Ecology And Biodiversity: Environmental DNA

Environmental DNA is known as DNA (nuclear, mitochondrial, chloroplast) that can be extracted from environmental samples without the prior isolation of any target organism. This DNA is usually released into the environment through organic waste such as feces, urine, gametes, mucus, perspiration, decomposition, and so on.

The objective of sequencing all the DNA present in an environmental sample is to study biodiversity and monitor the presence and / or changes in species without altering an ecosystem.

The environmental metagenomic is the study of the organisms present in a microbial community based on the analysis of DNA within an environmental sample.

Among the genomic methods for the study of environmental DNA are the following:

  • eDNA Metabarcoding

Each organism has a unique DNA sequence (barcode) associated with it that is used to identify a species. Often, it is usually the mitochondrial cytochrome oxidase 1 (CO1) gene or the 18S ribosomal subunit.

In the classic barcoding , the specific amplification of these barcodes is carried out for an objective species, so that its focus is directed detection, while in the metabarcoding the amplification and sequencing with universal primers allows detecting and identifying diverse communities, so which is a multi-species trial from a single sample.

  • Microbiomes and mycobiomas (16 S & ITS)

Sequencing is focused on a specific genomic locus using a pair of primers.

Microbiome: For prokaryotes, hypervariable regions (V1-9) in the 16S rRNA gene are analyzed

Mycobioma: For fungi, the ITS1 / ITS2 regions of the rRNA are used for the taxonomic profile.

  • Metagenomic shotgun

The DNA is extracted from all the cells present in a community and then crushed into smaller fragments that are sequenced individually. The sequences of these fragments are reassembled in their original order, based on overlapping zones, which ultimately produces complete sequences and the microbial composition of a diverse sample.

  • Long-range PCR

It is used to amplify long DNA sequences, such as mitochondrial genomes. These longer DNA sequences can help distinguish between species when smaller DNA barcodes have not been available. This approach is favorable for sequencing DNA that has not been degraded by the environment.

Starting samples


I usually



Decomposition material



Feathers, hair

Stool, urine


Biodiversity Study

Species monitoring

Migration patterns

Port monitoring

Impact of mining areas

Water analysis

Soil testing

Study of symbiotic organisms

Ecological remediation

Fig. The sequencing of eDNA is a powerful tool for understanding biodiversity. Available at: Overview of Environmental Metagenomics

Due to the high sensitivity of Illumina sequencing to detect eDNA present at low levels in the environment, it is possible to analyze trace amounts of DNA per species in a given sample, without knowing the types or abundance of species represented. Therefore, it becomes viable to profile thousands of species simultaneously from a single sample .

We invite you to read the Microbiology blog : The Scope of Sequencing to get into microbial genomics. In addition, you can request for free our infographic Sequencing shotgun and 16S / ITS , in which you can know the workflows of both methods.

by Abdullah Sam
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