Environmental DNA

What is environmental DNA?

The term ‘environmental DNA’ (eDNA) refers to the free DNA released by all living organisms into their environment. Monitoring using eDNA in bodies of water is a minimally invasive method, as it does not require the target organisms to be caught or removed from the water. The premise of this method is that every organism releases DNA into its environment through cell abrasion, excreta or secretion of DNA.

To illustrate this point, consider that a fish of 30-75g (for example, a small perch) releases more than 10⁷ copies of DNA per hour into the surrounding water. However, it is important to note that DNA is also subject to permanent degradation by various environmental influences.Indeed, the eDNA half-life was calculated to be around 6 hours, which indicates that more than 90% of eDNA copies will have degraded within 24 hours (Maruyama, 2014). Furthermore, DNA fragments measuring up to 300-400bp remain identifiable within the water for a period of only 1-2 weeks following the species’ removal (Dejean, 2011).The quantity of eDNA in the water undergoes a rapid decrease, meaning that a species can only be detected in the water if it is currently present or has just been present.

The result of an eDNA analysis is a snapshot. While DNA in nature can endure for extended periods, the detection of free-floating DNA fragments remains contingent on variables such as flow velocity, duration, and the true number of individuals, which can also be influenced by seasonal factors.

StarSEQ offers you a complete service for the analysis of your environmental samples: from DNA isolation to the preparation of metabarcoding or snapshot metagenome libraries or a qPCR to the bioinformatic analysis of the data.

Contact us to discuss your eDNA project:

eDNA@starseq.com

How does an eDNA project work?

StarSEQ can handle various sample types and advise on sampling strategies and methodologies. Please be sure to contact StarSEQ before you start the sampling and discuss the strategies with our experts.

eDNA workflow:

1. The customer is required to submit the sampling filters

• Sufficient eDNA filter systems are to be used; these can be purchased from one of several providers. These filters have a large PES membrane surface area and have been specially optimized for eDNA extraction
• After sampling, a lysis and storage buffer is to replace the water in the filter system. This lysis buffer can be supplied from StarSEQ or alternatively, we provide the customer with the protocol so that he can prepare the lysis buffer himself.
• The DNA can be stored refrigerated until dispatch.
• The closed filter system prevents contamination in the subsequent process.
• Filter can be stored in the freezer until the end of the sampling period
• StarSEQ will prepare the eDNA using our optimized protocols

2. The customer sends us extracted eDNA

• It is also possible to send in ready-made eDNA for analysis.
• Prior to the initiation of the sampling process, it is strongly recommended to contact StarSEQ to discuss the specifics of the project.

3. qPCR or Sequencing

• The choice of qPCR or metabarcoding, or snapshot metagenomic sequencing, depends on the requirements of the specific project.

4. Bioinformatic analysis

• Metabarcoding: The resulting data will be analysed by our experts using our own curated databases.
• Snapshot metagenomic sequencing: Depending on the project’s requirements, StarSEQ bioinformaticians will perform kmer-based analysis of the sequencing data using databases for amphibian, fish, insect, decapoda, mammalia, bacteria, fungi and plant, selected by the customer.
• qPCR: Analysis of qPCR data and species identification
• Report