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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