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The Loch Ness eDNA Project

Super Natural History

Launched 3rd June 2018

All life transfers skin cells, faeces, eggs, sperm, hair etc to the environment. So sampling the environment allows scientists to isolate and decode the eDNA and compare it against a database of known DNA sequences and thereby identify species. This is sSo much more elegant than our previous methodology!

The eDNA 'Super Natural History' project will involve shore-line, surface, mid and deepwater sampling at Loch Ness and three other lochs. The water samples will be filtered and sent to international labs.

International Participants
Personnel from the University of Otago, University of Bangor, University of Hull, University of Copenhagen, University of Grenoble, University of Canberra, UC Santa Cruz.

Local participants
The University of the Highlands & Islands
SEPA
The Loch Ness Project
The Loch Ness Exhibition Centre is hosting the fieldwork providing its boat and the Loch Ness Project lab facility.

Videography and images copyright Maralyn Shine 2018

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Prof. Neil Gemmell has assembled a top class scientific team with a wealth of experience and enthusiasm. and we look forward to taking part in the Super Natural History project.

Saturday 2nd June 2018

Team leader Prof. Neil Gemmell, Gert-Jan Jeunen and Cristina Di Muri arrived yesterday.

Sunday 3rd June 2018

Today there was a team meeting at the Loch Ness Centre. Sampling strategies and locations will be decided and equipment reviewed in the Loch Ness Project's laboratory. Some equipment is ready to go and some need a minor modification. A list is being assembled for a shopping trip to Inverness tomorrow and we are underway.

We were joined by Prof. Eric Verspoor and Lucio Marcello from the University of the Highlands & Islands. The Danish contingent (Tom Gilbert, Kristine Bohmann and Christina Lynggaard) had flight delays but are now en route from Edinburgh.

Protocols, equipment and ideas were reviewed and the plan now is to familiarise the team with MV Deepscan this evening.

 

adrian shine with John Minshull

Adrian Shine and John Minshull plan how to connect up the sampler. We have three samplers, the one Neil Gemmell is checking is a Marpet Sampler.
UHI

Prf. Eric Verspoor and Lucio Marcello detail where their Pioneer boat will coordinate some shoreline sampling.A second boat from UHI will be available from tomorrow to assist with sampling along the shoreline. It is essential that samples are processed quickly and the small UHI Pioneer can get in closer than Deepscan and run back to base with their samples. Deepscan will commence mid-water sampling tomorrow night.

Week commencing Monday 4th June 2018

Today sampling the water from the shoreline commenced. Some sites were easy to access by road but others needed a shallow draught boat to enable scientists to sample where the shore is too steep or a long walk in.The UHI provided their new Pioneer craft with Prof. Eric Verspoor at the helm and enabling samples to be ferried quickly back to the harbour for processing.

Processing the water entails extracting a full syringe of the sampled water and pushing it through a special fine pore filter. As more of the sample is pushed through the filter it becomes harder to push! This process concentrates the sample and indeed it is a very concentrated task! However the sun was ... but the midges weren't.

In the evening as the shore sampling drew to a close for the day, we boarded Deepscan to test the Friedinger water sampler. John Minshull and Adrian Shine had modified the release mechanism on the Friedinger earlier in the day. After several tests up to 100m we were all satisfied with the deployment routine and that the equipment was firing correctly.The weather held but there was a cool breeze so that repeatedly handling 100m of cold wet rope became just that bit colder.

Sampling at depth commences tomorrow.

The team heads north in the evening sun

J SKIPPER JOHNMINSHULL

Skipper John Minshull holds the boat head to wind while the sampler is deployed off the bows. The film crew are getting filmed too ... sorry !

TOMORROW NIGHT WE WILL DEEP WATER SAMPLE TO 200M.

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Out again at 6pm to go to the north basin to sample at two stations with 3 depths sampled with replicates.

Aboard Deepscan are Prof. Neil Gemmell, Adrian Shine, Cristina di Muri, Gert-Jan Jeunen, John Minshull, Maralyn Shine, Zander and Kieran.

It is yet again a beautiful night snd we very briefly skirt Urquhart Castle for a photo call before the serious work begins.

Now into seriously deep water we sample firstly at 200m, deeper than the height of the London Telecom tower. Motoring further south for the second station sampling, we had local sun-down and suddenley we are all in fleeces and hats and the loch looks lumpy and cold. When the boat heading falls off the wind she rolls and we keep one hand for the boat and one for ourselves. However the sampling continues and the processing is relentless.

At each station, firstly a profiler is lowered and its data uploaded to a laptop. Having read the data and being happy to proceed, the Freidinger sampler is scrupulously cleaned and lowered to the correct depth by a measured line from the ships bows. At the correct depth the messenger weight is put onto the line and it begins its descent to the sampler triggering mechanism which closes and traps the water.

The retrieval is from aft were though the electric hauler helps pull the sample up from the depths, that cold, wet rope must still be flaked by hand ready for the next drop.

We have along with us, Kieran and Zander to film and photograph the sampling and Maralyn Shine is filming for the Loch Ness Project and the Loch Ness Centre.

We finally head for home and arrive at the harbour at 10 pm and make our last visit to the Loch Ness Centre's lab. Local sunset turns the loch dark. Break out the woolly hats.The final samples are extracted efficientlyand fast, it was not plain sailing by 9.30pm.

Loch Ness Water Sampling processing DNA
The water is taken into a syringe and pushed through the special filter.

FILT 4

The eDNA has been separated and the excess water drains away.

Obviously sterility, labelling and correct storage is essential for a successful experiment.

photo op

Team talk.

sampler

Easy to guess where this was taken

proviler and sampler

The Freidinger with the RBR XR 420CTD profiler.

home

Heading for the labs at the Loch Ness Centre.

profiler

The water sample is immediately decanted into a sterile bottle and systematically pushed through filters, a buffer presevative is added, the tube labelled and it's ready to head off for lab processing.

It is meticulous and painstaking work especially when the sun has gone down, fingers are numb with cold and it's been a long day.

 

12th June 2018

Since last writing we had been very busy going out to the north and south deep basins and some river mouths to sample where methane was gassing from the sediments. The press had been with us but by the 12th June we were down to the core team.

The  weather calmed for the final sampling aboard the Loch Ness Centre’s research vessel. A variety of sampling devices has been used, the first being a metal Freidinger type supplied by Prof. Neil Gemmell of Otago University. The second was the transparent perspex Freidinger supplied by Adrian Shine of the Loch Ness Project and finally the Niskin Bottle brought by Prof. Eric Verspoor of the University of the Highlands and Islands. Also aboard  were Lucio Marcello (UHI) and Gert-Jan Jeunen (Otago Univ.) The skippers were John Minshull and Ali Matheson and the videographer was Maralyn Shine.

Water  samples were taken at every 50m down to 200m, from the north and south basins. Also the team visited two river mouths to sample water where methane was gassing from the sediment. As you can see from the video, everyone is enjoying the work and finally a quaich of water brought up from 200m is shared around to celebrate.

The visitors have now left leaving equipment stored in the Loch Ness Centre’s lab for possible further visits.
Adrian Shine said ‘DNA sampling is a new field for the Loch Ness Project though we are no strangers to water sampling and looking it the hard way, through microscopes. These concentrated eDNA samples bring a new elegance to biology.’

The samples are now being processed by an international team and some raw data will be ready later this year and the analysis in early 2019.

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