Friday, 22 July 2016

Immersive visualisation with the Oculus Rift and gaming engines ... by Steve Richardson

BGS staff held a hackathon on 19-20 July at its Keyworth headquarters. Nearly 50 developers, scientists and judges worked in teams addressing scientific challenges and developing prototype solutions in a relaxed, informal, collaborative atmosphere. In the first of our reports from Challenge Leaders, Steve Richardson describes his team’s 14 hours tacking ‘Immersive visualisation with the Oculus Rift and gaming engines’...

The title of our hackathon challenge was ‘Immersive visualisation using the Oculus Rift and Gaming engines’. The idea behind this challenge was to give our developers and scientists a chance to experiment with emerging Virtual Reality (VR) technologies and see whether visualising 3D data could help make our data more accessible, visible and exciting. Ideally we wanted to show how such tools could be used and demonstrated at conferences, BGS open days or even downloaded by users around the world.

For the two-day challenge, our specific goal was to:
“Build an INTERACTIVE, IMMERSIVE model (using a gaming engine) of the BGS geological walkway for players to EXPLORE (wearing the Oculus Rift)”.

We chose to use the BGS geological walk because it was an ideal site to demonstrate the concepts of visualising real-world locations in virtual environments. We could have chosen anywhere in the world but being on-site was the most convenient and familiar.

We also had a lot of data already available that would help us to get on with testing the technology in a time-restricted hack environment, such as a LIDAR point cloud dataset of the concourse captured in 2012:

Figure 1 LIDAR model of the BGS concourse
Figure 1 LIDAR model of the BGS concourse
Our team was a mixture of BGS developers (Steve Richardson, John Talbot) and 3D modellers (Bruce Napier, Luz Marina Ramos Cabrera) as well as a work experience student (Pierce).

After some hack-team planning we got stuck into the challenge at full speed, fuelled by bags of sweets and drinks provided by Patrick Bell and co.

The majority of our hack challenge tasks revolved around building a virtual world in the Unreal Engine 4 system.

First we used the concourse LIDAR model to use as a blueprint for the model, to make sure that all the buildings, trees, monoliths and paving were positioned correctly in relation to each other. This template allowed us to then start adding in the basic building blocks (cubes for buildings, spheres for the WSB atrium etc) of the built-up environment on and around the geological concourse.

Figure 2 Basic building-blocks of the concourse being added
Figure 2 Basic building-blocks of the concourse being added
With the rough outline of the concourse taking shape we then set about making it more realistic. To do this we took high-resolution photographs of the buildings, paving and monoliths, then using photo manipulation software we carefully stitched them together to form large digital wrapping paper to paint onto the bare shapes (buildings, pavement and monoliths). This is a slow and painstaking process which requires attention to detail and most importantly time – something which a hackathon is notoriously short on!

Figure 3 Creating seamless textures from high-resolution photographs
Figure 3 Creating seamless textures from high-resolution photographs
Once we had some textures the next stage was to paint them onto the models. This required us to have 3D models of each monolith, which requires LIDAR imaging or hand-building from scratch. As we were short on time we decided to use generic rock models which we downloading from the internet as placeholders.

Figure 4 Adding the new building textures onto the building model
Figure 4 Adding the new building textures onto the building model
At the same time as the modelling and texturing was taking place, other team members were searching for materials, models and text as the geological concourse content. As the walkway is in geological time order we wanted to place 3D models of fossils and (where possible) dinosaurs in their correct time sequence, to show how life evolved on the planet. We used the GB3D Type Fossils website to search for each time period, select an interesting range of fossils and then download their 3D model scan. This model was then imported into our concourse ‘world’ and placed into its correct location along the timeline. Virtual signposts were placed next to fossils and time periods to help players to understand how their geological time-travelling was going.
Figure 5 Showing a fossil and signpost on the SIlurian section of the concourse
Figure 5 Showing a fossil and signpost on the Silurian section of the concourse

Once the concourse had started shape we regularly tested it in the Oculus Rift, which is a 3D stereoscopic headset that tracks the user’s head movement, creating an immersive experience for the user. 
Figure 6 Testing the model while wearing the Oculus Rift
Figure 6 Testing the model while wearing the Oculus Rift
Viewing the concourse in the Oculus Rift gives the user a sense of scale which is not possible when viewing a 2D screen – especially when we started adding the big dinosaurs into the model!
Figure 7 Release the dinosaurs!
Figure 7 Release the dinosaurs!
All of this work was taking place under the loudly ticking hackathon-clock, constantly reminding us all of how little time was remaining!

Inevitably, we reached lunchtime of the second day with just enough time to whip up a short presentation for the judging panel.

Presenting our work to the rest of the hackathon judges gave us the chance to stop and review how far we had managed to come in such a short space of time. We had set out to produce an interactive, immersive and explorable model of the BGS concourse and in the short time our team had produced a substantial amount of work, with only the ‘interactive’ element of the task falling off the TODO list.
Figure 8 End-of-hack progress
Figure 8 End-of-hack progress

 Figure 9 Demonstrating the Oculus Rift to a willing volunteer
 Figure 9 Demonstrating the Oculus Rift to a willing volunteer

Our team learned a great deal from the #BGSHack in terms of what worked well but also what didn’t. We hope that the Hack gave scientists and other developers an opportunity to see what these technologies can achieve and look forward to seeing where we can take these techniques in the future.
 
Thanks to the team for their sterling work and efforts over the Hack, and thanks to Patrick and co for all their hard work setting up and running the inaugural #BGSHack!

Monday, 18 July 2016

INTIMATE: a Research and Training School in Palaeoclimate...by Stefan Engels

The training school
The INTIMATE network aims to better understand the mechanisms and impact of climate change by bringing together scientists working to reconstruct and model palaeoclimate through the INTegration of Ice core, MArine, and TErrestrial palaeoclimate records. Since the 1990’s, INTIMATE has held regular meetings and the active community of scientists has expanded across the whole of Europe.  A new initiative developed in 2013 (when INTIMATE was funded as an EU-COST Action) was the organisation of a training school that combined teaching about palaeoclimate research with conducting actual research on-site as well as following the school. Stefan Engels (Centre for Environmental Geochemistry, University of Nottingham and the British Geological Survey),  Christine Lane (University of Manchester), and colleagues recently hosted the 1st training school in Dörverden (Germany), where 20 early stage researchers (ESRs) from across Europe and beyond attended and enjoyed a week of science in a productive and social environment....

Explaining how to core peat sediments
 After months of intense preparation, budgeting and organisation, local organisers Michal Slowinski and Mariusz Lamentowicz (together with Stefan Engels and Christine Lane) hosted the training school in the beautiful surroundings of Stara Kiszewa, northern Poland. A total of 21 ESRs from 9 different nations joined the training school, from Ireland in the west to Russia and Bangladesh in the east. The first day of the meeting was aimed at formulating research questions, and analysing the palaeo-tool box we can use to answer these questions. This was mostly achieved in an interactive environment, where participants cooperated in different groups and then shared their ideas and findings in short presentations. Day two was used to get acquainted with the Quaternary history of the region during a very interesting field trip, before two days of hands-on training. Participants learnt a variety of techniques, including coring on a lake platform (piston corer) as well as in a peat bog (Russian sampler), lake-water sampling and a lab session was hosted where several proxies could be ‘sampled’ under the microscope. The final day was used to bring all the initial results and techniques together, and to apply all the knowledge that was gained during the previous few days to the research questions that were formulated on day 1. 

Students getting to grips with the cores
Aside from this busy daytime schedule, the evenings were filled with state-of-the-art lectures by experts in their various fields, including climate modelling (Didier Roche, Gif-sur-Yvette), age-depth modelling (Christopher Bronk Ramsey, Oxford), ice core science (Sune Rasmussen, Copenhagen) and lake sedimentology (Achim Brauer and Rik Tjallingii, both in Potsdam). These lectures truly formed a great addition to the program, and highlighted key aspects of palaeo-research. The final evening was (of course) used to have a big farewell party, and included the consumption of a locally shot wild boar as well as some local beers and snuff! We were introduced to local traditions by two Kashubian folk music performers, and the participants spent their final drops of energy learning to play the ‘devils violin’ (see picture) or the horsetail-in-a-barrel. A great end to a fantastic week, thanks to all the participants.

Stefan Engels is a Research Fellow within the Centre for Environmental Geochemistry, collaboration between the British Geological Survey and the University of Nottingham. 



Friday, 24 June 2016

BGS Hackathon... by Patrick Bell

BGS developers Wayne Shelley and Steve Richardson
get inventive at the NASA Space Apps Challenge Hack
held at the Met Office in 2014
BGS staff are holding a hackathon on 19-20 July at its Keyworth headquarters. Teams of 4-6 people will address scientific challenges and develop prototype solutions in a relaxed, informal, collaborative atmosphere. Example challenges include:
  • immersive visualisation of spatial data using video game engines
  • machine learning using Google technology
  • unleashing the BGS text corpus amassed over the last 180 years using new semantic web technologies
  • crowdsourced earthquake sensing using smartphones
  • enhanced processing of National Geological Repository digital assets

With more challenges still to be confirmed, this promises to be an exciting two days of interaction and creativity as our software developers, graphic designers and Communications team work together alongside our scientists to spark innovative uses of our technology and data assets to help answer key scientific questions facing society today.


Examples of BGS data delivery systems created by
our in-house software development team
At the end of the event, a judging panel will award the winning team with staff time to pursue their idea further. All teams will keep a video diary and write a blog so we’ll be able to share the outputs of their activities with you.
Keep an eye on our social media channels for updates throughout the event. And yes, we’ll no doubt be eating pizza!

BGS’s in-house software development team has extensive experience of creating award winning systems to visualise and provide access to geoscientific data and information. Examples include OpenGeoscience, UK Soil Observatory, OneGeology and the iGeology mobile app, which is now approaching nearly 300 000 downloads. We hope the hack will provide a springboard to a new generation of products.



We hope the hackathon will uncover exciting new ways to
visualise and interact with data like this augmented sandbox
If this sounds like fun, we are currently expanding our team and recruiting a number of positions including software developers, geospatial application developers, DevOps specialists and data scientists. These positions will be based across our Nottingham headquarters or Edinburgh office. This is a rare opportunity to join us and help shape our future as we expand and continue to modernise our Informatics skills to support our ambition to be a global leader of 'Informatics in geoscience' and remain relevant and competitive within the current IT landscape. For further details and to apply, please visit topcareer.jobs.

Why is Glastonbury so muddy? ... by Rachel Dearden

Muddy Glastonbury, courtesy of Amanda Borrhamm
The Glastonbury festival is famous for turning into a quagmire seemingly every year. It’s almost an expected highlight of the event!

But why is it so muddy?

The geology underlying the festival site near Pilton comprises the Blue Lias and Charmouth Mudstone Formation. The key is in the name ‘Mudstone’. This Sedimentary Bedrock was formed approximately 183 to 204 million years ago in the Jurassic and Triassic Periods when the local environment was dominated by shallow lime-mud seas.
The bedrock of an area directly influences the type of soil present at the surface and thus at the festival site; the soil is very clay rich (around a third of the soil is clay) and it forms a deep mud when it is churned up.
Glastonbury Festival bedrock and superficial geology map

Soils like those at Glastonbury are densely packed mixtures of fine clay- and silt-sized particles, with only very small amounts of sand and organic matter. David Entwisle, Engineering geologist, says that it’s the plasticity of the soil that really matters; as clay absorbs water, its consistency and behaviour changes. It’s volume increases (it starts to swell) and it becomes a malleable, or in less technical terms - a squidgy mess.
Muddy Glastonbury, courtesy of Amanda Borrhamm

At the Glastonbury festival site, the plasticity is medium to high, so when it rains, the ground will quickly become very wet and malleable, and it won’t drain away because the underlying rocks have low permeability too (so the water cannot soak away through them) and the site lies within a valley (a lovely bowl of mud).  Vehicles, wellies, shoes and feet remould the surface, mixing the water and clay together, reducing the flow of water into the ground even more and increasing the depth of mud.

If you want to find out more about the geology of the UK go to our Geology of Britain viewer  and if you’re particularly interested in soils explore our UK Soil Observatory Map viewer or our mySoil app (we’d love a soil description from a festival go-er).

Thursday, 16 June 2016

Continental Drilling and South Korea…by Melanie Leng

The ICDP Executive Committee on Jeju Island
In early June each year the International Continental scientific Drilling Program (ICDP) committee meets to assess applications for drilling deep holes in the Earth. This year the meeting was held on Jeju Island (off South Korea). Here Melanie Leng explains a bit about ICDP, the UK’s geoscience community involvement and her trip to South Korea...

The UK is a member of the ICDP and this enables consortiums of geoscientists from the UK (in collaboration with other member countries) to apply for funding to deep drill the earth through kilometres of sediments and rocks in order to get cores of pristine material for scientific study (take a look at the ICDP website for more information on current projects).

There are many reasons we want to take long cores through the Earth and, like many applications that were assessed in South Korea, they often involve assessing natural hazards including volcano and impact structures, searching for resources and understanding past climates.

Both workshop and drilling proposals were assessed at the meeting and the outcomes will be published soon on the ICDP website.

A volcano on Jeju Island (L) and steps up to the crater (R)
As well as assessing drilling proposals the ICDP committee visited some outstanding geological sites on Jeju Island. In 2007 the UNESCO World Heritage Committee listed “Jeju Volcanic Island and Lava Tubes” as a World Natural Heritage site in view of the islands outstanding examples of volcanoes and lava tubes. We visited a lava tube system at Manjanggul and the volcanic cinder cone of Seongsan Ilchulbong Peak. Both the lava tube and cinder cone are amazing examples of their types. The cinder cone can be accessed by a series of steps ascending the 200m to the rim, which reveals an almost perfect volcanic cone as a result of an underwater eruption approx. 5000 years ago. The lava tube, formed by a lava flow crystallizing from the outside inwards, now forms a 7 km long cave system (the central lava crystallizes more slowly was emptied from the tube leaving a long tube-like structure. We also had the opportunity to visit Jeju Stone Park, which was inspired by Jeju’s history of spiritual myths and legends associated with the creation of the volcanic island. There are amazing natural and manmade basalt sculptures...

Jeju Stone Park with sculpture from basalt 
Back to ICDP, the UK has key personnel within the program. Prof John Ludden (BGS Director) sits on the Assembly of Governors, I sit on the Executive Committee and Dr Kathryn Goodenough (BGS) is part of the Science Advisory Group.

Please feel free to contact us about ICDP activities. The next deadline for ICDP drilling and workshop proposals is January 2017. You can also keep up to date with ICDP-UK through our website.

For more information please contact Melanie Leng.



Thursday, 2 June 2016

Reconstructing Wildlife Populations in East Africa (Mara Triangle, Kenya) using Faecal Sterol Chemistry...by Christopher Vane

Chris Vane collecing elephant
dung samples

Introduction

Over the last few years the Organic Geochemists at the British Geological Survey (BGS) have been successfully analysing human sourced faecal waste in UK soils and sediments in order to assess the extent of treatment, frequency of raw sewage pollution release and how this corresponds to pollutants and pathogens. One outcome of this work has been to show that sediments often contain distinct faecal chemical 'fingerprints' from other sources namely, domestic and wild animals (Vane et al., 2011)

The Big Idea

Long–term collaborators Chris Vane (BGS) and Andy Kemp (University Tufts) teamed up with Chris Dutton, University of Yale to explore the idea of whether the faecal sterols (a class of organic molecules) found in animal waste and disseminated in sediments could be used to reconstruct past wildlife populations in Africa. Understanding how wildlife populations have changed over long periods (1000 years) through time is an important conservation goal particularly in Kenya and Tanzania where safari tourism is an important source of income for local communities. External funding was sought and won to evaluate faecal matter from a range of key species with the long-term aim to then apply this information to sediment cores from watering holes.

Field Campaign

Our study area was, close to the Kenyan-Tanzanian border, we camped in woodland on the edge of the savannah enabling a daily collection campaign like no other.  Fortunately, we were in good hands with knowledge and logistical support from the Mara Conservancy who gave permission to explore most of the conservancy via land rover and supplied an armed ranger for the collection of fresh samples on foot.  The team tracked and collected fresh faecal samples from a huge variety of animals including, elephant, ostrich, hippopotamus, zebra, lion, giraffe, baboon, wildebeest, buffalo, topi, hyena, leopard, cheetah, warthog, crocodile as well as domestic cattle and sediments from the Mara and Talek rivers. In order to account for dietary and locational/migratory differences we sampled from multiple individuals and herds across the Mara conservancy.

A selection of the huge variety of animals that were tracked and fresh faecal samples collected from.
From L-R: Black back jackal, elephants, lions, giraffes, hyena. 

Faecal Sterol Database

Organic Geochemists at BGS, Drs Chris Vane, Alex Kim assisted by University of Nottingham placement student Katherine Edgley are currently (May-August 2016)  busy preparing, separating and measuring the concentrations of 14 different sterols using Gas-Chromatography-Mass Spectrometry, a technique used to analyse and quantify organic compounds. The aim of this was to build a database from which the wildlife populations of the past can be tracked even in disseminated sediments. Preliminary results look promising with clear differences between major species.
                                                               

References

Vane, C.H., Kim, A.W. McGowan, S., Leng, M.J., Heaton, T.H.E. Coombs, P. Kendrick, C.P., Yang, H., Swann, G.E.A.  2010. Sedimentary record of sewage pollution using faecal marker compounds in contrasting peri-urban shallow lakes. Science of the Total Environment 409, 345-356.

video

For up to date information about this on-going  project or other Organic Geochemical studies at BGS please contact Chris Vane (email chv@bgs.ac.uk). 





Tuesday, 31 May 2016

More on our project investigating human impact on Malaysian wetlands...this time by Masters student Charly Briddon

Charly Briddon on Tasik Chini undertaking a diatom habitat
survey.
Hi, my name is Charly Briddon and I am Keele University student currently undertaking research for my MSc in Geoscience. For my international placement I have joined a collaborative project within the Centre for Environmental Geochemistry (a collaboration between the University of Nottingham and the British Geological Survey) involving supervisors at Keele University (Dr Antonia Law), University of Nottingham (Dr Suzanne McGowan) and the British Geological Survey (Dr Keely Mills). This has given me the opportunity to spend six months at the University of Nottingham Campus in Malaysia investigating how human activities within the lake catchment of a really special wetland system (Tasik Chini) has changed the lake ecology over time…

The diverse plant communities of Tasik Chini provide a range
of different habitats for microscopic diatoms. 
The Tasik Chini research project has been introduced in previous blogs by Prof Melanie Leng and Dr Stefan Engels. My role in the project is to primarily use diatoms to reconstruct past conditions in the lake over the past hundred years or so.  I have been analysing sediment cores collected from the various basins in the lake during the summer of 2015.  Fossil diatoms (types of algae with silica shells) can provide information about water quality, water level change and shifts in lake habitat structure. However, there is not a lot of previous diatom work on these types of shallow tropical wetlands and so I am supplementing this work by investigating where the diatoms are growing today. In April 2016 I collected diatom samples from plants, muds and waters in the lake to determine whether there are habitat affinities that I can use to interpret the core data.

The second part of my project is to try to characterise the organic material in the lake sediments. I started off by conducting loss-on-ignition analysis, which is literally burning the mud to give an estimate of the proportion of organic versus minerogenic material. I am also developing a technique to look at the fluorescence characteristics of the porewaters. We are using a UV visible spectrometer which provides 3-dimensional data on excitation and emission to provide information on where the organic matter in the sediments comes from- for example is it from soil erosion or from algal blooms in the lake.  This technique is quite novel and I am looking forward to using this piece of equipment which is brand new to the university, this part of my project is being supervised by Dr Shafi Tareq from the School of Biosciences in Malaysia.
Charly Briddon, Shafi Tareq and Suzanne McGowan
undertaking porewater flourescence analysis. 

Initial results from the diatom and organic analysis indicate that changes observed in the sediments appear to correspond with changes in human activities in the lake catchment, possibly associated with deforestation in the 1940s and the building of the dam around 1995. We also think that there might be evidence for acidification from atmospheric contamination in recent decades. However, we are waiting for dating of the core to be completed before these results can be interpreted with more certainty. I am looking forward to completing my laboratory work in mid-June when analysis of the results obtained and write up of my dissertation can start in earnest.

Charly Briddon is a Masters student at Keele University undertaking her project within the Centre for Environmental Geochemistry at the University of Nottingham and the British Geological Survey 







Friday, 20 May 2016

Reconstructing the pollution history of southeast Asian wetlands...by Stefan Engels

Stefan with field assistant Charlotte (MRes student
from Keele University) collecting plant samples.
How time flies! It has only been about 4 months since I started my new job as a research fellow with  Melanie Leng and Suzanne McGowan within the Centre for Environmental Geochemistry. The main aim of my research project is to reconstruct the pollution history of southeast Asian wetland systems, and one of the first locations that we selected as a study-site was Tasik Chini on the Malaysian peninsula, here I tell you about progress to date... 

Preliminary laboratory data obtained from short sediment cores that had been previously collected shows the first evidence of recent ecosystem change. To be able to study this in more detail, and to ensure that we have samples that predate the recent period of extensive human impact on the environment, we decided to revisit Tasik Chini this spring with the main goal of collecting longer sediment cores, hopefully dating back several thousands of years. I say ‘hopefully dating back’, as scientific data on this tropical wetland ecosystem is extremely sparse. We basically don’t know when or why it formed, nor did we know how long the sedimentary record goes back in time. Therefore, this project will yield a lot of surprises!

Suzanne showing some of the core sediments we collected from Tasik Chini.
On the 18th April I flew to Kuala Lumpur where I am met with Suzanne McGowan and Ginnie Pannizo (both University of Nottingham). We participated in a local workshop in Kuala Lumper on projects across SE Asia, followed by a great evening lecture by Professor David Taylor (National University of Singapore) on geostatistics, insect-borne diseases and climate change. A truly interdisciplinary topic! We then drove east to the more rural area of Pahang. On the 4-hr long drive I couldn’t help but marvel at the scale of impact that the Malaysian economy has had on the landscape: we basically don’t see anything but oil palm plantations. 

The core sediments have arrived
safely back in the UK!
Taking wetland core sediments in the tropics turns out not to be unlike coring in the subarctic, which is where I’ve done most of my previous fieldwork. One noticeable difference is the coring equipment: whereas the metal extension rods can freeze together in the subarctic, in Malaysia they get so hot that they left some of our field crew with some serious blisters! I was also kept awake by geckos that were “chatting” in my room all night (not something that happens in the subarctic). The trip was very successful though, we managed to collect long sediment cores from a number of locations across the wetland. I am now back in the UK and are subjecting these cores to a range of different laboratory-based analyses, ranging from classic measurements of the amount of carbon to modern molecular approaches where we can find out where the carbon came from (agriculture, mining, sewage). While the results of the project will take some time to become available, the memories of doing fieldwork in an area that is full of monkeys, monitor lizards and geckos will remain with me for quite a while.


Stefan Engels is a Research Fellow within the Centre for Environmental Geochemistry (University of Nottingham and British Geological Survey).  








Monday, 16 May 2016

Are land-use decisions by African elephants influenced by environmental geochemistry?...by Michael Watts, Lisa Yon and Stephen Cunningham

Background

This is a unique, interdisciplinary project involving environmental geochemistry, plant science, and animal health between a range of partners, including BGS and the University of Nottingham (UoN) to address research questions which have important and practical implications for wildlife health and conservation. In the first phase of the project, mineral levels in a range of biological samples (serum, hair, nails) from elephants at five UK zoos will be measured to validate their use as possible biomarkers of mineral status in wild elephants. The mineral content of food, soil and water consumed by these elephants will be determined.

The second phase of this project will apply these validated methods to a study of wild African elephants. The multi–element capability of ICP–MS for measuring environmental/biomonitoring samples enables an estimation of mineral balance and potential metal uptake. The working hypothesis is that the elephants in this study group are deficient in phosphorus, owing to a deficiency in the (soil and) forage in a South African National Park. This drives the elephants to supplement their phosphorus from the water, soil and forage on land surrounding a phosphate mine in close proximity to the National Park. Elephant incursion into nearby human settlements has resulted in human–elephant conflict, causing risk of injury and lost income. This project may identify key locations in the elephants’ home range where mineral–supplemented forage, or mineral licks, may be placed to reduce the drive to seek additional sources of phosphorus; this could reduce human–elephant conflict. This project provides opportunities for varied work: fieldwork in UK Zoos and South Africa for environmental/biomonitoring analyses of wild elephants, specialist laboratory and data interpretation training at BGS and UoN and translation into advice to relevant stakeholders.


Funding

This work will be focussed on a PhD project from the NERC Envision Doctoral Training Programme, with additional support from the Hermes Trust and Royal Society International Exchange scheme. The project is based on a Centre for Environmental Geochemistry collaboration between the Inorganic Geochemistry (Dr Michael Watts) and Stable Isotopes teams (Professor Melanie Leng) at BGS and Schools of Veterinary (Dr Lisa Yon) and Biosciences (Professor Martin Broadley) at the University of Nottingham. The collaboration is further strengthened by partners in five UK zoos and with partners in South Africa who have been studying elephant populations there for the past two decades, tracking elephant movements using GPS and GMS to better understand their habitat use.

Sample collection 

Recently, in April, the first sample collection was undertaken at Knowsley Safari Park, whose keepers were extremely interested in the possibilities of the project.  The keepers enthusiastically shared their immense knowledge on the measures they undertake to ensure the welfare of their elephants, the individual elephant dietary intakes and idiosyncrasies of each elephant.  We initially started with an evaluation of food and water intake through sample collections; these samples will be measured for ‘essential’ mineral content (e.g. zinc, iron) to determine dietary intakes and possible seasonal changes in forage and hay over the next 12 months.  These data will be related to mineral measurements in the elephants’ toenails, plasma, tail hair and faeces to validate methodologies for use and comparison with wild elephants.

Images from L-R: Elephant toe nail trimmings; tail hair clipping; Knowsley elephant team (Front row L-R (green shirts):
 Stephen Cunningham, Alex Spooner, Andy Doyle, Libby Ward. Back row L-R: Aurelie Devez, Michael Watts,
Daniel Middleton, Lisa Yon)
We would like to thank Stephen Cunningham and his team at Knowsley Safari Park for their enthusiasm and collaboration, particularly as part of the launch of the project and helping us to improve our planned methodology for sample collection and interpretation of data as the project proceeds.

For further information:
mwatts@bgs.ac.uk and lisa.yon@nottingham.ac.uk

More information will follow at:
http://www.environmentalgeochemistry.org/research/BiochemicalCycling.html 
https://www.knowsleysafariexperience.co.uk/ 
@KnowsleySafari, facebook.com/knowsleysafari 

Thursday, 12 May 2016

Bugs in soil prefer a good spread of food...by Barry Rawlins


Barry and the synchrotron
On my way to work I cycle past a field of grazing cows which is next to a milking parlour. A while ago I stopped to ask the friendly farmer, "Can I have a bit of the soil from your field?”

"Yes”, he replied, “but what do you want it for?"

I almost sighed. I knew if I had to explain thoroughly why I wanted it, my answer would be long and complicated. "Well, I want to do an experiment where I take lumps of your soil to a lead-lined room in Oxfordshire and shine light onto it that is 10 billion times brighter than the sun."

He looked over at his colleague with a confused expression, as if to say, we've got a right one here. But he did let me take some of his soil.

So, why did I need these lumps of soil? I want to understand what might help or prevent bugs (bacteria) in the soil eating their source of food – carbon. When bugs eat the carbon it is released to the air as carbon dioxide, the main greenhouse gas. If we understand this process better, we might be able to store more carbon in the soil and slow down climate change.

 A slice through a soil aggregate showing the
position of organic matter, minerals and pores.
Bugs in soil live in the pore spaces – the air- and water-filled gaps between the solid bits. The food which bugs want to eat – the carbon – is unevenly spread throughout each lump, which we soil scientists call ‘aggregates’. Sometimes carbon occurs as big clumps in only a few places in an aggregate, whilst in other aggregates the carbon occurs more frequently as lots of small pieces. The question I wanted to answer in my experiment was: in which of these two cases do the bugs eat more carbon?

A novel way to answer this was to do three things: first, measure how well the bugs fed on carbon in many soil aggregates in the laboratory; second, stain the carbon in these aggregates using a chemical, and finally put the stained aggregates of soil into a bright light source called a synchrotron. The synchrotron shows us in three dimensions the location of the stained carbon inside the aggregates. It also shows us the location of the pore spaces.

(When I was explaining this to the friendly farmer to make it sound exciting I said, "No one has done this before!" He still didn't look convinced.)

After the experiment I compared the amount of carbon the bugs had eaten with how it was spread out inside each aggregate. I found that the bugs had eaten more of the carbon when it was distributed more frequently, more pieces throughout the aggregate. I need to analyse more aggregates to have greater confidence in this finding, so I will have to visit some more friendly farmers and hope I can convince them to give me some lumps of their soil. I am expecting to see more confused expressions.

The research I describe above was a collaboration of several BGS scientists and other colleagues at the Diamond Light Source campus in Harwell. We wrote this paper and there is a movie on the BGS YouTube channel that shows me talking about the experiment at the synchrotron.