Environmental DNA: invasives species under investigation

Imagine that, from a small sample of water from a coastal area, it is possible to know the species existing in this area, even before they are spotted. It is based on this premise that the NIS-DNA project aims to combat and control early species that may become invasive. Avoiding the consequences for Portuguese coastal marine ecosystems is the basic idea at the core of this project, which uses DNA traces present in aquatic environments to discover non-indigenous species.

What if our environment was a large reservoir of DNA? According to the coordinator of the NIS-DNA project, Sofia Duarte, “it is possible to detect this molecule carrying the genetic code of all living beings present in an environment from a simple water sample collection”. This environmental DNA can thus become an inexhaustible source of information to discover more about living species yet to be detected in certain ecosystems. Who doesn’t remember police investigation series, where with a hair left at a crime scene, you can catch a criminal. This is how the Centre for Molecular and Environmental Biology (CBMA), at the University of Minho, uses a simple water sample or a “soup of organisms” to obtain DNA fragments and discover the biodiversity that left traces of its presence in a certain place.

Sofia Duarte, coordinator of the NIS-DNA project, from the Centre for Molecular and Environmental Biology //Diogo Martins

The researcher reveals that this project aims to “propose a protocol for early identification of non-indigenous species of fauna that are not native to the region”. Sofia Duarte adds that she intends to “optimise molecular tools” such as DNA barcoding and DNA Metabarcoding, i.e. tools or techniques that use DNA as a basis for identifying species to achieve the objectives of this project. These technologies used in the project allow the early detection of non-indigenous species, as it is possible to detect them at any stage of their life cycle and when in low densities, allowing to anticipate their growth, dispersal and areas potentially at risk of being invaded.

Sample collected within the NIS-DNA project //Diogo Martins

Traditionally, species classification methods are based on the morphological identification of organisms, based on their physical characteristics, the study of their shape and structure.

However, this approach may have limitations, such as the fact that this technique requires specialised knowledge and in some cases identification is difficult or even impossible. Furthermore, sometimes, in the case of very small living things (such as invertebrates), it is a challenge to find them in the ecosystem where they live and even to identify them.

Therefore, molecular tools can fill in the gaps of traditional classification and become an “inexhaustible” source of information about the respective species of each environment and, consequently, about the non-native and potentially harmful species to this same environment. 

Thus, the researcher reveals the importance of the innovative use of molecular tools, such as DNA barcoding and DNA Metabarcoding, for the preservation of the balance of Portuguese coastal ecosystems. Sofia explains that this technique “requires the extraction of DNA from organisms present in the places under study or else present in environmental samples, such as water, and, from this DNA collected, short sequences of standardised regions in the organisms’ genome are used for their identification”. The analysis of these sequences leads to the creation of genetic barcodes, in the case of DNA barcoding of a single species, and in the case of DNA Metabarcoding, of all species present in the sample. Subsequently, these unknown DNA samples are associated with species that have been previously registered in a reference gene library. The project coordinator points out the purpose of preventing and combating “the growing problem that non-indigenous species can bring, since by the time an invasive species is already established, it is very difficult to eradicate it”, which highlights the importance of this project.

Electrophoresis source, the device that confirms if the amplification of DNA was successful // Diogo Martins

Coastal regions are areas of great socio-economic importance for our country and non-indigenous species represent a threat to the sustainable and economic development of these regions, thus motivating the prevention of this problem.

In addition, the researcher explains that “Invasive species can be especially impactful in aquaculture areas”, exemplifying with the case of bivalve aquacultures in Ria Formosa, which were affected by invasive species, such as bryozoans and tunicates, which can translate into heavy losses for these cultures.

The Portuguese Institute of the Sea and Atmosphere, in the Marine Strategy Framework Directive [1] of 2018, states that until that date were referenced about 12,000 non-indigenous species, in marine and transitional environments, from the European Union and other European countries, and that of these, about 10 to 15% are considered invasive, translating, according to previous studies, ecological and economic impacts of invasive species, amounted to almost 5% of the world economy.

Nevertheless, these techniques are not infallible and, as such, they have limitations. For example, in the case of environmental DNA analyses, the persistence time of DNA in the environment can vary according to species (larger species in principle release more DNA) and according to environmental conditions (pH and temperature). In addition, DNA from species that are only found in certain locations can be carried by water currents, manipulating the results. In some species, DNA presents difficulties in being amplified, resulting in a greater difficulty in sequencing and, therefore, identification of these species [2]. And as the identification of the species relies on the data that are available in the reference gene libraries, their degree of fulfilment will affect the amount of identified species as they need to already have reference DNA sequences in these libraries. However, the project coordinated by Sofia Duarte, aims to optimize these methodologies and tools, leading the NIS-DNA project to its goal in the difficult and exhaustive world of combating invasive species.


[1] Diretiva-Quadro “Estratégia Marinha – Descritor 2 – Espécies não indígenas, Instituto Português do Mar e da Atmosfera, I.P – https://www.dgrm.mm.gov.pt/documents/20143/43971/IPMA_DQEM_2018_D2_FINAL_CP_22082019.pdf/110e6412-799a-0da5-d8a6-195565c6f72f

[2] Actes de la journée ADN Environnemental – Tristan LEFEBURE, Université Lyon 1 – Barcoding, Métabarcoding : petite entrée en matière – http://www.graie.org/zabr/zabrdoc/Actes_Adne_web.pdf

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