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Citizen science blog

5 Posts tagged with the genetic_diversity tag
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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.

 

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.

 

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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 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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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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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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I bet you have never wondered what microorganisms are living on London's iconic buildings. I certainly hadn't given it much thought until this August when I joined Dr Anne Jungblut, Lucy Robinson and volunteers Josie Buerger and Stephen Chandler, for an urban field trip. We visited four of London's iconic buildings to collect microorganisms and find out what on earth is living there. This would be the start of our citizen science project, The Microverse; a scientific exploration of the microbes that occupy our built environment across the UK.

 

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The Microverse team collecting samples from Westminster Abbey. Image credit: Josie Buerger

 

The Tower of London, The Gherkin, St Paul's Cathedral and Westminster Abbey all kindly accepted our request to swab their walls and DNA sequence the biofilms that we found. We carefully selected different types of building material and different sides of the buildings, so we could compare the community of microorganisms from these different aspects of the built environment. We took samples from different aged buildings, from cleaned and un-cleaned walls and even from the roof of St Paul's Cathedral.

 

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Collecting samples from St. Paul's Cathedral.

 

Samples were collected by dampening a cotton wool swab with sterile water and then rubbing this swab against the surface of the wall. The head of the cotton wool swab was then put into a tube of DNA preservative. Samples were stored in the freezer of the Museum until they could be DNA sequenced in the labs. We are currently analysing the lab results to see what communities of microorganisms were living on the different buildings. Will The Gherkin have less microorganisms than the Tower of London? Will south facing walls have more microorganisms than north facing walls? We hope to tell you what we have found very soon.

 

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Dr Anne Jungblut adding sample to DNA preservative at Tower of London. Image credit: Josie Buerger.

 

The Microverse is a citizen science project, suitable for A-level Biology students or equivalent, and community groups. The project takes you out of the classroom to gather microorganisms for DNA analysis, as part of our cutting edge research into the biodiversity and ecology of the microbial world. It's free to participate and you can find out more about the project and how to take part here.

 

Jade Lauren