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.

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.

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.

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.

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.

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.

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.

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."

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.

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.

MidKent College are one of the 140 schools and community groups to take part in The Microverse so far. We asked two of their students, studying for a BTEC Extended Diploma in Applied Science, to tell us what got them excited about microorganisms, DNA and taking part.

The team at MidKent College pausing for a group photo while collecting microbial specimens for The Microverse.

Here's Emmanuel Shobande:

We were informed about the Microverse project during a lesson and a majority of the class took a keen interest in what Alison, our lecturer, was saying. On the day, every member of the class went outside to collect biological samples from one side of the college building.

I took interest in the project as I wish to study Biomedical Science at university, so collecting data and analysing it is something I take an interest in. The course involves lots of research and analysis of data, so this project would be a great way to enhance my CV, thus making me more employable when applying for a job/placement.

But what inspired me was the fact that the data that I collected was going to be published and used for DNA analysis, which could help scientists identify the types of microorganisms with potential nutrient deficiencies, those living in wet/dry conditions and those which are housed in areas of high pollution from different areas and on different buildings. For scientists to say that they are to travel the whole world and swab every building for living microorganisms would be a very time-consuming and expensive task, which is why we, as future scientists, have been given such a great opportunity to get involved in the collection of data, which could one day help identify a new form of microorganism which may not have been studied prior to the project. Who knows, our data could one day be quite essential!

Emmanuel Shobande, studying for a BTEC Extended Diploma in Applied Science

And now for Max Squires:

To be part of an actual scientific project has helped me gain a range of microbiological skills which will help me with my Biomedical Science course at university. It has made me feel like an actual scientist by helping to gather data which will be analysed and be part of informative research about the microbiological life within urban ecosystems. As part of this, my class swabbed the exterior college building to hopefully identify the types of microorganisms that live in similar conditions across the UK.

This project has got me thinking of the life of microorganisms in urban environments. In built up environments, such as the college building which was swabbed, there are not many nutrients for microorganisms to thrive, there are high levels of pollution which can affect how microbes thrive and different weather conditions in which the microbes are exposed to (rain, hot weather, snow, etc.).

Could the high levels of pollution, possible lack of nutrients and harsh weather conditions inhibit microbiological life? In theory, microbes thrive in warm, moist, oxygen-rich environments and if one thinks about it, urban environments provide these factors, so it is very likely to find microbes in urban environments. Identifying specifically what microbes live in these environments will help us map out where each different microbe lives and possibly identify many new biofilms, which can give us an idea how microbes interact with each other to thrive.

It has been a great opportunity to be part of this research. It feels great knowing that an actual sample I collected will be analysed by top scientists and will be used in actual scientific research! It has got me thinking of the life in urban environments on a microscopic scale and has allowed me to develop my practical skills in science giving me a good start at university and in the future.

Max Squires, studying for a BTEC Extended Diploma in Applied Science.

The Microverse is a citizen science project, suitable for A-level Biology students or equivalent, and also 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. Free to participate, you can find out more at: http://www.nhm.ac.uk/microverse/