Environmental DNA is:

“… DNA that is collected from a variety of environmental samples such as soil, seawater, snow or even air [1] rather than directly sampled from an individual organism. As various organisms interact with the environment, DNA is expelled and accumulates in their surroundings. Example sources of eDNA include, but are not limited to, faeces, mucus, gametes, shed skin, carcasses and hair.[2] Such samples can be analysed by high-throughput DNA sequencing methods, known as metagenomics or metabarcoding, and can provide a rapid measurement and monitoring of biodiversity.

How DNA is used to make identifications

Virtually all species have unique DNA sequences at a number of “DNA Barcode” genes. To identify the species represented in an eDNA sample a search for matches is made between the DNA barcode sequences found in the samples and in a reference library of DNA sequences from known species (e.g. GenBank, BOLD).

What are some advantages of eDNA?

The analysis of eDNA has great potential not only for monitoring common species, but to detect and identify other significant species.[5] The method allows for biomonitoring without requiring collection of the living organism, creating the ability to study organisms that are invasive, elusive, or endangered without introducing anthropogenic stress on the organism. Samples (e.g. water, soil) can also be collected by non-experts. Access to this genetic information can make a critical contribution to the understanding of species distributions and community dynamics, especially for poorly documented species.

How long does eDNA last?

The length of time that eDNA remains viable depends on its exposure to chemical, physical and biological stressors. In some cases (e.g. permafrost) eDNA can last millennia, but more commonly its likely to represent organisms present within hours or days.

What kind of environments can eDNA be collected from?

Because of its versatility, eDNA is applied in many subenvironments such as freshwater sampling, seawater sampling, terrestrial soil sampling (tundra permafrost), aquatic soil sampling (river, lake, pond, and ocean sediment),[7] or other environments where normal sampling procedures can become problematic.[6]

[Source: https://en.wikipedia.org/wiki/Environmental_DNA; accessed and modified 12/04/2019]


Why eDNA is being recognised as a biological record in the ALA

It’s widely recognised that eDNA analysis can characterise biological diversity accurately and in great detail (Stat et al. 2017; Berry et al. 2019). Because of the high cost of conventional biodiversity surveys, the decreasing cost of DNA sequencing technologies, and advancements in eDNA practices, it is likely that eDNA will increasingly become part of biological survey toolkits, complementing conventional methods such as observation, trapping, and microscopy. Records from eDNA surveys will be a growing source of biodiversity information used to support environmental decision making. Presenting these records on the ALA is an opportunity to maximise their accessibility and use.

How to interpret eDNA records

eDNA records on the ALA indicate that a particular taxon was identified in an environmental sample collected from a specific location at a specific time. Each record is accompanied by information detailing the methods used to make the identification, or links to that information. This includes the sampling methods, the laboratory procedures, the bioinformatics workflow, the repository where the raw DNA sequences can be found, and the scientific manuscript that reports the results.

Accuracy of eDNA identifications

Studies comparing DNA barcoding to species identification by conventional means demonstrate that it is usually highly accurate (Sheffield et al. 2009; Pereira et al. 2013). Yet, like conventional methods, it has limitations. Prominent among these is that taxonomic assignment relies on those taxa being represented on DNA reference databases.  Where they are not, typical eDNA workflows will assign identities at higher taxonomic levels (genus, family, order etc, see  Huson et al. 2007).

Some taxonomic groups (e.g. Australian marine fishes) are very well characterised, whereas others (e.g. Australian crustaceans) are less well characterised (and comprise many species). The consequence of this is that fishes will more often be assigned to species level identity than crustaceans (e.g. Berry et al. 2015). Because of this eDNA identifications should be interpreted as representing the most accurate identification possible at the time based on available DNA reference sequences. Note that accuracy of identifications through eDNA analysis and DNA barcoding will continue to increase as reference libraries improve.

Multi-marker duplicates

Typically eDNA investigations will combine more than one DNA barcode in the survey toolkit to maximise the number of taxonomic groups targeted. For example, 16S rRNA often targets mammals, trnL for plants, ITS for fungi, etc. Because such markers can still pick up non-target taxa it’s possible that multiple records for the same taxonomic group may be detected from a single environmental sample.  This situation is analogous to a single observer recording the same species more than once at one place and time. In effect, such records are duplicates.

Submitting eDNA data

We encourage you to submit taxon records derived from environmental DNA analysis to the ALA.  Records must be submitted via spreadsheet in a prescribed format. We offer a basic format, as well as a more comprehensive format based on the internationally recognised MIMARKS system, which allows inclusion of detailed contextual environmental information.

DNA sequences

Please note that although the ALA uses DNA barcode sequences as unique identifiers, it’s not the intention that the ALA provide a repository for complete eDNA sequence datasets. These can be obtained from the links accompanying each record.  


Literature Cited

Berry O, Bulman C, Bunce M, Coghlan M, Murray DC, Ward RD (2015) Comparison of morphological and DNA metabarcoding analyses of diets in exploited marine fishes. Marine Ecology Progress Series 540: 167-181

Berry TE, Saunders BJ, Coghlan ML, Stat M, Jarman S, Richardson AJ, Davies CH, Berry O, Harvey ES, Bunce M (2019) Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events. PLOS Genetics 15: e1007943 doi 10.1371/journal.pgen.1007943

Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome research 17: 377-386

Pereira LH, Hanner R, Foresti F, Oliveira C (2013) Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? BMC Genetics 14: 20 doi 10.1186/1471-2156-14-20

Sheffield CS, Hebert PDN, Kevan PG, Packer L (2009) DNA barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studies. Molecular Ecology Resources 9: 196-207 doi 10.1111/j.1755-0998.2009.02645.x

Stat M, Huggett MJ, Bernasconi R, DiBattista JD, Berry TE, Newman SJ, Harvey ES, Bunce M (2017) Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment. Scientific Reports 7: 12240