Genetic Biodiversity Monitoring with NatureMetrics

Genetic Biodiversity Monitoring with NatureMetrics

A huge part of environmental management is that of biodiversity monitoring. This monitoring entails, or rather, should entail if done properly, not just overall population numbers, but monitoring of the genetic health and diversity of species in a given habitat.

Secondly, regular monitoring has a number of potential drawbacks, including a simple one – plain-old missing, or failing to recognise, the presence of a species in a said given area.

One biotech startup aims to overcome this issue – NatureMetrics. Based in Surrey in the UK, the team assists environmental managers by using DNA-based techniques to isolate species’ signatures from water or sediment samples “or from complex mixed-species samples of invertebrates”. These signatures then allow the technician to advise on which species are, or are not, present – invaluable information for the purposes of environmental management, monitoring, surveying and establishing of baselines.

A screenshot of part of NatureMetrics' home page
A screenshot of part of NatureMetrics’ home page

To quote from their site, they list the following as one of the reasons to use DNA-based biomonitoring:

“Ecologists are limited by a lack of biological data, usually as a result of a sampling bottleneck, a taxonomic bottleneck, or both. Combined these issues mean that (a) the true distribution and status of most species is unknown, and (b) total community level biodiversity is rarely assessed.”

Thus, we find a database of these samples, called eDNA (short for environmental DNA), explained within their glossary as:

…DNA deposited in the environment through excretion, shedding, mucous secretions, saliva etc. This can be collected in environmental samples (e.g. water, sediment) and used to identify the organisms that it originated from. eDNA in water is broken down by environmental processes over a period of days to weeks. It can travel some distance from the point at which it was released from the organism, particularly in running water. eDNA in soil can bind to organic particles and persist for a very long time (sometimes hundreds or thousands of years). eDNA is sampled in low concentrations and can be degraded (i.e. broken into short fragments), which limits the analysis options.

The benefits of this DNA-based approach to the monitoring of biodiversity are listed as the following:

  1. Many times faster
  2. Morphology and life-stage independent
  3. Reduced taxonomic bias
  4. Statistically powerful datasets
  5. Third-party verifiable
  6. Reduced observer bias

On the database, i.e. reference library side, NatureMetrics use both the National Center for Biotechnology Information (NCBI) database (known as GenBank) and the Barcode of Life Database (BOLD) as the basis for their species identification pipelines. That being said, given some claimed errors with these, the team have applied their own careful QA and curation methods to a version of their own that is used in their pipelines. As reference:

  • GenBank is the NIH genetic sequence database – an annotated collection of all publicly available DNA sequences – link: https://www.ncbi.nlm.nih.gov/genbank/
  • BOLD is a cloud-based data storage and analysis platform developed at the Centre for Biodiversity Genomics in Canada. It consists of four main modules: a data portal, an educational portal, a registry of BINs (putative species), and a data collection and analysis workbench – link: https://www.boldsystems.org/

A number of case studies of some of the work done by NatureMetrics can be found on their site at: https://www.naturemetrics.co.uk/our-work/case-studies/

Last year the biotechnology firm was announced as one of the first five firms to join the HS2 (UK high-speed railway development) for its Innovation Accelerator programme, the purpose of which…

…aims to develop technologies to be integrated into Britain’s HS2 high-speed rail project.

Check them out on https://www.naturemetrics.co.uk/

Update: 11 June 2021
NatureMetrics has been listed in Sifted‘s Sustain 100: the European sustainability startups to watch in 2021. In a news article published yesterday (10 June), NatureMetrics explained that:

Sifted cherrypicked the 100 most innovative startups across climate tech, cleantech, GreenTech and beyond. They have selected companies with sustainability at the heart of their mission and messaging. Each of the companies selected is recognised to be providing necessary tech solutions to the climate crisis.


References & Sources:

Boldsystems.org. n.d. Bold Systems v4. [online] Available at: https://www.boldsystems.org/

Cuenca, O., 2020. HS2 announces first five firms for its Innovation Accelerator programme – International Railway Journal. [online] International Railway Journal. Available at: https://www.railjournal.com/technology/hs2-announces-first-five-firms-for-its-innovation-accelerator-programme/

NatureMetrics.co.uk. n.d. Biodiveristy and eDNA Survey, Analysis & Monitoring | NatureMetrics. [online] Available at: https://www.naturemetrics.co.uk/

Ncbi.nlm.nih.gov. n.d. GenBank Overview. [online] Available at: https://www.ncbi.nlm.nih.gov/genbank/


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