Explore the molecular tools that allow us to generate your powerful datasets
DNA: it’s in our nature
Businesses are faced with a growing need to report on biodiversity, yet monitoring has traditionally been costly and difficult to perform at scale. We are all challenged by the need for better data on nature, whether it is for assessing the impacts of your business operations or monitoring the success of restoration efforts on biodiversity. NatureMetrics make biodiversity surveys possible at scale by giving you with the tools to collect DNA samples from your project sites and send them to us for analysis, generating data on unprecedented scales. The biodiversity monitoring landscape is being transformed thanks to our cutting-edge DNA technologies.
Environmental DNA
All living things leave a trace of DNA in the environment. Fish will leave a trail of DNA in the water as they swim, and this DNA comes from their mucus, scales and even faeces. Mammals shed DNA into the environment too, from pieces of hair, cells, skin and faeces. Birds, humans, insects, amphibians, reptiles and all other living things do the same. The environment is one big soup of environmental DNA (eDNA), and it is easy to collect, whether from rivers, ponds, oceans or forests.
Collecting eDNA samples
You can collect environmental DNA (eDNA) samples with the NatureMetrics iDNAture kits and send them to our labs for analysis. Easily collect eDNA from water, soil, sediments and more, to rapidly survey the biodiversity of your project sites.
Our eDNA from water service uses an easy-to-use filtering method in the field, which you can learn more about in the video below.
By leveraging eDNA for biodiversity monitoring, you can expect:
Single species surveys using qPCR
For single-species studies, we use qPCR, which is fast to perform as it does not require DNA sequencing. The qPCR process uses a unique species-specific primer to amplify the target DNA in your sample.
Because the primers are designed to only match the DNA of the target species, the qPCR reaction will only produce successful DNA amplification if the target’s DNA is present in the sample. The qPCR test simply measures the amount of DNA to determine whether amplification has taken place and infers species presence on that basis. Based on how quickly the amplification occurs, it is also possible to estimate the amount of the target’s DNA that was in the sample. This may be loosely related to the species’ abundance in the environment depending on the type of species and ecosystem.
We use qPCR for single-species eDNA surveys of Great Crested Newts and other aquatic organisms such as crayfish, eels and mussels (see full list here). Our lead scientist, Dr Cuong Tang, demystifies qPCR in our webinar titled “Your GCN eDNA Toolkit with NatureMetrics”.
What is PCR?
Polymerase chain reaction (PCR) is the process of making millions of copies of – or “amplifying” – a specific section of DNA. It uses primers, which are short sequences of synthetic DNA that bind to either end of the DNA segment you want to use for identification of a chosen species or taxonomic group. In the presence of a particular enzyme and a temperature regime, the primers replicate the DNA sequence between them, leading to exponential increase in the abundance of this DNA.
PCR is used in almost all our analyses including barcoding, metabarcoding, and single species tests (qPCR).
Multi-species surveys using metabarcoding
Metabarcoding is a method of identifying multiple taxa in a single reaction by sequencing many DNA barcodes in a highly parallel process known as High Throughput Sequencing. Metabarcoding can be applied to eDNA samples (e.g. water sample collected with the iDNAture kits), or from bulk samples of organisms (e.g. insects collected in a malaise trap).
Metabarcoding is carried out in NatureMetrics’ purpose-built facilities and sequenced on-site using our suite of Illumina MiSeq’s. Metabarcoding technology has enabled us to generate reliable, repeatable biodiversity data on a massive scale, informing critical environmental management decisions and altering how we describe the natural world.
The overarching workflow of multi-species metabarcoding surveys includes:
- Collection:
You collect an environmental DNA or bulk sample from your sites of interest. - Extraction:
At the NatureMetrics laboratories, we extract the DNA from your sample. - Amplification:
NatureMetrics amplifies a barcode region using primers optimised for your target group (e.g. fish, invertebrates, mussels etc.). This process makes millions of copies of the barcode gene for your chosen group, ready for sequencing. - Sequencing:
We use a high throughput sequencing platform (Illumina MiSeq) to sequence the amplified DNA, generating around 30 million sequences in just two and a half days. - Processing and species identification:
Our reporting team bioinformatically processes the raw sequence data to obtain a species by sample table ready for ecological analysis. - Analysis:
Our data science team can apply ecological statistics and data science to support better decision making from our powerful data sets.
Barcoding
DNA barcoding begins with DNA extracted from a specimen, such as a fish swab. The extracted DNA is amplified and sequenced using PCR to create a reference sequence for that species. This reference sequence is useful for documenting the known DNA fingerprint of a species that may not have been previously recorded.
Traditional barcoding requires collecting DNA from organisms so it can be time consuming for large-scale data collection across diverse groups. A traditional DNA barcoding approach is important for documenting a species’ DNA fingerprint for the first time, but there are also lots of species that have already been barcoded and are readily available in our DNA reference databases.
What can DNA-based monitoring achieve?
DNA-based technologies produce robust datasets that answer critical ecological questions for a range of applications. Our services can also be combined to address complex questions about biodiversity at the ecosystem or landscape scale.
iDNAture with NatureMetrics
Our technologies to collect DNA from the environment are available in a range of options, collectively known as the NatureMetrics iDNAture kits. These kits differ depending on the type of environment you want to sample and the purpose of your survey.
The iDNAture kits are available for:
eDNA from water
Great Crested Newt eDNA
DNA from Soils & Sediments
Invertebrates
Citizen Science
BSI Kitemark™ for Innovation Management
NatureMetrics is a proud recipient of the BSI Kitemark™ for Innovation Management, a prestigious award for pioneering organisations that demonstrate their innovation credentials in their vision, strategy, policy, and objectives. Recognised throughout the world, the BSI Kitemark is a symbol of quality and reliability.
