Explore the molecular tools that allow us to generate your powerful datasets. We have accomplished our proven workflows through years of research and development, based on a set of core technologies: environmental DNA and bulk metabarcoding, barcoding and qPCR. Our expert team are actively part of the scientific community that are setting the standards for DNA-based monitoring globally.
To read the science behind our services, you can also browse our scientific publications here. We have compiled a comprehensive set of answers based on the questions you ask during projects and webinars. Read our FAQs or get in touch with your questions.
DNA: it’s in our nature
At NatureMetrics, we utilise a fundamental component of life on earth – DNA – to bring power and pace to biodiversity surveys. In this video, our founder Dr Kat Bruce explains how we use DNA, and the building blocks (nucleotide bases) that make up DNA, to match DNA in the environment with the species it came from. We call this environmental DNA metabarcoding. It’s what we’re good at and it’s how we’re changing the way our clients see biodiversity.
Elevating biodiversity monitoring
Nature is in a state of decline. Responsive environmental management has never been more vital, yet this requires a constant stream of data about the natural world. Traditional tools and techniques for environmental management struggle to meet this demand effectively. Often, methods of classic sampling and taxonomy are expensive and time consuming to carry out, difficult to verify and inefficient in presenting data when it matters most.
We applied our DNA technologies to overcome those challenges and empower all, with accessible, ground-breaking science that facilitates effective, data-rich, biodiversity monitoring.
You can combine our technologies to answer questions about complex biodiversity.
Browse our core technologies and methodologies below:
Where does environmental DNA come from?
All living things leave a trace of DNA in the environment. Slimy fish leave a nice 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, maybe from pieces of hair, cells, skin and also faeces. Birds do the same, and humans, insects, amphibians, reptiles and all other living things. The environment is one big soup of environmental DNA or eDNA.
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, enabling the discovery of rare, elusive or cryptic taxa. This data is vital in conserving rare populations before they go extinct, and 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 and routine monitoring.
- Greater consistency and accuracy
Traditional taxonomy is hard to standardise due to variables such as subjectivity, interpretation, experience and skill-sets. Especially considering trained taxonomists are an endangered species in themselves. DNA sequences are digital and easy to curate and add to databases making it easier to verify this data by third-parties and audit.
Classic DNA barcoding is the method we use for creating reference sequences for different species.
Barcoding starts with DNA that is extracted from a specimen, for example from a fish tissue sample. The extracted DNA is amplified by PCR, and sequenced to generate a reference sequence for that species. There are ongoing efforts globally to barcode all life on earth, so you’ll often find that somebody has already barcoded your species of interest.
The eDNA metabarcoding workflow below relies on databases of these barcoded reference sequences, because the genetic data that is generated during metabarcoding is matched against a reference database of sequences. You can start a metabarcoding project without a full reference database, but it is a good idea to check whether the organisms you are interested have got reference sequences. If there are gaps in the reference database in your region, you could think about barcoding some key species for your study, and we can support you in making those decisions. We often include barcoding services with projects that are beginning in new areas, and we can catalogue the species found in your sampling region. You can contribute to global barcoding efforts whilst also making use of our bespoke databases of species we’ve barcoded and identified to date.
Species not yet in the reference database cannot be definitively identified without obtaining a reference sequence. However, in many cases there are sufficient references from congeneric species to make a confident identification at genus-level. In a scenario where only one representative of that genus is expected in the sampled community, a putative species label can be associated with the metabarcoding sequence we generate, pending confirmation from reference material. Species unknown to science would similarly be identified as best we can given their similarity with available reference data, but we cannot distinguish between gaps in the reference database and gaps in taxonomic knowledge.
Multiple species by Metabarcoding
Metabarcoding is a method of sequencing the DNA barcodes of many different organisms in parallel using High Throughput Sequencing to identify diverse taxa in a single reaction.
We have an Illumina MiSeq, and sequence your metabarcoding samples on site.
You can perform metabarcoding from a range of sample types- whether that be traditional bulk invertebrate samples or environmental DNA samples from water or sediment. DNA and eDNA metabarcoding allow us to generate sequencing data for many different species without having to use taxonomic expertise in the field. The taxonomic assignments are applied during the bioinformatics stage, and rely on barcoding and reference databases .
Metabarcoding technology has allowed us to produce robust, replicable biodiversity data at a remarkable scale, informing crucial environmental management decisions and changing the way we describe the natural world.
After we receive your samples for metabarcoding, there are five overarching stages in the metabarcoding pipeline.
Single Species by qPCR
We use qPCR for our single species analyses, and this does not involve sequencing the DNA at all. The qPCR process uses a very specific primer to amplify the target DNA in your sample. We use qPCR for Great Crested Newt eDNA surveys, and for single species detections from aquatic eDNA samples.
Unlike traditional PCR, quantitative PCR (qPCR) is able to quantify the amount of DNA being amplified whilst the reaction progresses. We can monitor reaction progression in qPCR assays by an increase in the fluorescence signal. A quantification cycle or Cq value can be determined when the fluorescent qPCR signal is detectable over the background fluorescence. We can use Cq values to evaluate the relative target abundance between two or more samples. We can also calculate absolute target quantities related to an appropriate standard curve.
This quantification approach is particularly useful for well-studied species such as the Great Crested Newt, where specific primers have been designed for that species, and we can use positive qPCR results as an indication of species present in the sample. For less well-studied species, primer development would need to be performed first before using qPCR for single species detection, or you may prefer to use metabarcoding and gather data on multiple species at the same time.
How does metabarcoding compare with classic DNA barcoding?
Although we use classic DNA barcoding for some things, for example when building reference databases, it is of limited use for biodiversity surveys for two main reasons. First, classic barcoding is too slow and expensive for generating large-scale data across diverse groups (e.g. arthropods and other invertebrates) because it requires a separate sequencing reaction for each specimen. Second, classic barcoding can’t be used on samples that contain DNA from a mixture of related species (e.g. environmental samples). This is why we use metabarcoding to bypass these limitations when generating large scale biodiversity data.
As global pioneers in our field, we’re constantly accelerating the scope and impact of our technologies and services.
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