Why biobanking is key to preserving biodiversity | Jacqueline Mackenzie-Dodds, Molecular Collections Facility Manager

Jackie Mackenzie-Dodds (in full cryo-gear!) decanting liquid nitrogen from the Molecular Collection Facility’s LN2 bulk tank. Copyright: The Trustees of the Natural History Museum, London.

Although estimates of extinction rates vary significantly [1], anywhere from losing hundreds to hundreds of thousands of species each year, it is widely acknowledged that we are in the midst of a biodiversity crisis. Ensuring we deliver a wide range of conservation measures to protect species is key to halting this decline across all taxonomic groups. A growing area of research is focussing on biobanking as an effective way to deliver this. But what does this mean in practice, how does it work and why is it important?

What is biobanking?

A biobank is a huge library of genetic information on animals, plants or humans, or more specifically “biological or medical data and tissue samples, amassed for research purposes” [2]. This focus on data and research is key – biobanking isn’t about locking specimens away, it’s about opening them up to researchers across the globe to carry out cutting-edge studies.

The term ‘biobank’ first appeared in 1996 and in the early days was mainly used to refer to the storage and use of human biological samples [3]. Since then, they have become an essential part of modern medical research, providing the opportunity to investigate the genetics of disease development. One of the most high-profile projects in the UK is the UK Biobank [4] which was set up in 2006 to deliver a large-scale biomedical database and research resource, containing in-depth genetic and health information from half a million UK participants. It has to date enabled over 20,000 researchers to use the data for scientific studies.

In more recent years, and as the cost of DNA sequencing has plummeted, the definition and applications of biobanking have expanded, branching out to include any biological material from animals and plants, as well as humans. Using cryopreservation techniques, the storage of samples in extremely cold sub-zero environments, we can now preserve ‘living’ tissues and cells of vast swathes of the natural world.

Biobanking at the Natural History Museum

The Molecular Collections facility at the Natural History Museum (NHM) was built in 2010, with support from the Wolfson Foundation, and opened in 2012. The facility enabled us to bring together valuable molecular collection genetic material, specimens and samples accumulated in research labs across the museum over decades for the first time, from dispersed local lab fridges to freezers bursting at the seams! It was also designed with space and facilities for other institutions in need of help to store their collections in a purpose-built secure facility. The molecular collection stores DNA, tissues and cell culture samples predominantly for use by the research and conservation community. It contains samples from lizards, frogs, birds and bees to mammals, spiders, fish, algae, flowering plants, ferns, mosses, crops and much more.

A specimen from the 45K UK Insect Pollinators Initiative Archive in the Molecular Collections Facility. Copyright: Jackie Mackenzie-Dodds.

We have the capacity to store over 2 million tubes, each containing a different sample from a different organism. These tubes are stored in freezers at -80˚C (home freezers operate at -20˚C). We also have a liquid nitrogen facility with tanks that can hold around 60,000 samples in liquid nitrogen vapour at -185˚C!

For research we need multiple samples from each individual and each species, so with ~10 million species so far described on Earth, achieving representation of all organisms across the tree of life in the biobank is a massive task. A task that is only possible if we collaborate and develop platforms for sharing this data with other biodiversity biobanks across the planet. We are in a race to beat extinction in the wild – some species now only exist in tubes!

Why is it important?

Maintaining and building these collections is essential to increase our understanding of the natural world both now and for future research. By storing and safeguarding genetic material from a wide range of taxonomic groups we can investigate an organism’s evolutionary history, resilience to global changes, as well as their relationship to other organisms and the environment. It provides a vital snapshot of biodiversity at the point in time when the sample was collected which is critical to conserving our ecosystems. As new technologies emerge, we are able to find out more and more about the world around us and how we can best preserve it, and by deep freezing high quality genetic resources now, we preserve our ‘options’ for future analysis – if not, we lose the opportunities forever!

Some research groups have also investigated how biobank specimens of sperm, embryos, oocytes, or cell lines (development of ‘stem cells’ from cell lines open up very exciting options) could even be used in breeding programmes for species that are at risk of extinction.

Future plans for the biobank at the Natural History Museum at Harwell include expansion of our liquid nitrogen cryofacilities. This will enable us to collaborate and provide more research groups and institutions with precious ‘viable’ i.e., living molecular collections stored in liquid nitrogen. This includes gametes etc listed above, for endangered and all other species. These resources represent the new ‘post-genomic’ molecular collections, unlocking next level cellular information from different species e.g., proteins, metabolites (transcriptomics and metabolomics) and much more. These NHM resources will be critical contributors to applied conservation research projects in the future, including informed breeding and habitat management programmes in the wild, for domestic and endangered species worldwide.

What kind of projects do you work on?

Darwin Tree of Life

A major project we are currently part of is The Darwin Tree of Life (DToL), a collaborative project led by Wellcome Sanger Institute and with a range of other research partners, to sequence the genomes of all 70,000 species in Britain and Ireland. The project aims to collect representatives of each species, use advanced DNA sequencing technologies to generate high quality genome sequences, and cutting-edge computational tools to understand how the DNA sequence translates into the diversity of life. The data is then released openly for all to use.  Meanwhile high genomic quality voucher specimens and DNA from DToL partners across the UK are stored at -20, -80 and liquid nitrogen in the biobank and made available to researchers worldwide. Understanding from the DToL data, protocols and outcomes will feed into the next ambitious genomics project, the Earth Biogenome Project, which plans to sequence whole genomes from all species on planet Earth.

CryoArks

Another major project is CryoArks, an initiative that aims to bring together the diverse collections of animal frozen material found in museums, zoos, research institutes and universities across the UK to make them accessible to the UK’s research and conservation community. The CryoArks partners include the NHM, Cardiff University, Nottingham University, National Museum of Scotland, and the Royal Zoological Society of Scotland. Several large new collections have been added to the NHM biobank as part of the CryoArks project, including deep sea species collected in the mid-Atlantic on the Discovery 100 Expedition in 2018, a renowned UK vertebrate frozen tissue collection from the Wildlife Veterinary Investigation Centre, Cornwall, and an incredible lifetime legacy collection of animal cell lines donated by Professor Malcolm Ferguson-Smith at the Cambridge Resource Centre for Comparative Genomics. Cell lines contained in this collection takes the NHM biobank into the future, with next generation viable biodiversity resources for research, and they are already being requested!

CryoArks’ hugely successful joint NHM and London Zoo (ZSL) Volunteer Programme (team of 8 working in pairs each week at both locations) has swung back into gear after lockdown helping ZSL and Institute of Zoology at London Zoo unlock their collections.

SCAN – Schistosomiasis collection

Over the last few years, we have also had a significant focus on building the schistosomiasis collections at the Museum – a global repository of schistosome parasites and their snail intermediate hosts. Schistosomes are parasitic flatworms responsible for a range of infections in both humans and animals affecting over 250 million people worldwide. The collection provides a secure and long-lasting repository of genetic schistosome material and associated ecological and epidemiological data for researchers looking to eradicate these diseases.

What’s next?

Ensuring we document and safeguard species in this way is essential for future research. If we can secure this information, it will continually be revisited as and when molecular analysis techniques advance.

Increasing recognition of the urgent need to preserve biodiversity molecular resources e.g., at COP26, has resulted in a renaissance of biobanking natural history collections in the UK and EU, with many new high impact projects and initiatives funded with biobanking included as an essential and major output . Examples include BIOSCAN (revealing species interactions and their dynamics), UKBOL (DNA barcoding of UK biota) and most recently a big new EU wide project Biodiversity Genomics Europe which aims to accelerate the use of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline. Governments and the public are now much more aware of the importance of biodiversity biobanking, and collaborations with e.g. Natural England, Environment Agency, DEFRA as well as active citizen science contributions and volunteer programmes are helping to expand natural history biobanking’s reach into wider society.

The future is ‘digital’ for biobanks, and all natural history molecular collections, specimens and samples will be ‘Born Genomic’, enabling easy, quick, and cheap unlocking and sharing of the genetic data they contain. Automated robotic workstations will be employed in biobanks to retrieve, deposit, sort, reformat and prepare very large numbers of molecular samples for downstream analysis, with streamlined molecular pipelines integrating biobanks with molecular biology research laboratories. Data Management is key, and we are developing integrated Collections and Laboratory Information Management Systems for this, with interoperable data portals which can connect with other biodiversity biobank data portals worldwide.  

Lastly, environmental sustainability as part of our commitment to net zero, is extremely important but a significant challenge for museum biobanking because of the ultracold storage required. We are currently measuring power usage by different storage units (-20/-80/LN2/Ambient -Room Temperature) to enable us to make recommendations on best practice going forward for biobanks everywhere. Alongside R&D to assess genome quality molecular resource preservation, we also plan to phase out high carbon footprint mechanical freezers in the biobank, replacing them with liquid nitrogen tanks  which are more efficient at preserving samples at a higher quality for a longer period, in parallel with increasing ambient (room temperature) dry storage formats.

All these steps are helping us to make sure biobanks and the information they contain are safeguarded long into the future – hopefully enabling us to answer questions we don’t even know we have yet.

And finally… did you know?

Each of our 40 freezers are named after a different animal or plant from Earths coldest environments…

Minus 80 °C Freezers. Left to Right: Polar Bear, Arctic Fox, Artic Hare, Snowy Owl and Reindeer. Copyright: Aidan Emery.

The Molecular Collections will eventually be rehomed at our new science and digitisation centre. To find out more about the project and to sign-up for email updates , including information on collections closures when available, visit the website.

If you enjoyed this blog please do feel free to share with your networks or on social media – you can also follow the project on Twitter and LinkedIn.


[1] e360.yale.edu/features/global_extinction_rates_why_do_estimates_vary_so_wildly
[2] http://www.lexico.com/definition/biobank
[3] pubmed.ncbi.nlm.nih.gov/24835262/
[4] http://www.ukbiobank.ac.uk/learn-more-about-uk-biobank/our-impact/celebrating-15-years-of-uk-biobank

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