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0

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.

 

Epipactis palustris Greywell Fen July-2005 020.FR.jpg

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

 

 

Epipactis palustris 728 [Fred Rumsey].JPG

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.

 

Goodyera repens (2) [Mike Waller].JPG

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!

 

Autumn Lady's Tresses - Eggardon Hill, Dorset 2011-09-02-19 [Chris Raper].JPG

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!

1

Today one of our Microverse citizen science project participants, Robert Milne, presents his own interpretation of the results of the microbial samples collected from Mid Kent College in Gillingham where he is a student:

 

The results:

 

Despite our best efforts, the samples we obtained for the Microverse project were taken in different weather conditions, at slightly different times, in slightly different areas of the building, and all three samples were taken from walls facing different directions. The materials of the surfaces we sampled were brick, glass and metal.

 

206A_JPG0001.jpg

Mid Kent College building, swabbed by The Microverse participants.

 

From the results below, it can be seen that all three surfaces have about the same number of OTUs, (Operational Taxonomic Units, a phrase to indicate taxonomic groupings in microorganisms), but this does not mean that each surface has the same number of individual microorganisms. The number of genetic sequences varies greatly.

 

 


Sample Area A

(brick)

Sample Area B

(glass)

Sample Area C

(metal)

Number of genetic sequences generated88,264120,49827,894
Number of OTUs2,1982,1071,960
% of sequences that were from Archaea0.02%0.00%0.00%
% of sequences that were from Bacteria75.62%88.76%87.75%
% of sequences that were from Eukaryotes24.36%11.24%12.19%

 

Table 1: Results from samples of microorganisms swabbed from brick, glass and metal, at Mid Kent College, Gillingham, (% rounded to 2 decimal places).

 

The glass surface has generated the most genetic sequences while metal has generated the least. This could mean that the bacteria on the surface of the glass are more successful than the ones on the metal, for instance.

 

206A_JPG0002.jpg

Sample Area A - Brick.

 

The image above shows the brick wall from which the first sample was taken. This wall had the most eukaryotic cells present, in which the majority of them contained chloroplasts (these are the organelles of plants that convert light energy into sugar).

 

This wall faces southwest and a wall facing south of any kind will always receive the most sunlight on it during the day, which could explain the increased chloroplast numbers compared to the other two surface areas we sampled. The fact that this wall was also close to a lot of grass could also play a part in these numbers.

 

 

206B_JPG0002.jpg

Sample Area B - Glass.


The image above shows the second surface sampled, which was glass. This had the most genetic sequences found out of all three of the surfaces we swabbed. There were, however, less eukaryotic cells on the glass and metal surfaces than on the wall.

 

This could be because the smooth surface of the metal and the glass meant that less eukaryote cells could remain on the surfaces for prolonged periods. The eukaryotic cells (represented by the mitochondria and chloroplast sequences in the sample) could have originated from natural wildlife around the area, such as a snail's trail or some spider webbing.

 

 

206C_JPG0002.jpg

Sample Area C - Metal.

 

Most of the eukaryote sequences found in all samples were chloroplasts, rather than mitochondria. This probably means the surfaces always have some form of sunlight on them, which is somewhat true since all the surfaces faced either west or east to some extent.

 

206 Relative abundance chart.jpg

Figure 1: The relative abundance of bacterial phyla, archaea, mitochondria and chloroplasts in the three samples.

 

Possible uses:

 

One of the prime examples for undertaking this feat of exploring more of the microbiological world is the need to find better antibiotics; resistance to antibiotics is an increasing threat in the world of medicine. Antibiotic discovery can occur via the identification of bacteria that produce chemical substances that kill or inhibit the growth of other bacteria. Once identified the chemical substance can potentially be cultured and used as a treatment to kill off bacterial infections.

 

Exploring the countless surfaces outside in the world is a treasure trove of information that could lead to the discoveries of new bacteria that can be used effectively as a source for an antibiotic.

 

However, it can also be considered that a new resilient bacteria could be discovered that can survive without much water for a long time, which may, just maybe, hold a specific DNA sequence to help relieve the effects of hunger and thirst in patients that must undergo a fast before an operation (such as colon screening). It can open up a number of new doors to the world of medicine, and with a huge percent of areas still not investigated, it could only be a matter of time before huge changes are discovered.

 

Robert Milne

 

Thank you Robert! Robert Milne is a student of Mid Kent College, who has just finished his second year of an Applied Science Level 3 course. He has a keen interest in biochemistry and genetics and hopes to enrol this Autumn on an Undergraduate degree in Chemistry at the University of Greenwich. To find out more about the Museum's citizen science projects, see our website.

0

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.

 

Image1 CocoPimlico.JPG

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.

 

Image 2 Crookshank OMH.jpg

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.

 

Image 3 Crookshank OMH.jpg

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.

 

Image 4 Hopkins NHM.JPG

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.

 

Image 5 Hopkins NHM.jpg

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.

 

Image 6 Crookshank OMH.jpg

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).

0

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)

 

IMG_6127.MW (3).JPG

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.

 

IMG_6127.MW (4).JPG

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

 

Frog Orchid (Coeloglossum viride)

 

Coeloglossum viride Ladle Hill 1.FR.jpg

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.

 

Coeloglossum viride Ladle Hill3.FR.jpg

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).

 

IMG_0523.MW (3).JPG

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.

 

lesser butterfly closeupMW.JPG

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

 

Greater butterfly close upMW.JPG

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.

2

Crystal Palace Transition Kids and Friends of Crystal Palace Dinosaurs swab the first ever dinosaur sculptures the world had ever seen, to help us identify The Microverse. Ainslie Beattie of Crystal Palace Transition Kids and Ellinor Michel of the Museum and a member of the Friends of Crystal Palace Dinosaurs report on the event:

 

Looming out across the lake in front of us are dinosaurs, 160 year old dinosaurs! They look huge, ominous and exciting! These were the first ever reconstructions of extinct animals, the first animals with the name 'dinosaur' and they launched the 'Dinomania' that has enthralled us ever since.

 

Never before had the wonders of the fossil record been brought to life for the public to marvel at. These were the first 'edu-tainment', built to inform and amaze, in Crystal Palace Park in 1854. They conveyed messages of deep time recorded in the geologic record, of other animals besides people dominating past landscapes, of beauty and struggle among unknown gigantic inhabitants of lost worlds.

 

justeaten.jpg

The Crystal Palace Dinosaurs were built in 1854 to inform and amaze. © Stefan Ferreira

 

Most people just get to look at them from vantage points across a waterway, but not us! Transition Kids (part of Crystal Palace Transition Town) and Friends of Crystal Palace Dinosaurs arranged special access to collect data for the Museum's 'The Microverse' project. The first outing of the newly formed Transition Kids group started with art and science discovery as we decorated our field journals (every good scientist keeps a field journal full of written and sketched observations, musings and potential discoveries) and observed the subjects from afar.

 

journal design.jpg

Transition Kids proudly presenting their field journals. © Stefan Ferreira

 

Then we started the trek over the bridge, through the bushes and onto the island. Wow, the dinosaurs are huge up close! Our CP Dinosaur ringmaster, Ellinor Michel, from Friends of Crystal Palace Dinosaurs, explained to the kids about the conservation of the historic sculptures and gave an overview of the science behind The Microverse project.

 

DSC_9166.jpg

The Microverse participants trekking over to dinosaurs island. © Stefan Ferreira

 

She introduced Dr Anne Jungblut from the Museum who developed 'The Microverse' project, which aims to uncover the diversity of microscopic life on iconic UK buildings. Anne explained what is interesting about the invisible life, called biofilms, on the surface of the dinosaurs. Our involvement in the project is trying to determine what types of organisms are living on the dinosaurs, by sampling and sequencing the DNA!

 

Our results will reveal whole communities of organisms, represented by many phyla of bacteria and archaea, living on each sculpture. Once we get the results back we will be able to investigate which variables affect these communities of organisms, such as substrate, compass direction and distance from vegetation. Then the Museum will compare our results with those from hundreds of other buildings throughout the UK, to look for broader patterns in microorganism ecology. We look forward to meeting again with the scientists to discuss what our results show.

 

sampling1.jpg

Transition kids collecting samples from the surface of one of the dinosaurs. © Stefan Ferreira

 

We also took some time to explore the surface of the dinosaurs, describing the textures and patterns that had been sculpted to represent dinosaur skin. Even today, scientists are still discussing the likely skin surface of these great beasts and there is evidence to suggest that some dinos had feathers!

 

The children also got the opportunity to sit and contemplate the size of the dinos, to look underneath them and across the lake at the diversity of species on display. Not only did they get to see the great big creatures, but also a few living animals when terrapins popped up, dragonflies zoomed past and ducks paddled by.

 

DavidVallade2.jpg

Resident artist David Vallade created a set of drawings the kids could use as a visual aid for exploration. © David Vallade.

 

During the summer break we will take the kids who participated in the Dino DNA event to the Museum to explore the science behind 'The Microverse' a bit further, and meet more scientists researching our environment in other ways. Starting with this adventure in deep time and now, Transition Kids are planning many more adventures in Crystal Palace Park and beyond.

 

To find out more about Transition Kids, please email Ainslie

 

And to find out more about the Friends of Crystal Palace Dinosaurs visit: http://cpdinosaurs.org/

 

A big thank you to all of the Museum staff and local community supporters who contributed to the event.

 

Full group.jpg

The whole dinosaur swabbing team. © Stefan Ferreira

 

CPTT.jpg FCPD2.jpg

Jade Lauren

0

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.

 

TheMicroverse_Green.jpg

 

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.

 

Untitled-1.jpg

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.

 

TrinityCatholicSchool226A.jpg

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.

 

Kev in MCF.jpg

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.

 

Jungblutfeild.jpg

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.

 

LooeBioblitz.JPG

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.

2

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!

 

Orchid Observers Team.JPG

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 volunteer Stephen Chandler, who has been supporting The Microverse project by using computer software to identify the taxonomic groupings of the DNA sequences revealed in the sequencing machine.

 

Due to the size of microorganisms, we have until recent years relied on microscopes to identify different species. The advancement of scientific technologies however has made it possible for scientists to extract DNA from microorganisms, amplify that DNA into large quantities and then put the samples into a sequencing machine to reveal the genetic sequences. In The Microverse project, my role begins when the sequencer has finished processing the samples.

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A raw data file from the MiSeq machine.

 

When the gene sequencer has finished decoding the PCR products it creates a file much like a typical excel file. The main difference is that this file can be incredibly large as it contains millions of DNA sequences belonging to hundreds if not thousands of species. This requires a powerful computer to run the analysis to identify what is in the sample.

 

At the Museum we use a number of servers with huge memory capacities and processing capabilities. To give an idea of the power these machines have compared to an everyday computer; a server at the Museum has at least 1.5TB (Terabytes) of RAM, that’s 300 times more processing power than your average computer, which has 4-6GB (Gigabytes) of RAM.

 

In order to use this computing power, the server needs to have a program designed to analyse and identify the DNA sequences, using a reference database of DNA for that group of organisms. To do this I use a program called QIIME (Quantative Insights Into Microbial Ecology).

 

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The QIIME terminal, where the computer code is inputed to process the sequences.

 

The process of turning a raw sequence file listing all the DNA sequences, hot from the gene sequencer, into something that can be used to create graphs is not an easy task, especially when you have hundreds of thousands of sequences, as for the Microverse project.

 

The first step is to remove low quality sequences that have errors. Then the sequences within a sample are grouped together into Operational Taxonomic Units (OTUs), according to their similarity. Sequences that are at least 97% similar to each other are grouped into one undefined OTU. The OTUs that are found are then compared to a reference database containing hundreds of thousands of specific species, and other taxonomic groupings, to identify which type of organisms they are.

 

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A nearly completed file. All the sequences have been identified, but now need to be put into an order.

 

Some of the bacteria that we find are common and you can find them living on most surfaces in our home or garden, but others are incredibly rare and have evolved to survive in the most competitive and extreme environments. And all this microscopic life and diversity can all be found living just outside the front door. Although in the Microverse project no sample or result seems to be quite the same, which makes this a very exciting project.

 

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Three coloumn graphs representing the relative abundance of different microorganisms identified in three different samples.

 

Stephen Chandler

 

Stephen Chandler obtained a degree in marine biology at Portsmouth University and then went on to complete his masters at Imperial College London in ecology, conservation, and evolution in 2014. Stephen’s ambition is to study for a PhD and he is particularly interested in studying microorganisms in marine environments.

 

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Stephen taking samples from the pocket roof of St Paul's Cathedral.

 

And now a brief word from Dr. Anne Jungblut, on careers in genomic science:

 

More and more research in biology, ecology and medicine is based on DNA and genome sequencing. The research relies on specialist software and programming in order to be able to analyse data sets as big as the Microverse sequence data, with future genomics projects likely to be much much bigger than our current project. 

 

Along with specialist software the field will also need more and more different types of experts working on DNA projects to tackle future challenges in science, ranging from people interested in going outside to collect field data, molecular biologists that know how to do laboratory work to extract high quality DNA and run sequencing machines, to people that love concentrating on data analysis by applying specialist software, writing programming scripts or even develop new bioinformatics programs.

 

Anne Jungblut

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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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