tomorrow.

an interesting bucket of jellies

Meanwhile, to help the kids at Churchtown think about this problem, the picture below has some good examples of the salps (the long, tubular jellies, connected in spirals) and the tiny jellyfish. Another rally interesting organism in this photo can also be seen, just about. The photo looks like it has a fine sprinkling of sawdust in it. These are tiny colonies of a photosynthesising bacteria called trichodesmium. It’s special in the ocean because it is a nitrogen fixer – it is able to use nitrogen gas dissolved in seawater, rather than the form of inorganic nitrogen (nitrate) that most phytoplankton need. That means they can grow in areas where nitrate is in very low concentrations, such as the large areas of open ocean in the sub-tropics. Finding them here is odd, because there is enough nitrate around and so the trichodesmium should not have any advantage compared to other phytoplankton. I’ll find out a bit more about them for another blog entry.

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salps and tiny jellyfish

Monday, 24 November 2014

The importance of zooplankton poo

Ocean research cruise blog of Jonathan Sharples


At dawn this morning we reached the end of the iron sampling transect, crossing onto the edge of the continental shelf at a depth of about 250 metres. Quite a stunning sunrise, with flat calm seas. Not what you’d expect for November. The dreadful-looking forecast for the end of the week also appears to have dissipated, so we might be able to push our work further north into the Celtic Sea.

end of iron transect

We are about to head southeast for an hour or so, to return to the shelf edge site that we spent 3 days on earlier in the cruise. We need to repeat some of the Snowcatcher work there, and also the zooplankton biologists on board want to find some more salps and jellyfish to try out some experiments to determine how much they are eating and also what happens to the waste material that they excrete. I’ve asked the children at Churchtown Primary School in Southport to have a think about this problem – how quickly does a salp waste pellet (i.e. a salp poo) sink through the sea? It’s an important thing for us to know about. A fast sinking particle doesn’t give the bacteria in the water much time to breakdown the organic material before the pellet reaches the seabed. A slow-sinking pellet can be broken down into inorganic material before it reaches the seabed, and that inorganic material is then returned to the water where it is accessible to the phytoplankton. Also, sinking quickly means that the carbon in the pellet is removed from the ocean surface (and the atmosphere) very quickly – you could argue that the stability of Earth’s climate owes a great deal to zooplankton poo.

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Sunday, 23 November 2014

Measuring growth of the microbes

Ocean research cruise blog of Jonathan Sharples


Yesterday started with another of our pre-dawn set of measurements. Fundamental biological measurements we need from these pre-dawn CTDs are how fast the microbial plants (the phytoplankton) are absorbing and using carbon and nutrients, and how fast the bacteria are growing by using the organic matter available in the water. Think of these as the two ends of a food chain, with the phytoplankton converting the inorganic elements into organic material, and the bacteria breaking down the organic material back into the inorganic. Between them we have the zooplankton, and other marine animals, eating the organic material provided by the phytoplankton, and in turn providing waste material that the bacteria use.

Radioisotope lab1

Measuring uptake of elements by phytoplankton and bacteria requires very careful laboratory work. The method involves using tiny quantities of radioisotopes of the elements we are interested in (carbon, nitrogen, phosphate, silicate) and incubating samples of seawater that have been treated with these isotopes. After a set period of time the sample is filtered to collect the phytoplankton or bacteria, and the activity of the samples counted to tell us how much of the element the organisms used. We have two laboratories dedicated to this work on the ship. Alex Poulton (National Oceanography Centre, Southampton) and Kyle Mayers (University of Southampton) are working in one to measure the phytoplankton rates. Sharon McNeill from the Scottish Association for Marine Science in Oban is dealing with the bacteria rates.
We steamed quickly over to the deep ocean side of the shelf edge yesterday afternoon, and at about 8 pm we started the second of our line of sample stations to measure iron in the seawater. This line started in a deep canyon, and we are working up the wall of the canyon back towards the continental shelf.

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Radioisotope lab2

Saturday, 22 November 2014

22 November, 2014 08:49

Ocean research cruise blog of Jonathan Sharples


We had a very successful day yesterday – managed to get through all that was planned, plus most of what I’d planned for the next day as well. Deploying the moorings began shortly after 0800. This tends to be a long, careful process as the mooring wire is gradually unwound over the stern, instruments are clamped onto it at the planned depths, buoys are slotted in at key stages to hold it all up in the water, and then finally the 500 kg clump of chain is attached and dropped into the sea. By lunchtime we had deployed the long temperature/salt logger mooring and also the bedframe with the current meters. The second current meter mooring has been delayed until today, while the techs sort out an issue with the memory cards that it uses. That allowed us to go and hunt for the wandering wirewalker mooring and also the glider that we deployed when we first got here from Falmouth, but which has refused to dive.

Both the wirewalker and the glider have been sending us regular position information via a satellite link, which meant that finding them and getting them on board was very quick. We arrived back at the mooring site just after sunset, ready to do some more zooplankton work.

It’s a lovely day today – a glorious sunrise (complete with dolphins) and an almost flat sea. However, we’ve just heard that the long-term forecast is looking a little grim. A particularly nasty-looking low pressure system is due this side of the Atlantic next weekend. Forecasts that far out tend to be a little uncertain, but it’s worrying enough for us to think carefully about when we can get back to this site to recover the wirewalker and the 2 gliders that are here.

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Friday, 21 November 2014

21 November, 2014 09:05

Ocean research cruise blog of Jonathan Sharples


We arrived at the central Celtic Sea mooring site yesterday at 0930. Recovering the moorings was delayed a couple of hours while we waited for the wind to drop a little, but we began pulling them out of the sea shortly after lunch.

We have a fairly complex array of instruments on the moorings out here. There’s a weather buoy, provided to our project by the UK Met Office, plus a Cefas Smartbuoy that samples the surface biology and chemistry. The Met Office buoy doesn’t need servicing – they are designed to stay at sea sending back weather information for about 2 years. The Cefas buoy is looked after by Cefas scientists also working on this project. That leaves 3 other components that we need to service. The first mooring is a vertical line of acoustic current meters, anchored to the seabed and stretched upward by large buoys. These current meters are being used to measure turbulence in the sea, which allows us to calculate the supplies of nutrients towards the sea surface and how carbon is being mixed downward.

curretn meter buoy recovery
The second mooring is a relatively simple steel frame containing two acoustic current meters; this frame sits on the seabed, with the current meters looking upward and every 5 minutes measuring the flow of water in a series of 4 metre thick layers throughout the entire depth. Finally, the most complex of the moorings is a line holding about 25 temperature and salt loggers, anchored to the seabed and stretched up towards the sea surface by several buoys. These loggers, sampling every 1 minute, show us how stratified the water is, where in the water the thermocline is, and also if there are any waves running along the thermocline. All 3 moorings came up OK, though the string of loggers popped up about 1 km away from where we expected it to appear, requiring a bit of nifty ship manoeuvring by the captain to grab the mooring before it drifted onto the Cefas buoy. Once everything was on board, the National Marine Facilities engineers, along with Jo Hopkins and Chris Balfour from the Oceanography Centre in Liverpool, downloaded data, re-batteried instruments, and got the new mooring wires wrapped onto the winches ready for deployment.

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bedframe recovery

Thursday, 20 November 2014

Off to collect the moorings

Ocean research cruise blog of Jonathan Sharples


We finished off the work at the shelf edge station with a set of samples collected using the Marine Snowcatcher. Quite a long process, with a good few misfires of the sampler, but all of the samples needed were eventually collected. At 0200 this morning we did another of the “pre-dawn” samples, collecting water from different depths to measure plankton growth rates and nutrient requirements, and the nutrients dissolved in the seawater. This was earlier than we would normally carry out pre-dawn work, but we need to get back up to the moorings further on the continental shelf with sufficient daylight to recover them all. We are due at the mooring site just after 0900. We’ll first collect a CTD profile of data adjacent to the moorings, which can later be used to help calibrate the mooring data, and then we’ll begin what will likely be a full day of manoeuvring and collecting the 3 mooring components.

We have a couple of hitchhikers aboard. Two storm petrels were found resting in the hangar by the CTDs last night. Both are currently having a sleep in a cardboard box, and Clare Davis is hopeful one of them will be OK to fly off later today. A few days ago we had an owl flying round the ship. Very exotic – cruises out here usually only attract tired homing pigeons.

Here’s a question for the year 3 ocean dynamic students back in Liverpool University. The water out here by the moorings will soon be completely vertically mixed, and I want to estimate the date when that will happen. The water is 150 metres deep, with a surface layer 60 metres thick and density 1025.6 kg m-3, and a bottom layer 90 metres thick and density 1026.0 kg m-3. The average tidal current amplitude is 0.45 m s-1, average wind speed is 12 m s-1, and the heat flux across the sea surface is 100 W m-2 (a heat loss to the atmosphere). That’s all the information you need, along with a handful of constants that are in your notes!

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Wednesday, 19 November 2014

Looking for particles (again….)

Ocean research cruise blog of Jonathan Sharples


We deployed the last of our gliders yesterday afternoon. This one is being piloted to patrol between the shelf edge and our mooring site, 100 km further onto the continental shelf; it will do this continuously from now until earl March when it will be picked up during another cruise. We then had a very successful night looking for particles. Starting just before sunset we deployed our two “Stand-Alone-Pumps” (SAPS). These pumps are lowered on a wire to a fixed depth, and programmed to pump water through large, dinner-plate sized filters typically for 1 or 2 hours.

Clare and SAPS
 Clare Davis, from the University of Liverpool, will analyse the filters to measure the ratios of carbon, nitrogen and phosphorus in the tiny organic particles caught on the filters – a vital part of the story of how carbon and nutrients are cycled through the sea, ultimately supporting the marine food chain and also absorbing carbon from the atmosphere. We also tried the large Marine Snowcatcher again, this time after some modifications carried out by the Ben and Tom the National Marine Facilities Engineers. It worked at last! Both the SAPS and the Marine Snowcatcher were deployed, first close to the sea surface and then at a depth of about 100 metres. This is quite a relief for us – knowing the make-up of the particles in the ocean is a vital part of what we are trying to measure.

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SAPS over the side

Tuesday, 18 November 2014

Shelf edge station begins

Ocean research cruise blog of Jonathan Sharples


Work at the shelf edge has started well. One big difference between the work here and the work that we did at the first station on the cruise is that we have no moored instruments here. The shelf edge is the most heavily fished part of the seas around NW Europe, so long-term deployments of moored instruments tend to be unsuccessful as the chance of moorings being snagged by fishing gear is very high. For the duration of our work at this site we instead hang a chain of instruments from the ship. Jo Hopkins and Chris Balfour, from the National Oceanography Centre in Liverpool, spent the previous day setting up about 40 temperature, salt and chlorophyll loggers so that their clocks were all synchronised and they all take measurements at the same rate (once per minute). The instruments were then clamped every 2.5 metres on a 200 metre wire lowered over the stern, with a 300 kg ball of lead on the end of the wire keeping it vertical in the water.

Jo with chain instruments

We are using this chain of instruments to track a particular feature of the shelf edge. As the tide moves onto and off the shelf, the steep slope in the seabed causes the tide to push the thermocline up (tide flowing onto the shelf) and down (tide flowing off the shelf). This up and down motion generates waves on the thermocline that move away from the shelf edge, both onto the shelf and away into the deep ocean. These underwater waves can be very large, 100 metres from peak to trough and 15 km long. They are important because they result in a lot of mixing at the shelf edge, bringing nutrients from the deeper water up towards the surface. Our chain of instruments will track this up and down motion of the thermocline wave, so we have a picture of how rapidly the physics of the water below us is changing as we collect all of the biological and chemical samples
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t-chain deployment

Monday, 17 November 2014

Dolphins everywhere

Ocean research cruise blog of Jonathan Sharples


We had an astonishing display of dolphins last night. While sat carrying out a couple of measurements with the CTD for the iron work, lots of small fish had been attracted to the ship probably because of the deck lights. They in turn attracted something like 40-50 dolphins, cruising up and down the ship, accelerating to chase fish, and leaping out of the water to catch fish that were trying to escape. The acceleration and the rate at which the dolphins could turn through 180 degrees were incredible to watch. [A good question for the Oceans Sciences and Marine Biology students back at Liverpool University – the dolphins were reaching easily 10 metres per second, what Reynolds number were they operating at?] With the light from the ship we could see the dolphins 2 or 3 metres below the surface, streaking along after their food. Two sharks also turned up for the feast – much more sedate than the dolphins, cruising slowly into the foray and just wandering about as the dolphins flashed around them. We got a good look at one of them as it passed right below us at the side of the ship – at least 2 metres long. Dolphins and sharks paid each other no attention at all. This whole theatre lasted a good 90 minutes. My camera wasn’t quite up to the task of night-time photography, but the best effort is below.
dolphin watching

A glorious morning for us today. The wave height has dropped below 3 metres for the first time this trip. We have now started our 3 day stint at the station at the shelf edge.
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dophins at night

Sunday, 16 November 2014

End of the iron line

We have nearly finished our transect sampling iron from the deep ocean back to the shelf. The iron group is fairly excited, because in all of the profiles we have done gradually working along and up a seabed canyon there has been evidence in the CTD data of lots of suspended particles near the seabed. There must be some flow of water down there that is pulling sediments, along with trace metals such as iron, up off the seabed which is exactly what the scientists are looking for.

iron nerve centre

Other lab work continues also, as the iron chemists need to know what else is happening in the water to help understand what they are seeing. Chata, a PhD student from the University of East Anglia, has spent the past 3 days trying to fix a machine she uses to measure argon, oxygen and nitrogen gas dissolved in seawater. The machine is refusing to work properly, so she is having to store samples for analysis later back at University. Oxygen and argon behaviour similarly in seawater, and in the rates they can be transferred from the atmosphere to the ocean. However, oxygen also has a biological component to how it changes – if the ocean’s microbial plants are growing, then (like all plants) they produce oxygen. Chata can compare what she sees the argon and the oxygen doing in the water, and any differences between them will tell her about how the biology in the ocean is working. She is also helping us by doing chemical analyses of water samples to measure the oxygen concentration, which will allow us to calibrate the oxygen sensor that we have on our CTD.

chata titrating oxygen samples

Due to finish this transect at about 0100 tomorrow. We then plan to start th second of our main study stations, this time sat at the edge of the continental shelf.

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Saturday, 15 November 2014

Sampling iron

Ocean research cruise blog of Jonathan Sharples


Starting in a depth of 2,500 metres we now plan to sample the concentration of iron in the sea at several stations, gradually working back towards the continental shelf. It might seem like an odd thing to look for, but iron is a vital nutrient to the microbial plants in the ocean. The plants only need it in minute concentrations, but in some parts of the ocean there is so little iron that the plant growth is inhibited. This was a big mystery in oceanography for a long time – there were areas where there was plenty of sunlight and plenty of the main nutrients (nitrogen and phosphorus, the sort of things you might give to plants in your garden), but very little growth of the ocean’s plants. Demonstrating that lack of iron was the problem took a long time because it is so difficult to measure iron without contaminating samples (for instance, with iron from the research ship). The CTD used to collect the seawater for iron analysis is entirely made of titanium and plastic, and the bottles on the CTD frame are always stored in clean conditions rather than being left on the frame as we do with the steel CTD. All of the iron analyses are done in a special clean chemistry lab on the ship, with the scientists having to wear very clean lab coast and gloves, and particularly attractive hats. Nobody is allowed into this lab without the right gear.

Iron is not a problem for the microbial plants that grow in the shallow shelf seas. The reason we are sampling iron is that the continental shelves are thought to be sources of iron for the adjacent open ocean, possibly resuspended in sediments from the seabed of the shelf and the deeper waters of the shelf slope where we are now.
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Friday, 14 November 2014

Into the deep water

We’re in deep water now. Not the deepest in the ocean, but enough to make a normally shelf-focused oceanographer a little nervous. The forecast suggests things should quieten a little over the next day or two, so we headed out over the shelf edge and into the deep ocean aiming for a depth of 2,500 metres. Crossing the shelf edge always looks like we are going over a cliff when you look at the echosounder. On the shelf the depth had increased from 150 to 200 metres in about 100 km, but then over the shelf edge the depth suddenly increases from 200 to 2000 metres in about 30 km. So a change of 1800 metres over 30 km: if you cycled a slope like that you might get a bit out of breath, but it’s not the cliff edge that the echosounder makes it look.

cup creations

 Scientists can be easily amused. The one thing we really like to do when we work in deep water is decorate polystyrene cups and then send them down with the CTD. Amber Annett from Edinburgh University remembered to bring a supply of cups, pens, and a pair of old tights to hold the cups on the CTD frame. The lab is a hive of creative activity. Why do we do this strange ritual? The cups compress under the pressure of the water; the greater the pressure the smaller the cups become. The decorations also compress, so that you end up with miniature, highly-detailed cups when the CTD returns to the deck. We are due to work gradually back up the shelf slope to the shelf edge, lowering the CTD into 2,000, 1,500, 1,000 and 500 metres, so we could produce a series of cups scaled by the depth of the water. It’s fun, and also a great way of demonstrating the concept of water pressure to school kids.

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deep ctd

At the shelf edge, and rolling….

Ocean research cruise blog of Jonathan Sharples


November 14th. We are out at the edge of the continental shelf. Work had to stop early this morning as the waves reached 7 – 8 metres, making it too difficult to get our instruments over the side safely. We are now sat here trying to get a weather forecast, so that we can decide whether to stay out here and wait for the waves to settle down, or turn back onto the shelf and work in the shallow water.

Yesterday’s work started off very well. We managed to do 5 out of 6 sets of measurements as we headed southwest from the central Celtic Sea. We have collected a great set of information on the distribution of the autumnal nutrients out towards the shelf edge. Unfortunately we couldn’t collect any information on iron in the sea, as the instruments used to do that use a wire that has a lower breaking strain – we are fairly sure it wouldn’t survive the sudden snatches the wire gets when getting gear back onto the ship in these waves.

We’re rolling heavily now! The ship has turned direction slightly to try to get a signal to our back-up internet connection – then we can get a weather forecast and start to plan the next few days.

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Thursday, 13 November 2014

13 November, 2014 21:38

Ocean research cruise blog of Jonathan Sharples


We finally finished our work at the mooring site yesterday evening. The marine snowcatcher work was not terribly successful. We are having difficulty in keeping them sealed, and also with the brass “messenger” that slides down the wire to trigger the catcher to shut. However, as usually happens, the Marine Facilities engineers on board have some ideas that might solve our problems so we’ll get another try in a couple of days.

We are heading southwest now, making a series of measurements with the CTDs across the continental shelf and to the shelf edge. There was some nasty weather during the night, with winds over 50 knots – dropped to 15 knots or so today, but it has left a decent swell for us to ride over on our way out. Over the next day the depth will increase slowly from 150 metres to 200 metres, then within about 2 hours the seabed will drop down to about 3000 m as we leave the continental shelf and head briefly into the open ocean. We will be doing a lot of iron chemistry out there, but I’ll explain more on what that is all about once we get started.

For now, work in the labs continues, on the samples we have collected since Monday and on those we collect during today. Invariably the lab work involved filtering lots of seawater, either because we want to analyse the pure seawater without any organisms in it (e.g. for dissolved nutrients), or because we want to filter out the organisms to study them more closely.

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Wednesday, 12 November 2014

Catching snow in the sea

Ocean research cruise blog of Jonathan Sharples


The last day on this station began with another 0500 early CTD, so that those scientists working on how fast the plankton are growing can start another set of experiments. During the afternoon we released another glider. This one has a special chemical sensor on it that has been designed at the National Oceanography Centre. It measures the amoung of nitrate in the water, a key nutrient required by the plankton. As with the glider yesterday, we are leaving this one in the water just while we are at sea; we aim to retrieve it just before we head back to Southampton in early December.

glider 2 deployed

We also had a go at using our “Marine Snow Catcher”. This large tube is designed to trap 400 litres of water at one depth. The tube is then brought back on deck, and all of the tiny particles in the water (plankton, bits of detritus)are allowed to settle in the tube. After 2.5 hours the scientists collect particles from near the top of the tube (which will be very tiny and will not have settled far), the middle of the tube and the bottom (containing the coarsest particles which settled quickly). We want to see how the organic matter in these different particles is being recycled by bacteria in the ocean; particularly we want to know if the bacteria recycle nutrients, such as nitrogen and phosphorus, more quickly than they recycle carbon.

Our communications are still suffering. It looks like we may be down to a limited email connection for the rest of the trip, with the problem with the main system having been narrowed down to a component that we don’t have a spare of.

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Glider away….

Ocean research cruise blog of Jonathan Sharples


Two new pieces of equipment deployed yesterday. First, the Ocean Microstructure Glider (OMG). A glider does exactly what the name suggests – it glides through the sea. By making itself heavier than the water, and tilting its nose downward, it glides downwards. Then, when it gets to the depth at which it has been instructed to turn round, it makes itself lighter than the water, points the nose up and glides towards the surface. Inside a glider are instruments similar to those on the CTD – measuring water temperature, salt and plankton. The OMG also has some specialised instruments for measuring the amount of turbulence in the water. That’s what the “microstructure” part of the name refers to – the sensors measure tiny changes in water currents associated with turbulence. We are really interested in turbulence, as it mixes nutrients, plankton and carbon through the water. The really neat thing about gliders is that when they surface they can stick their tail end out of the water and communicate back to shore via a satellite link, transmitting data back and also receiving new instructions. Our gliders are not controlled by us on the ship, but by scientists back at the National Oceanography Centre in Southampton and in Liverpool.

wirewalker deployment

 Immediately the glider was away, we moved the ship clear and deployed a “wirewalker” mooring. This again has instruments for measuring temperature, salt and plankton, but it moves up and down a wire fixed to an anchor on the seabed and a buoy at the sea surface. The action of the waves on the buoy provides the energy that the wirewalker needs to ratchet itself down the wire (so, a note to my nephew Ben there – yes we do now have things that use the waves’ energy to power them! Your idea was spot on); it then releases its grip on the wire and floats back up to the surface. With decent waves (of which we’ve been having plenty) the wirewalker can profile up and down the cable every 15 minutes or so. Jo Hopkins for the National Oceanography Centre in Liverpool is running this instrument – she is keen to capture the details of how the water is mixing as the weather cools into winter.

omg glider deployment2
We’ve lost a lot of our communications at the moment – certainly internet and phones are out. Zoltan, the NMF computer tech, is working through all possible causes and he’ll be calling on the ships ELT tech as well. Hopefully we’ll be fixed soon. We still have access to the National Marine Facilities Webmail though, so I can get these posts through OK.

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omg glider off

Tuesday, 11 November 2014

Sampling iron

Fantastic weather today. Winds 5 – 10 knots, and we have lots of blue sky. Other than a long, 2 metre swell you’d have to describe the sea as calm.
We have a group on board, led by Maeve Lohan from the University of Plymouth, who are going to measure the amount of iron in the sea. Iron is a nutrient that the microbial plants in the ocean need. It occurs in the ocean in very small concentrations, and so is a real challenge to measure. Much of the challenge is because ocean scientists need to make the measurements from steel ships, so there is huge potential for contaminating the samples with iron from the ship or our equipment.

The instruments used by the iron scientists are all made from titanium or plastic, and they do all of their work is a special “clean lab” on the ship, into which the rest of us are forbidden to go. When their titanium instruments come on board after collecting water samples, Maeve and her colleagues rush forward with a bag of polythene gloves which are all put onto the taps of the sample bottles so that they don’t get contaminated while on deck.
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Monday, 10 November 2014

Salp soup

The weather deteriorated a bit after the first CTD cast. Wind reached about 40 knots, so we had to stop working as the motion of the ship was putting too much stress on some of the equipment hanging over the side. However, things have calmed down nicely for the afternoon. A group of 6 or so dolphins has been hanging around the ship, probably feeding on the fish that often congregate underneath us if we stay in one place for a while.

zooplankton net

Sari Giering (University of Aberdeen) has started her sampling of the zooplankton – the tiny animals that feed on the microbial plants (and on each other). There is general surprise that there is so much biological stuff in the water, given the time of year. The zooplankton net, which is hauled vertically upward through the water to catch any zooplankton on a mesh at the end of the net, has come back with all sorts of stuff. The latest haul had a large colonial salp – a gelatinous filer feeder about the size of your finger, but that lives in long connected ribbons of several dozen clones.
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bucket full of sulps

The first data

Right on schedule, at 0500 our main set of instruments hit the water to collect the first data. This package of instruments (the "CTD") is made up of several sensors that measure water temperature, saltiness, oxygen concentration, and also how many of the microscopic ocean plants there are. The long grey tubes around the outside are used to trap water (20 litres at a time) from depths where the scientists want samples for their experiments.

CTD into sea

The first data is exactly what I was hoping for. Throughout the summer this part of the sea would have had a warm, sunlit layer above deeper, colder water. As autumn and winter approach this surface layer cools and starts to get thicker, until eventually the whole of the water from the surface to the seabed (140 metres deep here) reaches the same temperature. The red lines in the left panel of the computer screen show the temperature. It’s about 14 deg C in the upper 40 metres, then drops to 12 deg C in the deeper water. In summer it would have been about 18 deg C in the upper 30 metres, and 11 deg C below. So, we’ve got here just in time to see the change in conditions towards winter.
These early morning "CTD casts" are sampled a lot by the scientists. There was a big meeting last night to discuss who required how much water from what depths. Also the order in which the samples are taken is really important (samples for dissolved gases need to be taken first, while samples for salt can wait until the end).

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orderly queue

Sunday, 9 November 2014

Leaving Falmouth

Bang on time we left Falmouth Docks at 0830. The ship is so quiet many of us didn’t realise we’d started moving. We dropped the pilot off once clear of the docks. Ship pilots work for the port, rather than they ship. They know the sea in and around the port very well, so ships use them to guide into and out of the docks. Once we were clear of Falmouth, a fast boat came alongside us to pick up the pilot and take him back to shore.
The weather is remarkably sunny and calm. In fact we have some spare time as our first planned work is to start at 0500 tomorrow, and it’s about 15 hours to get to the work site. So, the ship’s crew have been testing one of the lifeboats – making sure that the davits (or cranes) that are used to lower it into the water work, and that the lifeboat’s engine is fine.

lifeboat recovery

Preparation of the laboratories continues, with the lab space gradually becoming clearer. Note in the picture below the typical fashion of the scientist at sea: lab coat, hard hat, lab groves, and also stell-toecapped boots. This is Matthew Bone (from the University of East Anglia); he will be working on how nutrients are released from the seabed at the start of winter.

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Matthew Bone

Saturday, 8 November 2014

Everyone aboard

Everyone has made it aboard now. We had our safety briefing this afternoon, learning about where to go if there were to be an emergency, how to operate the watertight doors, as well as other practical information such as where the laundry is and what time meals are served.

Snowcatcher Discussion

The scientists have continued getting the gear ready, and then all strapped down so that once we get to sea things don’t start rolling around the deck. We have two enormous "marine snow catchers" on the aft deck. These are used to capture 400 litres of water from key depths, which is then brought back onto the ship and sampled to see what particles are in it. For instance tiny animals (zooplankton), or bits of sediment from the seabed, or – very importanly – bits of zooplankton poo. Particles in the ocean sink, taking with them lots of carbon which ultimately was removed from the atmosphere. It’s what happens to these particles, and the carbon that they carry, that forms the basis of a large component of our work. One of the mooring components was also completed and strapped down, ready to take out into the middle of the Celtic Sea and dropped onto the seabed. This seabed lander has two devices for measuring the water currents using pulses of sound. It will sit on the seabed measuring currents until March next year.

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adcp bedframe