When planning an environmental DNA (eDNA) survey, one of the first decisions you'll face is which type of analysis to use: metabarcoding or qPCR. Both techniques are powerful tools for monitoring biodiversity and detecting species, but they are designed for different questions. Choosing the right one will save you time, money, and ensure you get data that are truly fit for purpose.
In this guide, we'll explore the key differences, ideal use cases, and decision points that will help you select the most suitable approach.
Metabarcoding uses high-throughput sequencing to identify all species present in a sample, based on DNA barcodes from voucher specimens from a chosen marker gene. This makes it a great option when you want a comprehensive community overview, for example, surveying all fish, amphibians, or invertebrates in a waterbody. Our metabarcoding tests are in the TaxaReveal range.
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Quantitative PCR (qPCR), also known as real-time PCR, targets a single species at a time, using highly specific primers and probes to confirm its presence or absence. This makes it ideal for projects where you need to know only about one (or a few) key species. Our qPCR tests are in the TaxaScreen range.
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The choice between metabarcoding and qPCR usually comes down to the question you're trying to answer. If your goal is to get a broad community-level picture then metabarcoding is the better fit. For example, if you want to see which species of fish are present in a catchment before a restoration project. Metabarcoding lets you detect multiple species from a single sample and build a comprehensive baseline for biodiversity.
On the other hand, if you need to know about just one or two species then qPCR is typically the most cost-effective and sensitive approach. For example, if you are tested fora legally protected species like the Great Crested Newt, or an invasive species like pink salmon which you're trying to eradicate. Because it focuses on a single target, qPCR can pick up even very low levels of DNA, givingyou confidence in presence/absence results.
Budget can also influence the decision. Metabarcoding usually has a higher per-sample cost but provides much more data per site, while qPCR allows you to spend less if you are testing for just a few species. Similarly, if you want to monitor population trends of a single species over time, qPCR is ideal because it can be repeated across seasons with highly consistent results, whereas metabarcoding is better suited to tracking changes in overall community composition.
The choice between metabarcoding and qPCR is less about which method is "better" and more about which one is fit for your question. Many ecologists use both methods together; metabarcoding to get the big picture, followed by qPCR to monitor a few species of particular interest.
If you're still unusre, we're happy to help you to design a study that uses the most appropriate eDNA method for your goals.
