Environmental DNA (eDNA) sequencing is a rapidly emerging method for studying biodiversity and monitoring ecosystem changes. As organisms shed DNA into their environments, eDNA analysis can provide clues about the species present without disrupting the ecosystem. Potential applications of eDNA include port monitoring, biodiversity surveys, ballast water testing, soil testing, and more.
Modern environmental DNA sequencing approaches allow characterization of both bacterial and eukaryotic species in aquatic, soil, and other samples. In the future, eDNA sequencing promises to be a vital tool for biomonitoring and conservation.
Scientists studying environmental DNA often analyze trace amounts of DNA per species in a given sample, without knowing the types or abundance of species represented. With next-generation sequencing (NGS), you can profile thousands of species simultaneously from a single sample. NGS also offers the sensitivity needed to detect eDNA present at low levels in the environment.
In contrast, physical surveys of natural environments require manual data collection and can be disruptive. Traditional DNA methods, such as bacterial cloning and Sanger sequencing, provide only a limited snapshot of a given sample. These approaches can be time-consuming and costly, and are not effective for processing large or complex samples.
“I think that eDNA could develop into one of the most powerful biomonitoring tools and become even more useful as the field matures.”
For some sample types, using a combination of environmental DNA sequencing approaches can help uncover the full breadth of diversity in an ecological sample.
Every organism has a unique DNA sequence, or barcode, associated with it. This DNA barcode is a highly variable region interspersed between conserved genomic regions. eDNA metabarcoding involves target-specific amplification and sequencing of these barcodes, often mitochondrial cytochrome oxidase 1 (CO1) or the 18S ribosomal subunit. These are useful approaches for distinguishing between higher-order eukaryotes.
Shotgun sequencing of environmental DNA is a suitable approach for studying species that are likely abundant in the sample, such as bacteria or small eukaryotes.Learn More
Environmental metagenomics has typically relied on sequencing the 16S or internal transcribed spacer (ITS) rRNA genes for detecting bacteria or fungi, respectively. Both 16S and ITS rRNA gene sequencing are well-established methods for comparing sample phylogeny and taxonomy from environmental samples.Learn More
Long-range PCR can be used to amplify large DNA sequences, such as mitochondrial genomes. These longer DNA sequences can help distinguish between species when smaller DNA barcodes are not available. This approach is favorable for sequencing DNA that has not been degraded by the environment.
Michael Bunce uses next-generation sequencing and eDNA metabarcoding to study ecosystem biodiversity.Read Interview
Professor Bunce takes us on an environmental DNA excursion as he explores the many facets of eDNA in the ocean.Read Article
The project aims to create a digital backbone of sequences from the tree of life that will serve as critical infrastructure for biology, conservation, agriculture, medicine, and the growing global bioeconomy.Read Article
These publicly available protocols support a variety of environmental DNA analysis methods, from 16S metagenomics to eDNA metabarcoding.
This protocol details the preparation of libraries for amplicon-based metabarcoding using mitochondrial cytochrome oxidase 1 (CO1).View Protocol
The authors of this study designed a primer pair for amplifying and sequencing mitochondrial genomes from environmental DNA.View Publication
This ITS protocol is designed to amplify fungal microbial eukaryotic lineages for sequencing on Illumina platforms.View Protocol
This Illumina-demonstrated protocol contains instructions for library prep and an example 16S metagenomics data set.View Protocol
This protocol describes primers targeting the 18S SSR rRNA, which are designed to be used with Illumina sequencing platforms.View Protocol
This study describes the design and evaluation of 18S rRNA gene primers for studying eukaryotic microbial communities.View Publication
Target enrichment captures genomic regions of interest by hybridization to target-specific biotinylated probes, which are then isolated by magnetic pulldown.Learn more about target enrichment
With NGS, environmental researchers can profile entire microbial communities from complex samples, discover new organisms, and explore microbial populations under changing conditions.Learn more about environmental metagenomics
Propel-certified labs provide demonstrated proficiency with Illumina NGS technology. They offer a variety of sequencing services.Find a service provider
NGS technology can be used for soil and agricultural metagenomics, targeted resequencing, and other plant and animal sequencing applications.Learn more about plant and animal sequencing