Thursday, 27 December 2012

10 - Final post

The blog has now finished as the RRS James Cook  is returning to Montevideo

Friday, 21 December 2012

9 - Collecting the creatures of the deep

When the ROV Isis  finds an interesting place on the seafloor, the sampling begins! Isis  is equipped with manipulator arms that can pick up samples to place them in boxes on the front of the vehicle, but as many deep-sea animals are very delicate, it is usually best to use the suction sampler (see image below). The suction sampler is like a vacuum cleaner, gently sucking up animals and sediment via a long tube. The animals can be deposited in any of five sealed rotatable chambers where they remain until the ROV is on board the ship again. As soon as the ROV is secured on deck and we are allowed near, all the biologists, armed with buckets, begin to move the animals and sediment samples to the sorting tables.

The suction sampler on ROV Isis  in use at E2.
The box in the background is attached to the ROV on swing arms and is used to hold samples

At the sorting tables, all samples are given individual numbers by Katrin Linse, so that we can keep track of what samples came from which place. One of each species of animal is preserved and safely stowed, so that, on our return, we can send them to taxonomic experts around the world for identification or if new to science, for description. All other samples are then divided up so that (hopefully) all scientists participating in this project get what they need to carry out their work. Sometimes different species go to different scientists. Or some species, like the yeti crabs, can also be shared – the legs to one person, digestive glands to another, gonads to someone else and so on. This means we make use of the entire sample and none of it is wasted. After all the large animals are sorted, the sediment that is left in the bottom of the buckets and chambers is sieved and then sorted under a microscope to find all the small animals that are difficult to see with the naked eye.

The samples are shared out because different scientists may analyse the samples in different ways as not everyone is studying the same thing. Below are explanations from each of the groups of scientists on board explaining how they analyse their samples and what they hope to understand from their work:

Katrin Linse (British Antarctic Survey) and Helena Wiklund (Natural History Museum, London)
Katrin looks at all the specimens collected to assess the overall biodiversity on a large scale. She wants to be able to describe the entire vent and off-vent assemblage of animals and answer questions such as which species lives where and with whom. Katrin and Helena also try to ascertain whether these animals are ‘specialist’ fauna (living only on the vents) or ‘background’ fauna, which come to the vent fields due to the greater availability of food (normally living in the general deep-sea waters of the Southern Ocean). Katrin and Helena also try to find the closest relatives of the animals we find by examining the DNA of each species. Also, looking into whether these animals have any special adaptations that allow them to live in these extreme environments. Helena has a special interest in polychaete worms and Katrin in molluscs.

Katrin with the first batch of samples on the sorting tables

Chong Chen (University of Oxford)
Chong is interested in snails! He is looking specifically at how species are connected with each other over distances of tens of metres to hundreds of kilometres. To do this he needs to compare the DNA of each snail collected, which he can get from small pieces of tissue taken from each specimen.

Leigh Marsh (University of Southampton)
Leigh primarily uses video footage to look at the spatial separation of animals around the vent habitats. In particular, she is interested in the yeti crab found at these vents. We have sampled crabs when abundant in hot areas close to the black-smoker chimneys and cooler areas further away. From this initial sampling, it has been found that females carrying eggs occur in the cooler areas further away from the hotter areas of the vent sites – it’s like a maternity ward for crabs! Leigh is also interested in examining how, when and where the yeti crabs reproduce to sustain their populations. That means, when samples are dished out, she measures the length of the carapace of each crab, identifies the sex of the crab and then removes the gonad tissue, which she then uses to assess the maturity stage.

The yeti crabs on the sorting table before being shared out to scientists

Clare Woulds (University of Leeds)
Clare uses the animal specimens to conduct experiments, which will help us to understand where the animals living close to vents derive their food and energy. For animals such as the brown snails that live on the vent chimneys, this involves placing them into aquaria filled with seawater from the site where they live. They are then kept at the temperature at which they normally live (in a high-tech fridge that she brought with her on the ship) for several days. The snails are unusual in that they have symbiotic microbes living in their tissues, and those microbes are able to harvest chemical energy from the mineral-rich hydrothermal vent fluid to make food (just as plants harvest sunlight to make food). She adds different chemical labels to the different aquaria, and these will allow her to see the uptake of different dissolved substances by the symbiotic microbes. Clare can then trace her chemical labels into the microbes’ DNA (and so figure out exactly which microbes take it up), and also, using cutting-edge microscope techniques, to be able to see exactly where the microbes are located in the animals.

Jane Heywood (British Antarctic Survey)
Chemosynthetic bacteria provide energy to deep-sea hydrothermal-vent ecosystems and support life. Many of these bacteria are found in symbiotic relationships with invertebrates such as the yeti crabs, brown snails and barnacles. Jane collects samples to examine the bacterial community from various tissues. For example, with the yeti crabs, she gives them a haircut, removing some of the hairs that grow from the underside of the shell. These hairs have many long chains of bacteria attached to them and Jane extracts their DNA and RNA and preserve samples for microscopy. Back on land genes will amplified from the DNA and sequence them to determine the diversity and community composition of these Kiwa-dwelling bacteria. Jane also performs similar analyses on bacteria associated with other hydrothermal vent fauna such as snails, barnacles and sea spiders and compare these to microbial communities in the surrounding environment; living on the rocks or free-living in the water. Assessing the microbial diversity and community structure will provide insights into the factors controlling these primary producers and the benefit, if any, that the animal gains from hosting these microbes.

Will Read and Chris Sweeting (University of Newcastle)
Chris and Will use a selection of animals for their food-web studies. Their primary goal is to figure out what these animals eat and how the energy sustaining life is transferred through the hydrothermal vent habitat. They start by removing various tissues (e.g. muscle, liver, gill) and freezing the samples at -81°C. The biological composition of the tissues will differ depending on their biological role, much like the way you see different percentages of fats, sugars and saturates written on food packaging. Taking different tissue samples will provide different types of information depending on the research question. The samples will then remain frozen until they get back to the lab in Newcastle where they dry the sample and process it for analysis. These data are used to figure out which animals are eating the bacteria at the base of the food chain as well as which animals are eating each other. We can also tell if the animal's diet changes with body size or spatial position within the hydrothermal vent habitat. The work links in with the research undertaken by the microbiologists and with those looking at the distribution of animals within the hydrothermal vent. By linking different aspects of the research together, it begins to provide a more holistic overview of the biological processes that occur at each location.

Wednesday, 19 December 2012

8 - From seabed to sample pot

We’ve now had several successful dives with ROV Isis  and still the call of ‘she’s on deck’ brings eager and excited faces to get the rare fluid samples collected during the dive. The chemists on board can immediately tell whether their fluid samples are good quality, as they smell sickeningly awful if they are collected from inside the vent chimneys without mixing with too much seawater. The worse the smell of rotting eggs, the happier the chemists!

Scientists collecting the samples from ROV Isis  after she returns from a dive.
So what makes the fluids smell so terrible? The answer lies in how these vents form. Shallow bodies of molten rock (magma) pool in the Earth’s crust in areas close to tectonic activity, such as mid-ocean ridges where new ocean crust is created. Seawater trickles deep into the Earth’s crust through cracks and fissures on the seafloor in these tectonically-active areas, where they are heated to extremely high temperatures. At such high pressures and temperatures, the seawater reacts with the surrounding rock and transforms into a highly acidic, metallic and chemically-rich fluid which rises back up through the crust owing to its buoyancy. This process of circulation also strips oxygen from the fluids, causing sulphate (a major component of seawater) to reduce to the strongly odorous chemical, sulphide. As the fluids emerge into the cold water of the deep sea (about 0 °C), lots of the dissolved elements precipitate from solution as metal-sulphide minerals. These are black in colour and as a result, the vigorously-venting fluids look just like black smoke.

We are really interested in these fluids, as their chemistry can provide us with information about the deep-ocean crust, the processes of hydrothermal circulation and the origins of many important elements in seawater. As a result, we are keen to collect pure fluids from within the vents, before they mix with seawater, as well as water samples from inside the black smoke.

For collecting fluids directly from within the chimneys, we use large syringes made from titanium, which can withstand the extremely high temperatures. The manipulator arms of the ROV insert the syringes right into the chimney, and we wait for our temperature sensors to reach about 350 °C to indicate that we are in pure hydrothermal fluid. We then fire the syringes, sucking the precious fluids into our sample barrels as you can see in the pictures below.
Top: ROV manipulator arm guiding the titanium syringes towards the venting fluids
Bottom: inserting the probes into the chimney orifice.

Once the samples are on deck, we have to process them quickly as oxygen in the air reacts with the sulphide in the fluids resulting in the chemical composition of the fluids changing. We preserve the samples for the analysis of tracers of magmatic gases, pH, sulphide, carbon cycling, metal content and many other chemicals.

Throughout the world’s oceans there are hundreds of sites of hydrothermal activity, pumping fluids enriched in many different elements into seawater. Despite being a few miles down in the deep sea, these elements can be transported up through the water column in the rising hydrothermal plume, and swept away on ocean currents. Some of these elements are essential nutrients and stimulate primary production - the first rung of the food ladder - if they reach the surface waters.

Tuesday, 18 December 2012

7 - The uncertainties of planning scientific expeditions in Antarctica

When we set out on this expedition we had a clear route plan. We were to go from Punta Arenas direct to E9 (see map), then on to Kemp and Adventure craters and then finish at E2 before steaming back to Montevideo. The best laid plans...

Not long after leaving Punta Arenas we started checking the daily ice maps for Antarctica ( They showed that ice was still present as far north as 59°S and along the 30°W longitude. As E9 and the Kemp and Adventure craters are at approx. 60°S and 30°W, we could not get to them in the RRS James Cook as it is not an ice-strengthened ship. So we changed direction and went to our last station E2, where we spent a productive week examining the biology and chemistry of the vents there and making detailed maps of the vent environment.
Map showing JC080 cruise proposed destinations
Each day, even before breakfast, we logged on to the Polarview website to check the ice conditions. Over the last week the satellite images of the ice show a very slow retreat close to our southern stations. This may be the effect of the South Orkney Ridge and the southern end of the South Sandwich Island chain being relatively shallow and as a result the ice has frozen deeper relative to the water-column depth. In the open sea at the same latitudes the ice appears to be breaking up nicely. We are also in the austral spring after one of the most extensive freezes for many decades in Antarctica and ice melting is taking much longer.

So we have decided to move south and use our CTD to check for chemical evidence of vents in each of the segments of the East Scotia Ridge. Today we are at E5 and then we go on to E6 and E7 (see map), which may be close to the ice edge, although we hope that by the time we get there, it will have receded southwards. We have been lucky in all other respects, in that the seas are lovely and calm and the sun is shining.

All this shows is that even the best laid plans can be thwarted by nature. We have back-up plans and will use them until, we hope, our southern stations are free of ice.

Monday, 17 December 2012

6 - Surrounded by whales

It was just after 7.30 and breakfast was under way. The ship’s doctor, Molly, said she had just seen ten or so whales on the port side of the ship. This lead to a general exodus for those not on watch, onto the aft deck armed with cameras. Little did we know what the rest of the day had in store for us!

Off to the port beam we could see three whales, and as almost all of us have no experience with whale watching, a quick discussion developed concerning which species we were seeing. Some rapid photo images with long lenses soon showed these were enormous humpback whales. Humpbacks have a number of readily recognisable features including a white underside to the tail, white bellies, a low dorsal fin, nobbly protruberences (tubercles) on the head and often have barnacles growing on their chins. Even at a distance these features became recognisable.

Two humpbacks, one showing dorsal fin and the other the tail
Within 30 minutes there was a snorting noise immediately beside the ship and looking over the gunwhale we saw the massive outline of a humpback whale. It then arched its back, showing off the small humps behind the dorsal fin, and sank from sight with the last part seen being the massive tail with its knobbly-trailing edge and white underside. Over the next six hours, these three humpback whales were joined by others within their group (totalling eight at one point) and they playfully swam alongside, round the stern and even under the ship. They rolled over, flicked their tails into the air and then appeared to ‘stand’ on their tails with their mouth and rostrum pointing skyward (spy-hopping). It was truly remarkable to see these large animals so close, almost within touching distance, seeming to be enjoying themselves, and the clatter of camera shutters was almost deafening.

Humpback spy hopping; see barnacles on chin
What had attracted the whales to this area was the high density of krill that occurred in the top 150m of the water column. The krill could be seen clearly on the Isis’s cameras during her deployment and recovery. There are thought to be five or six sub-populations of Humpback whales in the Southern Ocean. They usually spend the austral summer around the Antarctic before migrating north, probably up the east coast of South America, the west coast of South America or up to West Africa.

As we continued to look out to sea in the afternoon, we could see spray all around the ship from whales in the distance. Our day was completed when some of the individual whales began to breach. This is when they leap completely out of the water and crash back into the sea sending up massive amounts of spray. The whales stayed with the ship all day until our time at station E2 ended with the recovery of Isis  and steaming south with the fresh memory of a truly remarkable experience.

Humpback expelling air as spray

Saturday, 15 December 2012

5 - ROV-ing at E2

Over the last four days, we have completed three ROV dives at the E2 site (refer to map). We have split this site into two areas – north and south. The south is the area we have explored on previous cruises and thoroughly over the last few days. The north is a poorly-known site where strong signals of hydrothermal activity have been picked up previously with the CTD, however no ROV exploration has been done as yet.

At E2 South, we have been using distinct features of the terrain to navigate (in a similar way to using sign posts when driving). We always start our ROV dives at ‘Dog’s Head’. This is the only black-smoker complex that we know of at E2 and was found in 2010. There are bacterial mats, anemones, yeti crabs, gastropods, limpets and sea spiders living on this chimney complex.

Image of the black-smoking Dog’s Head with bacterial mats
(Rogers et al., 2012).
Moving south from ‘Dog’s Head’, there are a series of chimneys, some extinct and some emitting diffuse flow with limited fauna. The names given to these sites range from ‘Poached Egg’ to ‘Cricket Stumps’ and take inspiration from what they resemble.

There are six other areas of interest at E2 South – ‘Sepia’, ‘Cinderella’s Castle’, ‘Dreaming Spires’, ‘Crab City’, ‘Crab Spa’ and ‘Anemone Field’. Sepia is a chimney that rises off the seabed and then balloons out into a large spherical structure with lots of flanges. It looks like a giant button mushroom. This is probably the area with the second highest abundance of fauna at E2.

Image of a flange at Sepia with anemones and bacterial mats on
the chimney below (Rogers et al,. 2012).
‘Cinderella’s Castle’ is another diffuse-flow chimney that balloons towards the top into a structure with flanges, but this time, there are many smaller chimneys on top (like the turrets of a castle- called chimlets). This site also has the full complement of vent fauna, similar to ‘Dog’s Head’ and ‘Sepia’. ‘Dreaming Spires’ is very similar to ‘Cinderella’s Castle’.

Image of the undescribed gastropod from E2 surrounding one yeti crab.
There are also limpets on the gastropods, anemones  and one sea spider (bottom right)
(Rogers et al., 2012).
‘Crab City’, ‘Crab Spa’ and ‘Anemone Field’ are all diffuse-flow patches amongst pillow and rope lava. ‘Crab City’ is a large aggregation of yeti crabs and bacterial mats found in 2010. ‘Crab Spa’ is a series of smaller patches of yeti crabs, which were found on this cruise. We originally thought of naming it ‘Crab Holiday Park’ but decided ‘Crab Spa” had a nicer ring to it! ‘Anemone Field’ is pretty self explanatory – a large flat-ish area with lots and lots of anemones.

We have managed to get many biological and chemical samples from the E2 South site and the ‘Hows’ and ‘Whats’ of that will be a coming blog entry.

Over tonight and into tomorrow, we intend to send ROV Isis  down to explore the E2 north site. Fingers crossed we find something exciting!

Tuesday, 11 December 2012

4 - Mapping the hydrothermal landscape

The cruise is ten days in now. In the coming days, the team will do a series of back-to-back ROV dives at the E2 vent site. In addition we will be placing equipment on the seafloor and carrying out visual observations along transects. But how will we know where exactly to go? What kind of environment do our samples come from? Understanding the surroundings of the chemosynthetic sites and the spatial structure of the habitats is important for the final interpretation of any experimental results. It is also important in its own right, because marine habitat maps are increasingly used as the main source of information to support decisions about marine protected areas and the conservation of endangered species.

So how do we go about creating a map of the seafloor and hydrothermal habitats? Unfortunately, visual light doesn’t travel very far in water, so we can only use photography and video at very close distance to the seabed. However, it is (currently) impossible to video or photograph the entire world’s ocean floor – this would take hundreds of years! Instead, the tool of choice for mapping the seabed is sound: by using different types of echo-sounders and different frequencies, we can map the morphology and reflectivity (which gives an indication for the sediment type) of the seabed.

A single beam echo-sounder measures the time between a sound signal being sent from the ship and the echo from the seabed to coming back, and converts this into depth below the vessel. This is continuously repeated while the ship travels on, and results in a profile of the seabed plotted on the screen. A multibeam echo-sounder basically does the same, but has a whole fan of acoustic beams going out from the vessel. The seabed depth is measured for each of these beams, and by repeating this ping after ping, a 3D morphological image of the seabed is created (see Figure). In addition, the strength of the echo in each of the beams tells us something about the seafloor type, with strong echoes from rocky or gravelly substrates, and weak returns from a muddy seabed.

This swath bathymetry animation is courtesy of the COMET Program. See below for credit.

Unfortunately, there is one trade-off: due to the geometry of this fan of beams, and the absorption of sound in the water (although less than the absorption of light), mapping in deeper water needs a lower frequency sound source and results in lower resolution in the final map. Typically when working in 1000m water depth, the pixels in the map represent about 25x25m patches on the seafloor, while in around 100m water depth this can be reduced to 2.5x2.5m.

So, to get a better picture of the vents, we have to bring the multibeam system closer to the seafloor, which we do by putting a system on the ROV! Flying the ROV at about 40m above the seabed, we create ultra-high resolution maps, with pixels of around 30x30cm, although we cover less ground in the same time. It’s a real challenge for the pilots as they have to fly in the dark: at 40m altitude we cannot see the seabed! It may come across as a fairly tedious activity, slowly moving along the survey lines at a speed of 0.4 knots, not seeing very much, but it is still fascinating to see the map being created on the screen, line after line! Combining this information with the video interpretations will provide full-on habitat maps of the hydrothermal landscapes.

So far we only have been able to map one area (E2) with this technique during this cruise, but hopefully we will do this at Adventure Crater also. The results of the ROV mapping provide unprecedented insights into the shape of the hydrothermal vents, and we hope the weather will be kind enough to us to allow a few more detailed maps to be made!

Swath bathymetry animation
The source of this material is the COMET® Website at of the University Corporation for Atmospheric Research (UCAR), sponsored in part through cooperative agreement(s) with the National Oceanic and Atmospheric Administration (NOAA), U.S. Department of Commerce (DOC). ©1997-2011 University Corporation for Atmospheric Research. All Rights Reserved.

Monday, 10 December 2012

3 - Plume Hunting

For the last two nights we have been deploying the CTD (conductivity, temperature and depth) profiler. The CTD is the most versatile and well-used piece of oceanographic equipment on the ship. It was by using a combination of CTD and novel new sensors from Japanese colleagues in 2009/2010 that we were able to identify these East Scotia Ridge hydrothermal vent sites to within ten metres of where they were.

Doug showing Alfred the method for sampling methane from the water samples collected
in the grey Niskin bottles on the CTD profiler in the background.
Alfred collecting water samples from a Niskin bottle on the CTD profiler
Having found these sites, we now use the CTD to look at the complex flow of chemicals exiting the vents. By collecting water samples in 10 litre plastic bottles on the CTD, we can investigate which chemical species are present in vent fluids and how they may affect the wider ocean including the impacts of nutrients like iron. Iron has a strong effect on primary productivity and consumption of CO2 in shallower waters. With this research we will see if our small hydrothermal vents have a much wider, global impact on marine life and our planet.

In addition to the chemical species being investigated, the microbiologists are particularly interested in the changes in the microbial community and the effects these microbes have on communities living in the plume environment.

On Saturday night, a CTD was used to pinpoint the major black smoker on E2. We sampled at various depths where the hot buoyant chemically-rich plume rose through the water column. We collected water samples to analyse for gases, metals and nutrients. Some of these will be analysed on board and others will be taken back to respective labs in the UK. Last night a series of CTD dips were conducted over the northern end of the E2 site to prospect for a new site for which evidence was found in 2009/2010.

This type of work normally leads to very excited geochemists and biologists catching up on their sleep!

Friday, 7 December 2012

2 - To the East Scotia Ridge

We said goodbye to Punta Arenas and set sail in the early hours of the morning, stopping first at a fuelling station to fill the ship’s colossal tanks. Our journey south began with the Straits of Magellan, a historic passageway connecting the Atlantic Ocean with the Pacific through the island labyrinth of the Tierra del Fuego. The ship was a buzz of activity as boxes were unpacked, lab equipment was secured to benches and work tops, and cabins were adjusted to feel like home. We had a safety briefing with tours of the lifeboats and some of us had a go at getting into immersion suits should disaster call us to abandon ship.

Claire Woulds modelling the one-size-fits-all immersion suits in the main lab.

Over the next couple of days as we approach the East Scotia Ridge where we will begin our science, we are all getting used to the rolling of the ship and adjusting our body clocks to match the watches we’ll be doing on site. We’ve already been visited by a spectacular array of bird life, including many different species of petrel and the remarkable Wandering Albatross, which have wing spans up to 3.5 metres!

A Wandering Albatross skimming the waves behind the ship.

1 - Mobilising in Punta Arenas

Before setting sail from Punta Arenas in Chile, we had a few crucial days to mobilise. During this time, crew and scientists flew in from around the world to board the RRS James Cook. They moved into their cabins and got familiar with the ship and each other. The ship was also loaded with all the equipment that scientists and technicians had freighted out to Chile weeks ago. Provisions (water and food) for the next six weeks were also packed on to the ship.

This was also the last chance for scientists to buy any snacks and equipment that had been forgotten. Among the purchases were a lot of chocolate, a cafetiere, some Christmas-tree lights and a bag of carrots for snacking. The scientists also got the chance to dine on some ‘wild’ Chilean meat – beaver, hare, goose, guanaco (similar to llamas) and rhea.

Where is Punta Arenas?

View Punta Arenas in a larger map

A bird’s eye view of Punta Arenas

We got the lovely surprise of having the RRS James Cook  docked next to the R/V Nathaniel B. Palmer  of the US Polar Sciences programme. It isn’t often that two world-class research ships are docked together!

The RRS James Cook  docked next to the R/V Nathaniel B. Palmer