◄Previous: 2.3 Detecting old and new pathogens

# 2.4 Improving biodiversity surveys

Environmental DNA (eDNA) refers to genetic material that organisms shed into their environment through skin cells, mucus, scales, faeces, urine, gametes, or decomposing tissue. This DNA can be collected from environmental samples such as water, soil, sediment, snow, or air, without needing to capture or even directly observe the organisms themselves.

In practice, scientists collect an environmental sample (e.g. a litre of river water), filter it to trap DNA fragments, extract the DNA, and then sequence it, as you learned in the first section.

This greatly reduces the cost and effort of sampling compared with traditional methods that rely on trapping, visual surveys, or species‑specific assays. Because organisms do not need to be seen or captured, eDNA is particularly effective for detecting elusive, rare, or endangered species that are difficult to observe directly.

Metagenomics also enables simultaneous detection of entire communities, providing a comprehensive picture of biodiversity with minimal disturbance to ecosystems.

## Box 3 Invasive species and their importance

Invasive species are organisms introduced – intentionally or accidentally – outside their native range that establish, spread, and cause harm to ecosystems, economies, or human health. They are now recognised as one of the five major direct drivers of global biodiversity loss, alongside habitat destruction, climate change, pollution, and overexploitation.

Invasive species thrive because they often escape their natural predators, parasites, and competitors, allowing them to outcompete native species, alter food webs, change ecosystem processes, and in some cases drive native species to extinction. Their impacts are particularly severe on islands, freshwater systems, and coastal ecosystems, where native species may have evolved in isolation and lack effective defences against novel competitors or predators. Beyond ecological damage, invasive species impose enormous economic costs, affecting agriculture, fisheries, water infrastructure, forestry, and public health.

Many invasions go undetected for years, meaning management often begins only after populations are widespread and expensive – or impossible – to eradicate. As a result, early detection, including using environmental DNA and metagenomics, can be a very cost‑effective strategy for invasive species management.

View document
Figure 9 (interactive) Invasive species of major global importance.

The advantage of using eDNA for studying biodiversity is well exemplified by a study on fish diversity in the Danjiang River in the Shaanxi Province, China (Deng et al, 2024). Fish diversity is a key indicator of freshwater ecosystem health, but traditional survey methods such as netting or cage trapping are time‑consuming, costly, and can miss rare or elusive species.

By using eDNA metabarcoding of water samples, scientists identified 59 fish species belonging to 8 orders, 19 families, and 40 genera. Several dominant species were identified, alongside eight rare species and two non‑native (exotic) species, highlighting both conservation value and potential ecological threats.

Interestingly, when compared with historical data and conventional ground‑cage sampling, eDNA revealed significantly higher species richness, showing it to be more sensitive and comprehensive.

- What advantage did eDNA metabarcoding have over traditional fish sampling methods in this study?

- eDNA metabarcoding detected more fish species than ground‑cage sampling because it can identify DNA from species that are rare, elusive, or difficult to catch.

◄Contents►Next: 2.5 DNA is in the air

OpenLearn - The metagenomics revolution: an introduction
Except for third party materials and otherwise, this content is made available under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 Licence, full copyright detail can be found in the acknowledgements section. Please see full copyright statement for details.