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Citizen science blog

13 Posts tagged with the uk_biodiversity tag
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This week we hear back from Kath Castillo, our Orchid Observers Project Officer, about what orchids you can search for in the field this month.

 

August is nearly here and with it the start of the holiday season, so if you are planning a walking holiday or a bit of wildlife photography in the UK, there are some stunning species on our list to look out for and photograph for Orchid Observers.

 

Flowering now and into late August, the Marsh Helleborine (Epipactis palustris) is a fairly large orchid with loose clusters of pink and white flowers with a white frilly lower petal. The species, which grows in wetland areas such as fens and damp dune slacks, can flower on a grand scale, with tens of thousands of plants creating a carpet of flowers. Although it may occur in profusion in some areas, the Marsh Helleborine is declining in England and Wales due to habitat loss.

 

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A flower of the Marsh Helleborine. Photo credit: Fred Rumsey.

 

 

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Marsh Helleborine photographed flowering in large numbers last summer at Berrow Dunes, north Somerset. Photo credit: Fred Rumsey.

 

If you are up in northern England and in north-east parts of Scotland and likely to be visiting and walking in woodland, particularly pine woods, then look out under the pine trees on the forest floor for small spikes of creamy white flowers which are very hairy! Take a look at the leaves; if the veins are distinctively net-shaped (rather than parallel as in most UK orchids) then you may well have found Creeping lady’s-tresses (Goodyera repens).

 

Please take a photograph and record the location and date and upload your data to the Orchid Observers website.

 

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Creeping lady’s-tresses at Eden Valley, Cumbria. Photo credit: Mike Waller.

 

A similar looking species, but in another genus altogether, is Autumn lady’s-tresses (Spiranthes spiralis) which is found in southern England, most commonly by the coast This small orchid has tiny white flowers arranged in a single spiral around the stem resembling braided hair, hence the common name. An interesting fact is the leaves develop in autumn and photosynthesise throughout the winter but wither before flowering – this is an adaptation to hot dry climates. Germination to flowering takes 14 years. This is a Mediterranean species that only grows on calcareous grassland with very short turf. Look out for it in late August and into September on chalk downs, fixed dunes, cliff tops and even lawns and old grass tennis courts!

 

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Autumn lady’s-tresses at Eggardon Hill in Dorset. Photo credit: Chris Raper.

 

The Orchid Observers team would once again like to thank all our participants who have been out photographing orchids and collecting records from all over the country; nearly 1600 records have been submitted so far!

 

Kath Castillo

 

Kath is a biologist and botanist working as the Orchid Observers project officer and along with the Zooniverse web team developed the Orchid Observers website. She now tries to get out into the field whenever she can to find and photograph wild orchids!

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This week Dr. Della Hopkins tells us about how the Decoding Nature project takes school students out on field trips and involves them in the Museum's science research.

 

In June, a group of ‘scientists in the making’ from Pimlico Academy joined up with a small band of research scientists from the Museum as part of a long running project called Decoding Nature. Decoding Nature is a Museum-run venture which delivers residential science courses to school children aged 8-18.

 

The courses take place at The Old Malthouse School near Wareham in Dorset, and combine learning with original, ongoing scientific research. Over the years the project has evolved and included a wide range of scientists with varied areas of expertise. Each course is different, ensuring that the children are taking part in cutting edge research that will be used for publication.

 

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Amazing lichen communities on Dorset trees - a winning photo from the photography competition. Image credit: Coco from Pimlico.

 

For this particular course our budding scientists from Pimlico Academy were set several tasks, to aid renowned Lichenologist Holger Thues with several important research questions. The week began with an introduction to lichens and a recap on classification and how to use keys, before launching into investigations into the species composition of spice lichens; bags of mixed lichen species sold as cooking ingredients in many Asian supermarkets.

 

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Recording the lichens on coastal trees. Image Credit: Annabel Crookshank, The Old Malthouse.

 

Next we took to the fields to carry out an air quality survey (designed by the OPAL project), using nine target lichen species growing on tree branches to give an indication of pollution levels. Three of these lichens are very sensitive to pollution, three are ‘intermediate’ and the final three are nitrogen-tolerant. The children’s findings were of great interest, showing that the presence of sheep dramatically altered the lichen community, with the nitrogen sensitive species nowhere to be found. Less than a mile away, by the coast, these species were flourishing.

 

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Comparing the lichen species on trees in grazed fields. Image credit: Annabel Crookshank, The Old Malthouse.

 

Once they had honed their lichen-identification skills we headed out to Dancing Ledge, a beautiful area on the coast where the cliffs meet the sea. The students carried out a series of transects to answer questions about the habitat preferences of the coastal lichens, such as whether the rocks were sea- or land-facing, vertical or horizontal, and how close to the sea they were. We made some surprising discoveries, and were able to make some collections to take back to the Natural History Museum.

 

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Making a (permitted!) lichen collection at Dancing Ledge.

 

Finally we used DNA barcoding techniques on a number of European and British samples of the lichen Verrucaria pachyderma. This involved working in the laboratory to extract DNA, and amplify it to a level which could be taken to the museum for the sequences to be read. This was very important work, and great care was needed with the samples. Everyone managed the task superbly, and we were successful in extracting the DNA.

 

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Ready and prepared for DNA extraction.

 

Once we left Dorset, and returned to the museum, the DNA samples were sequenced. Genetic analysis of the lichens collected from Europe show that the British collections may in fact represent an entirely separate species. The next step is to expand the collection range and analyse more genetic markers, but the results so far are already a big surprise and wonderfully exciting.

 

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Holger Thues explaining the different habitat preferences of the lichens. Image credit: Annabel Crookshank, The Old Malthouse.

 

The week was full of games to encourage learning, especially with the more tricky subjects such as DNA barcoding. The children entered each challenge with enthusiasm, whether they were in the lab extracting DNA, or buzzing around the field as worker bees collecting their sand pollen. We also found time to learn about other techniques used by scientists in botany (plants) and entomology (invertebrates).

 

To find out more, visit our Decoding Nature webpage.

You can also find out how to participate in OPAL surveys here.

 

Della Hopkins

 

Dr Della Hopkins has worked at the NHM for 6 years, and has managed the Decoding Nature project for the past 5. She previously worked on seed conservation with the Millennium Seed Bank at Kew. She studied Environmental Biology at Royal Holloway University of London, followed by an MSc in Ecology (Bangor) and her PhD from London investigated heathland conservation and restoration.

 

Della runs the Decoding Nature project with Dr Robert Dyer (molecular laboratory assistant).

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For July, the Orchid Observers team are simultaneously excited and fretting. We're excited because we're planning field trips to see the next orchids on our hit list, but we're also concerned about the flower spikes scorching in the sun and wilting. It might be a race against the sun this month to catch July's finest orchids. Not only that but this month's highlight species are some of the trickiest to spot and identify. Please don't let this deter you, take up the challenge and see if you can locate and photograph these beauties.

 

Bog orchid (Hammarbya paludosa)

 

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The bog orchid (Hammarbya paludosa) is the tiniest of the UK orchid species. © Mike Waller.

 

Being the tiniest of the UK orchids, the bog orchid can be rather inconspicuous. It's just 4-8cm tall and green and there are only 25 flowers on the flower spike, which are said to smell sweet and cucumber-like.

 

As its name implies this species lives on bogs, growing among clumps of sphagnum moss. It needs to live in areas that don't dry out, even in a hot summer. When the summer is hot it flowers earlier than when the summer is cool and wet.

 

Being a bog plant it's our Scottish contributors that are going to have most opportunity to find this one. But there are a few colonies dotted around England, in Cumbria, northwest Yorkshire, Northumberland, one-site in Norfolk, Cornwall, Devon, Dorset, Hampshire and some in the west of Wales.

 

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The bog orchid (Hammarbya paludosa) has very distinct flowers, that small sweet and cucumber-like. © Mike Waller.

 

Frog Orchid (Coeloglossum viride)

 

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Keep an eye out for the frog orchid (Coeloglossum viride) which is found across the UK. © Fred Rumsey.

 

The frog orchid can be found across the UK, but only in small localised patches. It is more easily found in the north and west of the UK, having declined in the south due to changes in land management.

 

It is quite a hard plant to spot as it is only 5-15cm tall and mostly green in colour. But you can find it on short chalk or limestone grasslands in the south, and in all sorts of places in the north, from railway embankments and road verges, to grasslands and dune slacks.

 

The flowers of the frog orchid have a very enclosed green hood and a long red lower lip, which is lobed at the end. It's classified as vulnerable, so please take extra care when you find this orchid.

 

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The frog orchid (Coeloglossum viride) can be found on chalk and limestone grasslands in the south of England. © Fred Rumsey.

 

Now for a last chance to see:

 

Lesser butterfly-orchid (Platanthera bifolia) and Greater butterfly-orchid (Platanthera chlorantha).

 

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Its a last chance to see the greater butterfly-orchid (Platanthera chlorantha). © Mike Waller.

 

Distributed across the UK the lesser butterfly-orchid and greater butterfly-orchid are really quite difficult to tell apart. But here are some top features to help you distinguish between the two.

 

Compared to the greater butterfly-orchid, the lesser butterfly-orchid is shorter, it carries less flowers and it usually flowers a little bit later. It can be found on damp heathlands and moorlands, or in deciduous woodland, whilst the greater butterfly-orchid is found on deciduous woodland and chalk grassland.

 

But the most reliable way of telling the two apart is in the positioning of the pollinia (the pollen bearing structures of the flower). In the lesser butterfly-orchid the pollinia are closer together and parallel to each other, while in the greater butterfly-orchid the pollinia are further apart and slant inwards at the top.

 

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The lesser butterfly-orchid (Platanthera bifolia) can be identified by its parrallel pollinia. © Mike Waller.

 

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The greater butterfly-orchid (Platanthera chlorantha) has pollinia that are further apart and slant inwards.

 

Of the two, the lesser butterfly-orchid is classified as vulnerable, due to large declines, particularly in south-eastern regions, so again please be extra vigilant when locating this species.

 

If you manage to find any of the 29 species of orchid we are conducting our research about, then don't forget to take a photo and upload it to the Orchid Observers project here. And if it just gets too hot to go outside then get online and help us transcribe data from our orchid herbarium sheets.

 

Find out more about our Orchid Observers project and how you can get involved.

 

Jade Lauren

 

Jade Lauren Cawthray is Citizen Science Project Officer in the Angela Marmont Centre for UK Biodiversity, where she develops and runs citizen science research projects. Having studied an undergraduate degree in Ecology and Conservation and then a master's degree in Science Communication, Jade is combining her two passions, nature and public engagement, by pursuing a career in citizen science.

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Citizen Science Project Manager Lucy Robinson introduces a Q&A with Dr. Anne Jungblut.

 

In an earlier blog post, a group of students from Bedford Girls’ School described their recent visit to the Museum. The girls had taken part in The Microverse, collecting samples of microorganisms from buildings and sending them to the Museum for DNA analysis, and were keen to meet the scientists involved to find out more. We arranged for them to meet the lead researcher on the project, Dr. Anne Jungblut, to ask her some questions about the project and her wider research. We thought you might like to hear her responses:

 

Q. What inspired you to set up this project?

 

A. Of all the life on Earth, only a relatively small proportion are the plants, animals and fungi that we can see – the vast majority are microscopic. My research takes me all over the world, where I collect samples of microorganisms and study them using DNA technologies to better understand these important organisms. I’ve done a lot of work in the Antarctic, but I thought to myself that it would be really cool to also look at the microorganisms in the UK, in particular on buildings. There’s been very little research into the microorganisms that live on buildings in towns and cities to see what role they are playing in urban ecosystems. So I contacted Lucy and Jade in the Museum’s citizen science team as this research would require lots of samples to be collected across the country and I thought citizen science – collaborating with members of the public – could be a good option. Together we developed The Microverse project.

 

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Q. What are you looking for in the data – what kind of patterns?

 

A. Firstly, I’m looking for the overall diversity of microorganisms. They are such an understudied group that these data will give us a baseline understanding of microorganism diversity on buildings. I’m also looking for differences between building materials – we asked participants to sample three different building materials so we will have a lot of different materials to compare.

 

We also asked you to record a number of different variables that might affect diversity for example the distance to the nearest road and the nearest vegetation. These variables show us possible pollution levels, or semi-natural habitats that microorganism may have colonised the wall from. I’m interested to see what influence the proximity to roads and vegetation/soil has on the microbial diversity.

 

I’m also keen to see whether unique locations have different communities of microorganisms. Some sample sites are quite unusual e.g. on land contaminated by heavy metals, and on a pier over the sea. Will these buildings have very different communities of microorganisms to the other samples?

 

This research will also allow us to formulate more detailed hypotheses and refine our research questions. We are also inviting participants to suggest new hypotheses and future directions for the research. Ideas can be emailed to microverse@nhm.ac.uk.

 

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Arachnula impatiens, a microorganism found on walls, is a predatory protozoan

 

Q. How will the Museum judge how accurate the data are?

 

A. The schools and community groups taking part in The Microverse are carrying out exactly the same method to collect samples as a professional Research Assistant would have done. This means that samples need to be collected under sterile conditions, following a strict protocol.

When we were developing the project, we chose A-level students (or equivalent) as the main audience as they’re committed to science, and we felt they would be more likely to carry out the survey correctly and understand the importance of sterile working compared to other potential audiences we considered e.g. primary school students. Collecting samples in the right way is the first step to ensuring data accuracy.

 

Once we receive the samples, there are a number of ways we can check the accuracy of the data. After the PCR step, gel electrophoresis checks whether enough genetic material is present in the sample. The sequencing process also removes low quality sequences (ones that are too short in length) which will not give reliable results. The great thing about using DNA technologies for identification is that it’s very accurate and doesn’t rely upon human ability to make a correct identification.

 

Participants record details about their building surface, but we also ask them to send us photographs, so we can double check if we are unsure about the accuracy of a piece of information, or if it’s an unusual building surface that we need to be able to see to properly interpret the results.

Finally, when we sequence the data, the output shows us how many mitochondria sequences were generated which indicates how much animal DNA there was in the sample. If a sample had been contaminated e.g. by someone’s hands touching the swab, it would show up as a very high number of mitochondria and we would be able to exclude that sample from our analyses. Luckily this hasn’t yet happened.

 

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Students from Trinity Catholic School collecting samples for The Microverse project

 

Q. Have you seen any microbes in The Microverse samples that you haven’t seen before?

 

A. Not yet. Samples are still coming in and are being sequenced so we only have very early results from a few sample sites. I will know more when all the samples have been sequenced and analysed. The sequencing we are doing is not always able to identify a microorganism to species level, it may be identified to a Genus or Family. Where they are identified to species level, it takes time to work through the data and explore further any sequences that look particularly interesting. We are keeping The Microverse samples frozen in our Molecular Collections Facility so that we, and other researchers, can go back to them in years to come to conduct further research.

 

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Kevin Hopkins, in our film The Microverse in the Lab, placing specimens in the Molecular Collections Facility

 

Q. What are the long-term impacts of your research?

 

A. I work in the polar regions where environmental change is happening at a very fast pace. The deep ice sheets in this area also hold a record of microbial life going back hundreds of years. Understanding the impacts of climate change on all life, not just microorganisms, is an extremely important area of research at the moment. Polar regions are very delicate habitats that have been changed by the introduction of non-native species e.g. reindeer in South Georgia which have had a massive impact on soil quality there. Understanding the microbial life within healthy soils can help us to restore these damaged habitats.

 

In the UK, microorganisms are largely beneficial, through cycling nutrients such as oxygen, carbon dioxide, nitrogen and sulphur. But they may also be affecting the colour, moisture levels and other characteristics of buildings – understanding these potentially negative impacts may help the conservation of historic buildings and monuments.

 

In a much longer-term view, it is likely that new active chemicals and medicinal drugs will be derived from microorganisms, so research into microbial diversity facilitates this.

 

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Dr. Anne Jungblut collecting samples in Antarctica

 

Q. You described The Microverse as ‘citizen science’ – what do you mean by that?

 

A. Citizen science is the involvement of volunteers in scientific projects that contribute to expanding our knowledge of the natural world, through the systematic collection, analysis or interpretation of environmental observations. Many of the big research questions of our time require large datasets to be collected over large geographic areas. It just isn’t possible for professional scientists to travel the country gathering samples or observations, so we collaborate with members of the public who volunteer their time, effort and expertise.

 

The Museum has a range of different citizen science projects where you can help our researchers to better understand the natural world. We have a project photographing orchids for climate change research, one recording seaweed distributions around the UK coast to monitor the spread of invasive species, and online projects where you can copy information from handwritten labels on museum specimens to make these data available to our researchers and curators. If you want to see how you can get involved, have a look at the Take Part section of the Museum’s website.

 

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Professional and Citizen Scientists collecting data at Looe Bioblitz, 2013

 

Lucy Robinson

 

Lucy Robinson is Citizen Science Programme Manager in the Angela Marmont Centre for UK Biodiversity. She has been working at the Museum in the field of citizen science for 7 years, initially on the Big Lottery Funded OPAL project and has worked on projects studying earthworms, lichens, seaweeds, urban invertebrates, microorganisms and many other areas of biodiversity.  Lucy has a BSc in Zoology from the University of Bristol and a MSc in Biodiversity and Conservation from the University of Leeds.

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This week we get an update on the Orchid Observers project, from Project Officer Kath Castillo.

 

It’s been a busy time for Orchid Observers! The project got off to a great start when the website went live on the Zooniverse platform on 23 April; the very first of the season’s field records was uploaded on day one!

 

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The Orchid Observers team, from left to right: Jade Lauren Cawthray, Jim O’Donnell (Zooniverse web developer) Lucy Robinson, Mark Spencer, John Tweddle, Kath Castillo, Chris Raper and Fred Rumsey

 

At the time of writing this blog we now have 567 registered users on the website who have enthusiastically completed 11,044 classifications, by verifying and transcribing data for our historical specimens and identifying species and flowering stages for around 700 photographic records already submitted by participants. The field records collected span the country, from Cornwall to Perth in Scotland, and from Pembrokeshire across to Norfolk. So far, for early-purple orchid (Orchis mascula) and green-winged orchid (Anacamptis morio) approximately 9% of the records are from new/unknown sites (as measured by 2 km square/tetrad); this is valuable information, particularly for green-winged orchid which is considered at risk of extinction in the UK.

 

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A herbarium sheet of green-winged orchid (Anacamptis morio); one of around 10,000 historical specimens available online for data verification or transcription

 

Whilst we have not been able to fully compare the Orchid Observers phenology data with our museum records (as yet, the relevant, verified, 2015 UK weather data has not been released) we have already been able to see that the median date of this year’s flowering of two species (early-purple and green-winged) is at least 10 days earlier than the museum data (which mainly covers 1830 to 1970). These are early figures only, and the full data set will be analysed later this year.

 

We are immensely grateful for the time and good will of all our participants - without this effort we would not have been able to collect this data. And we’ve still got the rest of the summer to collect more data for all our 29 species in the survey!

 

The Orchid Observers team had a very busy in May, showcasing the project to the public at the Lyme Regis Fossil Festival, in Dorset and on Fascination of Plants Day and at Big Nature Day at the Natural History Museum.

 

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Orchid Observers at Big Nature Day

 

Some of us in the team have also managed to get out to various sites to record and photograph orchids ourselves. Here’s a snapshot of our recent activities:

 

Visit to Stonebarrow Hill, Dorset, 1 May

 

After a busy day on the stand at the Lyme Regis Fossil Festival, Kath, Mike and Chris drove up to the National Trust’s reserve at Stonebarrow Hill to look for orchids and found two beautiful ancient hay meadows of flowering green-winged orchids (Anacamptis morio), including the occasional white variety in a sea of purples.

 

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Kath photographing green-winged orchids (Anacamptis morio) at Stonebarrow Hill, near Lyme

 

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Green-winged orchids (Anacamptis morio) at Stonebarrow Hill

 

BBC News report at Darland Banks, Kent, 19 May

 

Next up, Mark and Kath travelled down to Darland Banks, in Kent, to film a piece for BBC South East News, with reporter Charlie Rose. The south-facing chalk grassland slopes were abundant with the man orchid (Orchis anthropophora). You can see the film piece here.

 

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Orchid Observers in the News: The man orchid (Orchis anthropophora) at Darland Banks

 

Visit to Box Hill in Surrey, 29 May

 

At the end of May, and despite a weather warning to expect heavy rain later in the day, a group of us left Victoria station in the morning sun and headed down to Box Hill to search for and photograph orchids. Box Hill forms part of the North Downs and is a well-known site to spot many of our wild orchids – there are around 17 species here. We were able to find and photograph 5 of our 29 target species: common spotted-orchid (Dactylorhiza fuchsii), common twayblade (Neottia ovata), bird’s-nest orchid (Neottia nidus-avis), white helleborine (Cephalanthera damasonium) and fly orchid (Ophrys insectifera), by the time the skies darkened. Some species, such as the bird's-nest and fly, are hard to find at the best of times, and were particularly difficult to photograph in a thunderstorm!

 

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Lucy, Jade and Mike collecting photographic records for common spotted-orchid (Dactylorhiza fuchsii)

 

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The beautiful bird's-nest orchid, (Neottia nidus-avis) in woodland

 

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Drenched but happy: orchid observers Jade, Sally and Lucy at Box Hill

 

We’ve also been busy filming a piece which has just launched on the Museum’s citizen science Orchid Observers webpage. Kath organised with the Museum’s Broadcast Unit team to film a short piece to explain the research behind the project. So, mid-May saw Kath, together with Emma Davis and Hannah Wise, setting off early one morning with two carloads of film equipment, a group of Museum volunteers and Mark Spencer. The team went to Oxfordshire, to a couple of the Berkshire, Buckinghamshire and Oxfordshire Wildlife Trust’s finest nature reserves. We are very grateful to BBOWT’s Giles Alder and Laura Parker for hosting us.

 

Find out about why the Orchid Observers research is so important by watching our film here.

 

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Filming for Orchid Observers in Oxfordshire

 

Kath Castillo

 

Kath is a biologist and botanist working as the Orchid Observers project officer and along with the Zooniverse web team developed the Orchid Observers website. She now tries to get out into the field whenever she can to find and photograph wild orchids!

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This week we hear from Freya Bolton and Emily Stearn, students at Bedford Girls' School, about their experience of visiting the Museum to meet with the Angela Marmont Centre for UK Biodiversity team and Dr Anne Jungblut who leads the Microverse project.

 

On 30 April, we (eleven International Baccalaureate students from Bedford Girls' School) had the opportunity to come and visit the Natural History Museum, having participated in the Museum's exciting project 'The Microverse'. For many of us, despite the fact we'd visited many times previously, we knew this time it was going to be something slightly different, being able to explore the Museum in a new, unique and fascinating light. Having spoken to Jade Cawthray, she kindly agreed to arrange a behind the scenes tour especially for us!

 

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So much to identify so little time. Florin Feneru with a draw of specimens for identification.

Photo credit: Aarti Bhogaita

 

We were greeted by Lucy Robinson, who explained to us, as we travelled through the Museum, that within there were over 80 million different plant, animal, fossil and mineral specimens. After this, we were introduced to Dr Florin Feneru at the Angela Marmont Centre for UK Biodiversity, who confessed that he would receive specimens sent in from thousands of people each year, from the UK and abroad, in the hope that he could identify what exactly they were.

 

He explained that the most common specimen query was the "meteorite" (or as he would like to call them "meteo-wrongs") from members of the public who wanted validation for the rocks they believed to have mysteriously entered from outer space. Dr Feneru did however then excitedly show us, an ACTUAL meteorite received earlier this year, letting us hold it. It was extremely heavy for its size - not surprisingly as it was composed of mainly iron.

 

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An actual meterorite, and not a "meteo-wrong!"

Photo credit: Aarti Bhogaita

 

He then led us into the Cocoon: an eight storey building with 3 metre thick walls, containing just over 22 million specimens. The building was kept at a particular humidity and temperature in order to keep the specimens in good condition. The storey we entered was maintained at 14°C - 16°C and kept at 45 percent relative humidity. We were shown by Dr Feneru a range of butterfly species on the ground floor, and he explained that, before the Cocoon was built, the curators had to use mothballs to prevent infestations with pest insects.

 

After we'd visited the Cocoon, we were shown to a workshop area, where we met Dr Anne Jungblut, one of the founders of the project we have been participating in. She gave us a brief talk about her other current projects, including an expedition to Antarctica, and we had the opportunity to ask her about The Microverse and what inspired her to create this project. We were informed that one hundred and fifty four schools had taken part, and that Dr Jungblut was looking for a difference in diversity of microscopic life in different urban environments.

 

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A group photo with Dr Anne Jungblut.

Photo credit: Aarti Bhogaita

 

Following this talk, we had two hours remaining to ourselves, before it was time to depart back to sunny Bedford. Instinctively, we headed first to the cafes and shops before exploring the more scientific parts of the Museum. Full stomachs and emptier purses in hand we chose to explore the Marine Biology and Dinosaur galleries (naturally). One of the pupils explained that she hadn't been to the Dinosaur exhibition since she was 5 years old, as a consequence of being absolutely terrified of the animatronic Tyrannosaurus rex (she had many nightmares apparently). She confirmed that he definitely was not as scary as she thought he was at the time - that being said, she is now 17.

 

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Sophie the Stegosaurus, looking very friendly.

Photo credit: Aarti Bhogaita

 

Returning back to Bedford with new knowledge of both 'The Microverse' project, marine biology, and dinosaurs, as a whole group we would like to thank the Museum staff members and the teachers at Bedford Girls' School who made this amazing experience possible.

 

Freya Bolton and Emily Stearn

 

Thank you to Freya and Emily for writing their blog post and to Bedford Girls' School for coming to visit. It was an absolute pleasure to have them with us!

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This week Sally Hyslop, one of the trainees on our Identification Trainers for the Future programme, gives an update on the results of our 9-year-long Bluebell Survey:

 

The arrival of bluebells each spring is an iconic sight. The floods of nodding colour characterise our ancient woodlands, support a commotion of insect life and make up an important part of Britain's natural heritage. Our native bluebell species is widespread in Britain; in fact half of the world's population is found here. But the introduction of non-native bluebells, planted in our parks and gardens, may be threatening our native species.

 

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Bluebells are iconic to our woodlands. Copyright: Mike Waller.

 

The introduced Spanish bluebell is deceptively similar to our native species, except for a few subtle differences in its features. It is broader in size, its petals flare out a little more, and the pollen is not white, but characteristically blue.

 

Spanish bluebells can breed freely with our native species, creating a hybrid plant with features from both species. Since the Bluebell Survey started in 2006, citizen scientists have been carefully identifying bluebells across Britain and recording the whereabouts of native, non-native and hybrid forms. This helps us to investigate these changes.

 

Exploring change in Britain's bluebells is no easy task, but by submitting their records, citizen scientists have created a nationwide picture of our bluebells. Using this data, scientists at the Museum have gained a greater understanding of the threats to our native species.

 

For example, we now know that, although large populations of native bluebells exist in the countryside, in urban areas hybrid bluebells are increasingly common. Each hybrid bluebell has a mixed genetic make-up, inheriting a blend of features from both its native and non-native parent. The mixed hybrids may cope better with changing environments and could out-compete our native species.

 

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A native bluebell with characteristic bell shape and nodding tip. Copyright: Mike Waller.

 

To better understand the threat of hybrid bluebells, we have been asking citizen scientists to record flowering times for the bluebells they identify. Using this data, scientists will uncover how native, non-native species and their hybrids are responding to climate change.

 

Due to natural fluctuations in climate, scientists need many years of data to accurately interpret the effect of climate change on flowering time. This is why records from the public continue to be so important! If you have been or want to take part, by collecting this information over several years and for the same plants, you can provide scientists with consistent data to study our bluebells.

 

The effect of climate change on Britain's biodiversity is likely to be vast, but by collecting data we can start to work with the unpredictable, anticipate the future and direct change. If you'd like to help discover more about Britain's bluebells take part in 2015's Bluebell Survey.

 

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Illustration Copyright: Sally Hyslop.

 

Thanks Sally! As part of her work as an Identification Trainee at the Museum, Sally has been collating and managing the records that you have been sending in for this year's Bluebell Survey.

 

And, for another take on the Bluebell Survey, see the latest from the Wildlife Garden blog.

 

Jade Lauren

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Advances in DNA sequencing technology are occurring at an incredible speed and Kevin Hopkins is one of the Museum's Next Generation Sequencing Specialists working with the sequencing technologies used at the Museum to produce relevant data for our Microverse research.

 

"The challenge is being able to bring together the technology, often developed in biomedical settings, and the samples at the Museum, where limited and often damaged DNA from specimens is the only chance we have of sequencing them. My job involves designing methods that work for our unusual samples, extracting DNA and producing sequencing ready samples from it, and running our MiSeq and NextSeq next generation sequencing platforms."

 

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Kevin Hopkins is a Next Generation Sequencing Specialist at the Museum.

 

What is DNA sequencing?

DNA sequencing is the process of reading the order of nucleotide bases (adenine, guanine, cytosine and thymine) in a particular strand of DNA. Sequencing can be used for many different applications, such as defining a specific gene or a whole genome. The best way to sequence DNA is in sections; this is because there are a number of challenges to sampling the whole genome of a species in one go.

 

There is so much data within a genome that it takes an incredibly long time for any sequencing machine to process the information. In the Microverse project we are analysing short strands of DNA. At least 60 samples are loaded into the sequencer at a time and the analysis takes a total of 65 hours. If we were to analyse the whole genome rather than smaller parts, it would take a considerably greater amount of time, but luckily we don't need to do it for The Microverse project.

 

Another challenge for sequencing can be old DNA that has been degraded into very short sections, in this situation it is difficult to gain enough DNA from all the microorganism in the samples, to study the community composition. To avoid this in The Microverse project, we asked the schools to return the biofilm samples in a DNA preservative to minimise the degradation of the DNA.

Lab work

When Kevin receives the samples from Anne, the lead researcher on the project, he performs two quality control checks before loading them into the DNA sequencer: these are the concentration of the samples and the average DNA strand length. It is important to know both of these factors as they allow us to estimate the number of DNA fragments that are in each sample.

 

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We are using the Illumina MiSeq machine to sequence The Microverse samples.

 

The equipment that Kevin uses to sequence DNA is an Illumina MiSeq which can sequence up to 75,000 samples per year. Having equipment like this allows scientists at the Museum to carry out research such as looking at plant DNA to reveal the history of their evolution in relation to climate change, and using molecular work to benefit human health by understanding tropical diseases such as leishmaniasis, as well as exploring microbial diversity in soil, lakes and oceans.

 

During DNA sequencing the DNA double helix comprising two strands of DNA is split to give single stranded DNA. This DNA is then placed into a sequencing machine alongside chemicals that cause the free nucleotides to bind to the single stranded DNA. Within this sequencing cycle when a nucleotide, which is fluorescently charged, successfully binds to its complementary nucleotide in the DNA strand (A with T and vice versa, G with C and vice versa), a fluorescent signal is emitted. The intensity and length of this fluorescent signal determines which nucleotide base is present, and is recorded by the sequencing machine. The sequencer can read millions of strands at the same time.

 

Why is this important?

 

DNA sequencing is vitally important because it allows scientists to distinguish one species from another and determine how different organisms are related to each other. In the Microverse project we are using the sequencer to identify the taxonomic groups of the microorganisms in the samples that you have sent to the Museum.

 

Katy Potts

 

Katy Potts is one of the trainees on the Identification Trainers for the Future programme, who is based at the Angela Marmont Centre for UK Biodiversity. Alongside her work on the Microverse project she is developing her skills in insect identification, particularly Coleoptera (beetles).

 

If you are taking part in the Microverse project the deadline for sending us your samples is Fri 29 May.

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We take a diversion this week from the Microverse and our newest project, Orchid Observers, to introduce one of the projects that wouldn't get anywhere without the general public reporting sightings, the UK Cetacean Strandings Investigation Programme (CSIP). Cetaceans are the infraorder of marine mammals that includes whales, dolphins and porpoises, and the Museum has been involved in recording their strandings on UK shores for over a century. So it's over to Rebecca Lyal, Cetacean Strandings Support Officer at the Museum, to introduce the project and what she does as a part of it.

 

Warning: You may find some of the images that follow upsetting as they are of stranded and injured animals.

 

The CSIP was created in 1990 to unite the Museum with a consortium of interested parties to formally investigate the stranding of any cetacean, seal, shark and turtle upon the UK coastline. The Museum has actually been recording strandings since 1913 when the Crown granted it scientific research rights for the collection of data on the 'fishes royal'.

 

The first recording was a Cuvier's beaked whale that stranded in Northern Ireland during the summer of 1913. Since then there have been over 12,000 logged reports of whale, dolphin and porpoise strandings, that have ranged from the mighty blue whale to the common harbour porpoise, and even a rogue beluga whale found in Scotland.

 

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A stranded Cuvier's beaked whale.

(Photo credit: Department of Environment, Marine Divison, Northern Ireland)

 

On the eve of submitting this very blog entry I was contacted via London Zoo - a CSIP partner - with a report of a common dolphin found dead after being stranded in Burnham-on-Sea in Somerset. As soon it was confirmed that someone could help me move an animal weighing upwards of 100kg I jumped into the car and followed the afternoon sun westwards.

 

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Common dolphin found stranded in Burnham-on-Sea.

 

A few hours later I arrived at a blustery Sedgemoor council depot where amid a multitude of dustbins and trucks was the dolphin. It was female, roughly 170 cm in length, and appeared in 'good condition' (i.e. it had suffered minimal decomposition), the latter being crucial to making an accurate assessment for the cause of death.

 

For animals smaller than around 2 metres in length, I can transport them to London Zoo for a post mortem in the back of the car (with the back seats pushed down of course…) so our first job was to wrap the specimen in a large polythene bag to protect it from immediate damage and shield the car from any leaking wounds.

 

With a fair amount of careful heave, ho-ing she was settled in the boot and resembling a slightly malformed Christmas cracker. Like with any stranding, I am extremely grateful for those who help with this strenuous and often fairly messy part, so my sincere thanks go to those at Sedgemoor council who assisted with this collection.

 

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Once wrapped in polythene, the dolphin can be safely transported to London Zoo for an autopsy.

 

Upon returning to London, I took the dolphin to the fridges at London Zoo where she'll be taken for a post mortem. During this procedure, a sample is taken of each organ, as well as one of the ribs and any unusual parasites found. It is also examined for unusual markings or damage that could have been caused by predation or unnatural damage. Watch this space for an update on the results…

How you can get involved

If you find a dead, stranded cetacean, seal, shark of turtle, please contact the CSIP hotline (0800 6520 333) and leave your name, number and as much detail about the stranding as possible (location and date found, species - if you know it - and the overall length and condition of the animal.)

 

I hope to provide a guide to identifying different species in a future blog post.

 

Rebecca Lyal is the Museum's Cetacean Strandings Support Officer, one of the partnership organisations of the CSIP. She completed her undergraduate degree in Marine Biology at Newcastle University and joined the Museum as the strandings officer in August 2014.

 

Jade Lauren

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A new and exciting citizen science project has begun and it's time to get involved with Orchid Observers! This research project, in partnership with Oxford University's Zooniverse platform, aims to examine the flowering times of British orchids in relation to climate change.

 

In order to achieve this, we are inviting the amateur naturalist and professional botanical community, alongside nature loving citizens from across the country, to help us collect and sort orchid data.

 

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The bog orchid (Hammarbya paludosa) is our smallest UK species. It usually grows on mountain peat bogs and can be found from July to August.

 

We want you to go out in the field and photograph any of 29 selected UK orchid species and upload your images onto our dedicated website, www.orchidobservers.org. Flowering times from each of your records will then be collated and compared with the extensive Museum herbarium collection, and data from the Botanical Society of Britain & Ireland (BSBI), totalling a 180-year-long time-series of orchid records.

 

The primary aim is to further our understanding of the impacts of the climate on the UK's flora, using orchids as a model group. The extensive data set that you will be contributing to, will tell us how different species of orchids are responding to changes in temperature and rainfall across the UK.

 

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Get out in the field and support us in our research on orchid phenology.

 

Field work: We are asking observers - like you - to record orchids by simply photographing the flower spike and uploading the image to our website, with a location and a date. To aid you with identifying the orchids, we have painstakingly produced a lavish ID guide (PDF) complete with images, descriptions, flowering times, and distribution maps. There's also a short guide (PDF) for how to take the most helpful photographs for the project.

 

Online work: We have over 10,000 herbarium orchid specimens from around the UK, stretching back over three centuries. In order to calculate any change in flowering times we need you to help us sort through images of our herbarium sheets and transcribe key information such as the species, location and flowering condition. This is one that can be done at home on your PC, or when out and about from a mobile device.

 

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The Pyramidal orchid (Anacamptis pyramidalis) adds a splash of colour to the alkaline grasslands of high summer. Keep an eye out for it in June and July.

 

If you would like to get involved with the project either online, or in the field, then go to visit www.orchidobservers.org. The orchid season runs from April until the end of September so the first species are starting to flower right now - time to get your camera out!

 

Mike Waller

 

Mike Waller is one of the new identification trainees working at the Angela Marmont Cente for UK Biodiversity. His passion lies in botany and ornithology with a particular specialism in European orchids.

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Hello! I'm Filipa, the laboratory assistant in the Microverse project. My role is to prepare all the samples that arrive from schools and community groups for DNA sequencing.

 

Each group collected 10 samples from three different locations, which they labelled A, B and C. I select one sample from each location and I set up my lab bench with everything I need, including micropippetes, tubes and the reagents necessary for DNA extraction.

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Filipa's workbench, ready to extract DNA from the samples.

 

Then I label all the tubes I'm going to use with the respective sample code, so that none of the samples gets mixed up, otherwise that would lead to misleading results. Then I extract the cotton wool, where all microorganisms are, from the wooden stick with the help of a pair of forceps and I use the reagents - following a specific protocol - to extract the DNA from the microorganisms. Finally I get a tube with DNA in it!

 

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DNA extracted from the microorganisms.

 

We then use this DNA to carry out a PCR (Polimerase Chain Reaction) - a process through which we are able to amplify a specific DNA region, by producing millions of copies. We chose to sequence the gene for the 16S rRNA, which is regarded to be an excellent genetic marker for microbial community biodiversity studies due to it being an essential component of the protein synthesis machinery. That will enable us to identify which microorganisms are present in the sample. We amplify each sample three times (with different DNA concentrations), plus a negative control (with no DNA) to make sure that there isn't any contamination in the reaction.

 

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This is the machine to visualise PCR products on an agarose gel using electrophoresis.

 

Then we run the PCR products on an agarose gel to see whether we have amplified the right size fragment - we expect our gene (16S rRNA) to be a 300-350 base pair fragment, which we compare with the ladder on the left - and that the control sample does not show up at all. The result is something like this:

 

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A photograph of the PCR products after gel electrophoresis.

 

Everything worked! For each sample we have three bright bands in the position for 300-350 base pairs and a blank one, where we put the control.

 

Lets imagine that this was not the case and some things hadn't worked so well. For instance, if we didn't get a bright band from our samples it would mean that the DNA fragment wasn't amplified. In this case it would mean that an error occurred during the PCR set up and as a result we would need to repeat it.

 

It could also happen that we found a band in one of our negative controls, this would reveal a contamination in the PCR reagents, which are not supposed to have any DNA. To solve this, we would need to start again with brand new reagents (and be more careful!).

 

In the control sample, and in some of the samples with DNA, we see a short faint fragment, this is a by-product of the reaction called a primer-dimer. To remove this we do a PCR clean-up. When that is done the samples are almost ready to be sent for sequencing, and soon after we will find out what microorganisms inhabit the surfaces you've been swabbing!

 

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Filipa Leao Sampaio, laboratory assistant.

 

Filipa is a laboratory assistant at the Museum, she began her career with an undergraduate degree in Biology and then a masters in Biodiversity, Genetics and Evolution in the University of Porto, in Portugal. For her dissertation she worked on a project where she studied phylogenetic relationships and patterns of genetic diversity in reptiles from the Mediterranean Basin.

 

Since September 2013 she has been working at the Museum carrying out molecular lab work on different projects - snake vision evolution, Antarctic soil microbial diversity and UK urban microbial diversity. Later this year she starts a PhD in London where she will receive training in different areas of environmental sciences.

 

Jade Lauren

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This blog post is a guest blog from the Natural History Investigators at Oxford Univeristy Natural History Museum (OUNHM).  After visiting us in London, to find out more about The Microverse research and to support us in our development of the project, museum educator Sarah Lloyd, took the project back to Oxford to involve students at both the OUNHM and the Oxford University Botanic Garden.  Here is what the Natural History Investigators got up to.

 

One snowy Saturday morning we unpacked our Microverse pack and lay out the scientific looking contents.  We are Natural History Investigators, a group of 14 to 16 year olds who meet every Saturday morning at OUNHM. We carry out our own research using Museum specimens. Before we begin our individual project work, we always spend some time doing something together. We've been into the Museum's spirit store, we have handled live tarantulas, but this week we were to collect samples to contribute to The Microverse project.

 

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Investigator, Gemma George investigating the similarities and differences between domestic and wild cats.

 

We divided the tasks amongst the group. Three of us were photographers. Six of us were keen to glove up and become swabbers and sample collectors.  We read through our instructions carefully and began collecting the grime that has accumulated on the outside of the neo-gothic museum building since 1860. We were very thorough and very efficient. Freezing temperatures definitely focus the mind!

 

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Abdullah Nassar collects samples from the north wall of the Museum.

 

With everything packaged up we eagerly wait to find out how many species exist in this special environment. Our individual projects have been based on things we can observe and hold in our hands.  So we are really keen to find out more about the process of studying life that you can't see or hold!

 

Natural History Investigators, OUNHM

 

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I can confirm that the samples from OUNHM have arrived at the Museum's laboratory.  Our lab assistant Filipa will be starting the PCR process very soon and then they will go into the sequencer.  In just a couple of weeks we'll be able to send the results back the Natural History Investigators, for them to explore.

 

Jade Lauren

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Meet the citizen science team

Posted by JadeLauren Jan 25, 2015

Meet the Museum's core citizen science team. First up, it's Lucy:

 

Lucy Robinson

Citizen Science Programme Manager

 

"Hello! As Programme Manager, I oversee all of the Museum's citizen science activities. My role is to update and promote our existing projects, and to work with our researchers, curators and public engagement staff to develop exciting new projects that support the Museum's scientific research.

 

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Lucy Robinson, worm charming for the OPAL soil and earthworm survey.

 

A key element of the citizen science programme is to support other citizen science practitioners to develop their own projects. We do this by producing knowledge exchange guides and publications, and I regularly represent the Museum at national and international citizen science conferences. I am a member of the global Citizen Science Association and the European Citizen Science Association, within which I lead a working group that aims to share best practice and build capacity in citizen science across Europe.

 

I've been working at the Museum in the field of citizen science for 7 years now, initially on the Big Lottery Funded OPAL project, and now as the Museum's programme manager. I love being at the interface of science research and public engagement, and am fortunate that my job means I'm working alongside world-class researchers. Over the past 7 years I've worked on citizen science projects studying earthworms, lichens, seaweeds, urban invertebrates, microorganisms and many other areas of biodiversity, and I love this variety in my role."

 

Jade Lauren Cawthray

Citizen Science Project Officer

 

"As Citizen Science Project Officer I am responsible for setting up and running citizen science projects here at the Museum. I work with staff from across the Museum, to define a research question, develop the data collection method, produce the resources that support participants in collecting and analysing the data, and communicate the results at the end of the project.

 

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Jade collecting leaf samples in the Bialowieza Forest, Poland.

 

Really important to furthering our work in citizen science is my role in advocating and communicating citizen science and the projects that we run. Not only do we need to communicate to the public what projects they can contribute to and how they might benefit from getting involved, but we also need to demonstrate to research scientists how working with citizen scientists can support them in fulfilling their research ambitions.

 

As both an ecologist and a science communicator, I combine knowledge from both fields to developing public engagement opportunities that support people in engaging with and better understanding nature.

 

I started working at the Museum nearly 3 years ago as a Science Educator, delivering the Museum’s learning offer to school and family groups. I then joined the citizen science team in August 2014."

 

John Tweddle

Head of the Angela Marmont Centre for UK Biodiversity

 

"With a background in palaeoecology, I - like Lucy - also worked on the OPAL citizen science programme for many years as OPAL Project Manager. That time was spent developing and delivering new citizen science projects as well as coordinating the taxonomy, public events and exhibitions, and voluntary natural history societies aspects of the OPAL programme.

 

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John teaching identification skills to Cubs, out in the field.

 

I subsequently left my role in OPAL to become Head of the Angela Marmont Centre for UK Biodiversity (AMC). The AMC forms a hub for partnership-based UK natural history engagement, training and research, and provides a focus for the Museum’s citizen science programme. Our mission is to inspire and support the development of existing and future naturalists.

 

Projects range from citizen science surveys, to answering public identification enquiries, provision of wildlife identification resources and training, and research into critical aspects of the UK’s biodiversity.

 

The AMC also acts as a free drop in resource centre where UK natural history enthusiasts of all abilities can further their interest by accessing UK reference collections, library materials, microscopes and expertise.

 

I am a founding Steering Committee member for the global Citizen Science Association and a member of the British Ecological Society Citizen Science Special Interest Group."

 

So, that's a quick introduction to each of us. In our next blog post, we’ll introduce you to our latest citizen project... see you there.

 

Jade Lauren