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.

Turning nature into data

Years of research and development have yielded efficient workflows centred on our core technologies: environmental DNA, barcoding, qPCR and metabarcoding.

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Environmental DNA - NatureMetrics

environmental DNA

qPCR - NatureMetrics

qPCR

Metabarcoding - NatureMetrics

metabarcoding

Environmental DNA

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.

eDNA Discovery with NatureMetrics

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: 

  • Higher detection rates
    eDNA detects organisms present in the area without the need for their presence in the physical samples,. This enables the discovery of rare, elusive or cryptic taxa, providing vital data for conserving endangered and protected species as well as finding invasive species before they become established.

  • Higher throughput
    DNA Metabarcoding analysis can process diverse samples at vast scales and in parallel, providing critical ecological data many times faster than traditional methods, which is vital for establishing effective long-term monitoring.

  • Greater consistency and accuracy
    Research shows that visual identification produces a high level of error, especially for invertebrates and juvenile life-stages. Molecular analysis overcomes observer bias, leading to a greater level of consistency in identification, as well as species level IDs for groups and life stages that can’t be identified morphologically (e.g. flies).

Environmental DNA

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, although this is only loosely related to the species’ abundance in the environment.

We use qPCR for single-species eDNA surveys of Great Crested Newts and other aquatic organisms such as crayfish, otters and mussels (see full list here). Our lead scientist, Dr Cuong Tang, demystifies qPCR in our webinar titled “Your GCN eDNA Toolkit with NatureMetrics”.

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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.

PCE is used in almost all our analyses including barcoding, metabarcoding, and single species tests (qPCR).

See more definitions in our glossary
Multi-species surveys using metabarcoding

Multi-species surveys using metabarcoding

Metabarcoding is a method of identifying multiple taxa in a single reaction by sequencing the DNA barcodes of a whole taxonomic group using 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 an Illumina MiSeq platform. 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:

  1. Collection:
    You collect an environmental or bulk sample from your sites of interest.
  2. Extraction:
    At the NatureMetrics lab, we extract the total DNA from your sample.
  3. Amplification:
    NatureMetrics amplifies a barcode region using primers optimised for your target taxon group (e.g. fish, arthropods, molluscs etc). This process makes millions of copies of the barcode gene for your chosen group, ready for sequencing.
  4. Sequencing:
    We use a high throughput sequencing platform such as the Illumina MiSeq to sequence the amplified DNA, generating around 30 million sequences in just two and a half days.
  5. Processing and species identification:
    Our reporting team bioinformatically process the raw sequence data to obtain a species x sample table ready for ecological analysis.
  6. 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 tissue sample or a 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.

NatureMetrics Webinar - Episode 1

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eDNA increases the power and pace of biodiversity surveys

The NatureMetrics scientists are active members of the scientific community and we are collaborating across industries to establish a global standard for DNA-based monitoring.

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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.

We can detect and identify multiple species from a single environmental sample (water, soils, sediments, faeces or invertebrates from an unsorted trap sample) using DNA metabarcoding from water samples or soil and sediment samples. We perform DNA metabarcoding analysis which uses the DNA present in these samples to identify the species present.

If you’re looking to understand the diet of an animal, we use metabarcoding to perform a diet assessment from faecal samples.

We’ve had great success helping Citizen Scientists to leverage these revolutionary methods of analyses to discover animal communities in water samples, using the NatureMetrics eDiscovery Lab. This can be used by individuals or families looking to explore their local wildlife, or as community activities and team-building exercises.

We use qPCR to test for the presence of a single species in water samples.

If you are looking for a single species, contact us to see how we can use qPCR for highly specific DNA-monitoring of your target taxa. We have highly optimised workflows for a range of species.

We can perform Species ID analysis using Sanger Sequencing. We mostly use this for identifying bat species from faecal samples.

We can compile a reference database for your survey area using available reference sequences, and where there are gaps in the reference database, you can collect tissue samples and send them to us. We will barcode them using Sanger Sequencing, and add them to your genetic reference library to enable identification of species during your metabarcoding projects.

We have developed workflows to rapidly gather species distribution data, so get in touch with our team and we can tell you which DNA sequences have been attributed to  your geographical area of interest, and where there might be gaps in the reference database that may need improving by performing species barcoding.

We offer integrated biodiversity surveys on large scales and across a diverse range of taxonomic groups – from water to soils and sediments, and barcoding for reference databases. These can produce detailed baselines against which to monitor and assess the effect of mitigation activities, as well as evaluate progress towards net gain or no net loss goals.

Use our suite of tools to determine whether key species are returning to areas of restored habitat, and whether the biological community is being effectively preserved or enhanced.

Data generated from metabarcoding can be used to generate fine-scale biological maps of ecosystems across a landscape, highlighting which are most ecologically distinct, particularly rich in species, or support species that do not occur in other parts of the landscape. This enables you to make more informed environmental management decisions, minimising overall impacts to biodiversity.

Learn more in our FAQs

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:

iDNAture with NatureMetrics - eDNA from water
eDNA from water
Great Crested Newt eDNA
DNA from Soils & Sediments
Invertebrates
Species from Faeces
Citizen Science Icon - NatureMetrics Services
Citizen Science

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