Environmental DNA Metabarcoding for Biodiversity Assessment

Environmental DNA metabarcoding is a molecular approach that retrieves genetic material shed by organisms into their surroundings to survey biological communities across terrestrial, freshwater and marine ecosystems. By extracting DNA from soil, water or air samples and targeting taxonomically informative regions of the genome, researchers can amplify mixed-template sequences simultaneously, enabling rapid detection of multiple taxa in a non-invasive manner. Developments in high-throughput sequencing and bioinformatics have refined workflows from sample collection through primer design, library preparation and sequence data filtering, accelerating biodiversity inventories at unprecedented spatial and temporal scales. Applications span from invasive-species monitoring and conservation assessments to ecosystem health surveys and palaeoecological reconstructions. Challenges remain in standardising primer sets to minimise taxonomic bias, calibrating sequence reads to estimates of abundance or biomass, and interpreting eDNA transport and degradation in variable environments. Integrating eDNA metabarcoding with conventional field surveys and ecological modelling is delivering robust, scalable tools for tracking biodiversity change in the face of global environmental pressures.

Research from Nature Portfolio

Advances in riverine ecosystem assessment have demonstrated that spatio-temporal sampling of environmental DNA can resolve animal community dynamics across tens of kilometres and multiple seasons. By combining systematic sampling of rivers in Europe and North America with flow, pH and temperature data, this work quantified beta diversity as driven predominantly by species turnover rather than downstream DNA transport, and detected seasonal life-history events of migratory fish. In parallel, deep sequencing studies have revealed that human genomic fragments are routinely co-captured in eDNA surveys, a phenomenon termed human genetic bycatch. This finding highlights both new possibilities for environmental surveillance and the need for ethical frameworks to address privacy, consent and data ownership in large-scale eDNA projects.

Environmental DNA Metabarcoding for Biodiversity Assessment publication trend

The graph below shows the total number of articles in environmental dna metabarcoding for biodiversity assessment across all publications each year (not limited to Nature Index journals).

Technical terms

environmental DNA (eDNA): Genetic material released by organisms into environmental substrates such as water, soil or air.

metabarcoding: Simultaneous amplification and sequencing of a standardised genetic marker from mixed DNA samples to identify multiple taxa.

high-throughput sequencing (HTS): Automated platforms that generate millions of DNA sequence reads in parallel.

beta diversity: A measure of species composition change between spatial or temporal samples.

primer bias: Differential amplification efficiency of DNA sequences due to mismatches between primers and target regions.

spatio-temporal resolution: The scale and frequency at which biodiversity data are sampled and resolved in space and time.

human genetic bycatch: Unintended recovery of human DNA sequences during eDNA metabarcoding surveys.

References

1. What determines plant species diversity along the Modern Silk Road in the east?. iMeta (2023).
2. An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding. Nature Communications (2024).
3. Pest Alert Tool-a web-based application for flagging species of concern in metabarcoding datasets.. Nucleic Acids Research (2023).
4. Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA. Nature Ecology & Evolution (2023).
5. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology (2017).