Shelf Sea Biogeochemistry blog

Thursday, 14 May 2015

Working with mud!

By Sarah  Dashfield  and  Joana (Jo) Nunes

This is our first SSB cruise, as well as our first cruise overall!!! Exciting stuff!

Bulk coring team

On the second benthic cruise we are responsible for doing lots and lots of coring, i.e. lots of mud to shovel off the side of the ship!! Sarah’s work, who is mainly responsible for all the fauna (the beasties) that live in and on the seabed, involves both the NIOZ and the SMBA box corer. These corers collect a 0.1m2 and a 0.5m2 sample of the seafloor, respectively. Epifauna is collected with the Jennings trawl, a 2m net that is very slowly dragged over the seabed – the nets collect lots of bivalves, starfish and sea mice (furry and iridescent worms! Yes, really!),  snappy Nephrops norvegica (scampi!) and sometimes even some monkfish, which we don’t keep!

Sea mice


Jo is responsible for the flux coring. Here, we also use the NIOZ box corer, but each core is shared by several people. It is Dave who collects for nutrient flux incubation, Gangi who collects cores for oxygen profile incubations, and Helen who collects cores for a pulse-chase experiment.  This experiment quantifies the exchange of nutrients between the sediment and the overlaying water.
Jo sub-samples around everyone else:  50mL syringes for pigments and microbial analysis, surface scrapes for nitrification rates, and, the most fun of all, 10cm diameter cores for denitrification rates, which get whizzed up with a blender-like piece of kit.  The samples are treated with different chemicals to stop the nitrification process at different stages, incubated for a minimum of 24 hours and fixed with zinc chloride.  Finally, they are ready for analysis when we return back to PML.

Jennings trawl 
The fauna that we have collected from the trawls and cores will be identified, counted and weighed when we return to the benthic lab in PML.  This information together with the microbial data and the chemical analyses can be statistically analysed to discover whether there is a relationship between them. Finally, this information can be added to enhance marine models such as ERSEM (the European Regional Seas Ecosystem Model) which then will be used to predict how the marine environment may change in the future.

Flux coring

Wednesday, 13 May 2015

Calm Seas

Calm seas: Credit: Gary Fones

12th of May saw some much appreciated calm weather and lots of science activity aboard the RRS Discovery. Lunchtime saw the deployment of the PML Buoy Profiler, which is a SSB PhD project (more of this in a latter blog from Rich Sims, PML).

 Picture of PML Buoy. Credit: Gary Fones

Sediment coring followed this, this is a key activity of any benthic cruise. We are using a number of coring devices to collect sediment from the seabed beneath us, which is 100m down. On this research cruise we are using a NIOZ corer which is used to collect sediment (mud) from the ocean floor,  a mega-corer (able to take up to 12 undisturbed samples in clear plastic tubes),  and a large SMBA box corer which is designed to take a 600mm square, undisturbed sediment sample up to a maximum depth of around 450mm.

 NIOZ corer recovered to deck. Credit: Gary Fones
Wednesday 13th of May started with calm seas and a lovely sunrise. This was followed by a very successful recovery of the NOCL mini-stable lander that has been on the seabed the last few days gathering in-situ data (more of this in a latter blog) which will be used by the scientists to understand processes happening at the boundary between the sea bed and water column.

Recovery of Lander: Credit:Richard Cooke

Friday, 8 May 2015

Rough seas and science finally starts

Deploying the CTD. Credit: Gary Fones

The core aim of DY030 is to collect samples and data to understand how the chemistry and biology of the Celtic Sea link together to drive healthy and productive conditions, as well as how those conditions might change with climate change. After sailing we experienced some weather more associated with March than May – a number of scientists took to their cabins or just sat on deck staring at the horizon wishing the waves away! Those with their sea legs carried on and continued preparations in their various laboratories on the ship waiting for the science to start.

CTD. Credit: Torben Stichel
We eventually started work on the 6th May at one of our main Benthic Process sites – Benthic G. First up is always some CTD work even on a benthic sediment sampling research cruise. CTD (Conductivity, Temperature and Depth) is the stock instrument of any oceanographic cruise and enables us to understand the water column structure using a number of on-board sensors and collecting water samples from per-determined depths for subsequent analysis. After a slow start it is always nice to get the first sampling underway.

CTD. Credit: Richard Cooke

Tuesday, 5 May 2015

The Start: DY030

4th May 2015 saw the commencement of DY030 aboard the RRS Discovery, the latest cruise in the Shelf-Sea Biogeochemistry (SSB) programme. The aim of the NERC Shelf Sea Biogeochemistry research programme is to take a holistic approach to the cycling of nutrients and carbon, and the controls on primary and secondary production in UK and European Shelf Seas, and to increase understanding of these processes and their role in wider biogeochemical cycles.

RRS Discovery. Photo credit: Jessy Klar
Of the 4 main work packages this cruise will mainly focus on Work Package 2 (Biogeochemistry, macronutrient and carbon cycling in the benthic layer) and Work Package 3 (The Supply of Iron from Shelf Sediments to the Ocean), but with facets of the CANDYFLOSS Pelagic Work package. All Work packages contribute to the overall Integrated modelling effort of Work Package 4.

Aboard RRS Discovery. Photo credit: Richard Cooke
This mainly benthic focussed cruise is the third of four benthic cruises following on from DY008 in Spring 2014 and DY021 in March 2015. DY030 will include the use of a number of benthic lander systems, Autosub 3, gliders, benthic trawl equipment, benthic flumes, CTD water column sampling, Sediment Profile Imaging (SPI) camera and various coring systems.

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.