A powerful tool for studying ecosystem biodiversity

NGS offers the ability to analyze complex environmental DNA samples

Environmental DNA Sequencing

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.

An Effective Biomonitoring Tool

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.

Alt Name
eDNA Metabarcoding

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

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
16S and ITS Metagenomics

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

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.

Featured Environmental DNA Sequencing Research

eDNA Sequencing
eDNA Sequencing Offers a Powerful View of Biodiversity

Professor Michael Bunce uses next-generation sequencing and eDNA metabarcoding to study ecosystem biodiversity. Learn why he thinks environmental DNA could develop into one of the most powerful biomonitoring tools in the future.

Read Interview
Driving Insights Through Microbiome Profiling
Driving Insights Through Microbiome Profiling

This metagenomic shotgun sequencing workflow, co-developed by Illumina and PerkinElmer, enables accurate DNA detection from soil.

Read Article
Earth BioGenome Project
Earth BioGenome Project Builds Foundation to Sequence Life

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
  • Organisms shed DNA at different rates, which can affect measurements of relative abundance in environmental samples.
  • Environmental DNA can become degraded due to temperature and other factors.
  • The availability of species-specific DNA barcodes depends on the quality of existing databases.
  • Certain environmental DNA sampling, extraction, and storage methods are more prone to contamination than others.
  • DNA extraction methods should be optimized for the sample type and species of interest, to ensure detection of species present in low abundance
  • Strategic assay design is key to achieve selective enrichment for specific targets and avoid cross-reaction between species.
Sailing the Seven Seas for an Epic Plankton Study

The Tara Oceans Expedition united a group of researchers as they collected and analyzed hundreds of oceanic samples.

Read Interview
Dual-PCR Method for CO1 eDNA Metabarcoding

This protocol details the preparation of libraries for amplicon-based metabarcoding using mitochondrial cytochrome oxidase 1 (CO1).

View Protocol
Long-Range PCR for Mitochondrial Sequencing

The authors of this study designed a primer pair for amplifying and sequencing mitochondrial genomes from environmental DNA.

View Publication
ITS Illumina Amplicon Protocol

This ITS protocol is designed to amplify fungal microbial eukaryotic lineages for sequencing on Illumina platforms.

View Protocol
16S Metagenomic Sequencing Library Preparation

This Illumina-demonstrated protocol contains instructions for library prep and an example 16S metagenomics data set.

View Protocol
18S Illumina Amplicon Protocol

This protocol describes primers targeting the 18S SSR rRNA, which are designed to be used with Illumina sequencing platforms.

View Protocol
Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers

This study describes the design and evaluation of 18S rRNA gene primers for studying eukaryotic microbial communities.

View Publication
MiSeq System

The MiSeq benchtop sequencer enables targeted and microbial genome applications, with high-quality sequencing, simple data analysis, and cloud storage.

View Product
MiSeq Reagent Kits v2

MiSeq sequencing reagents in pre-filled, ready-to-use cartridges. Micro and nano formats are available for low output applications.

View product
MiSeq Reagent Kit v3

Optimized chemistry to increase cluster density and read length, and improve sequencing quality scores, compared to earlier MiSeq reagent kit versions.

View Product
Target Enrichment
Target Enrichment

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
Environmental Metagenomics
Environmental Metagenomics

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
Sequencing Services
Sequencing Services

Propel-certified labs provide demonstrated proficiency with Illumina NGS technology. They offer a variety of sequencing services.

Find a service provider
Plant and Animal Sequencing
Plant and Animal Sequencing

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