Environmental DNA: A Promising Tool for Biodiversity Monitoring

An eDNA survey can help determine if artificial and natural barriers, such as waterfalls, are limiting the migration of fish species from the river to the sea. Photo credit: R. Stirnemann.

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Published: 21 August 2023

In Samoa, eDNA survey techniques were used to assess the potential effects of a proposed dam on freshwater ecosystems.


Freshwater ecosystems, including streams, lakes, and rivers, play a vital role in ensuring livelihoods and protecting biodiversity. They are a source of clean water for drinking and irrigation and support human communities, agriculture, and industries, including energy production. They are essential for food production, with fish populations in rivers, lakes, and streams providing sustenance for millions of people worldwide. They play a significant role in nutrient cycling, flood regulation, carbon sequestration, and climate mitigation. They also offer recreational, cultural, and spiritual value for many communities.

These ecosystems are often biodiversity hotspots, especially in Asia and the Pacific, providing habitat for a wide range of species, including migratory, endemic, and endangered ones. They cover only 0.8% of the Earth’s surface yet host approximately 15,000 fish species, corresponding to approximately half of the known fish diversity.

Despite their importance, these ecosystems are under growing pressure. Habitat fragmentation (due to the proliferation of dams and habitat conversion), invasive species, climate change, and untreated pollutants’ discharge have significantly affected a large part of rivers worldwide, leading to a biodiversity crisis of massive magnitude.

In many of the Pacific nations, rivers and streams are critical in ensuring food security and providing a source of fresh water, especially under recent climate emergencies. The remoteness of certain countries and the limited resources available for biodiversity and water management research have resulted in a notable knowledge gap in the abundance, diversity, distribution, and threats to local biodiversity. The potential outcomes are that these countries are losing biodiversity and freshwater resources without even knowing they exist.

Considering the limitations of expertise and the necessity of achieving development goals, some emerging technologies can help to fill this knowledge gap and ensure that the impacts of developments are accurately assessed and potentially avoided. One of these tools is the so-called Environmental DNA[1] (or eDNA) that was used during the preparation of the Alaoa Multipurpose Dam in Samoa. The proposed project will help to attenuate catastrophic river floods, increase the resiliency of the country’s capital water supply, increase renewable energy production capacity, and contribute to biodiversity conservation.

How It Works

In the natural environment, various species release eDNA through their urine, fecal matter, and skin cells, which disperses into the surrounding ecosystems, such as rivers, oceans, soils, and even the air. Rather than directly observing or capturing the species, the utilization of eDNA survey techniques allows for the identification of species within their habitats or environments by collecting water (see Figures 1and 2) or soil samples and conducting genetic material analysis. These survey methods based on eDNA offer greater sensitivity, cost-effectiveness, and environmental preservation compared with conventional species monitoring approaches commonly employed in both developed and developing nations.

Figure 1: eDNA water sampling in a river in Samoa to determine the species present. Photo credit: R. Stirnemann.

Figure 2: An eDNA sample was taken along the river to determine if artificial and natural barriers were limiting the migration of fish species from the river to the sea. Photo credit: R. Stirnemann.

Assessment and management of priority species require reliable information on species occurrences and distribution, and conventional survey techniques can be hindered by habitats that are difficult to access (such as remote rivers) and the rarity or the cryptic nature of some species. eDNA sampling can overcome these limitations. With only a fraction of the search effort of a conventional survey, eDNA can find cryptic species, including those that elude traditional survey methods.

Surveys of eDNA freshwater environments can also be more cost efficient than conventional methods, providing a rapid alternative to intensive fieldwork. As a result, rapid and comprehensive datasets can be developed showing locations of key species of interest. eDNA techniques not only allow for a greater understanding of species distributions in difficult-to-sample habitats but also offer unprecedented information on ecosystem composition because these can provide information on all species present.

Technical Challenges and Future Research

As with any newly developing field, there are still challenges with eDNA sampling. The DNA libraries used to identify species are not yet complete, especially for invertebrates, and therefore there are still limitations on how the process can be applied. The process is also extremely sensitive to the introduction of material from other places. For example, false positives can occur through contamination from clothes or from what the biologists eat for lunch (Figure 3).

Figure 3: Field researchers Moe and Fia take an eDNA sample carefully to avoid contamination of the water. Photo credit: R. Stirnemann.

Some species may be present but not yet detected using eDNA. During the Alaoa dam survey, a fish called Kuhlia (Figure 4) was detected by traditional snorkeling survey methods but not by eDNA despite being abundant in a pool where the sampling took place. This may be an effect of water flow and eDNA stratification since the species hides under rock ledges. It is crucial to acknowledge the nascent nature of eDNA sampling as a method that is currently undergoing refinement and that the efficacy of species detection can be influenced by the specific sampling protocols employed.

Figure 4: Kuhlia salelea (Salele) was detected during the Alaoa survey using traditional snorkeling techniques but not by eDNA. This may be because of eDNA water stratification. Combining traditional and eDNA surveys can be useful for getting a full understanding of what species are present. Photo Credit: R. Stirnemann.

Initially, research on eDNA primarily focused on identifying the presence of species. Nevertheless, there is a growing trend in eDNA studies to examine the quantity of eDNA as an indicator of species abundance. While controlled environment studies have validated these associations for certain fish species, the correlation in natural environments remains somewhat uncertain. Consequently, we still rely on conventional methods to estimate species abundance. However, when both conventional and eDNA techniques are combined, the outcomes become more comprehensive, enhancing our comprehension of species distribution and potential restoration.

The Use of eDNA in the Pacific

Oceanic islands are generally known for their abundant endemic species but with moderate species richness compared to mainland areas. While this poses challenges for understudied regions like countries in the Pacific, where some endemic species may be undocumented in the eDNA global databases, the lower species richness facilitates more efficient data collection campaigns. Identifying and sequencing[2] DNA of specimens can be achieved within a shorter timeframe compared to regions with higher species richness, such as the Mekong River and its remote tributaries in Southeast Asia.

The eDNA sampling for Alaoa included the collection and sequencing of some species that were not present in the genetic libraries (Figure 5), contributing to future monitoring of freshwater biodiversity in Samoa and to the global advancement of eDNA science. Although the costs of conducting initial baseline surveys and campaigns for genetic sequencing may be higher compared with traditional methods, these activities establish a reliable starting point for future monitoring. This approach can ultimately lead to substantial cost savings in the long term, especially for Pacific countries where specific freshwater biodiversity expertise is lacking.

Figure 5: The Stiphodon hydoreibatus species had eDNA sequenced for the first time as part of the Alaoa survey and was added to the DNA reference library. This will enable easier detection in future surveys. Photo Credit: R. Stirnemann.

The potential of using eDNA in developing countries is significant. Due to gaps in biodiversity knowledge, limited expertise and funds, and the urgency of certain developments, decisions that could harm biodiversity may be made without adequately assessing alternatives or monitoring mitigation measures. The Samoa Alaoa Dam example demonstrated that incorporating novel technologies like eDNA enabled the implementation of effective mitigation and offsetting measures. It also established a monitoring protocol (Environmental Management and Monitoring Plan or EMMP) to identify changes in river biodiversity, including accidental release of invasive species (Figure 6) and presence of endangered, endemic, or migratory species. This provides developers with the opportunity to take appropriate actions to reduce or further mitigate biodiversity impacts during construction or implementation of the dam.

Figure 6: The technique can be a useful method for mapping the locations and spread of invasive species, such as Tilapia fish. Image credit: R. Stirnemann

Looking Ahead

The use of eDNA has the potential to revolutionize biodiversity conservation, sustainable development, and climate change response.

eDNA is a non-invasive way to detect the presence of species in the environment, even if they are rare or difficult to observe. It is now under development also for terrestrial ecosystems and sampling soil or even air. This makes it a powerful tool for understanding species distribution, monitoring ecosystem health, and detecting invasive species.

The Pacific region, in particular, is home to several endangered and endemic species, making it an important area for eDNA application. eDNA monitoring can help to bridge knowledge gaps about these species and inform conservation efforts. It can also help to protect the cultural and economic value of these species for local and indigenous communities.

[1] The DNA, which stands for deoxyribonucleic acid, is a molecule that contains the instructions for building and maintaining living organisms. It is made up of four chemical "letters" or nucleotides (A, T, C, G) that form a unique code for each individual.

[2] Genetic sequencing determines the unique order of nucleotides in the DNA or RNA of an organism. This sequence serves as a distinct genetic fingerprint, differentiating each species.


Francesco Ricciardi
Senior Environment Specialist, Office of Safeguards, Asian Development Bank

Prior to joining ADB, Francesco worked for about 10 years as a researcher focusing on the impact of environmental contamination on natural ecosystems and wildlife. After leaving academia, he worked as an environment and ecology consultant in several projects around Asia, including renewable energy plants, large coastal infrastructures, and natural resources development and protection. He is a passionate underwater and wildlife photographer. Some of his photos have been published in international magazines and papers.

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Rebecca Stirnemann
Consultant, Asian Development Bank

Rebecca is an interdisciplinary scientist and consultant focused on environmental management and conservation action. She has worked around the world on marine, aquatic, and terrestrial projects. A key part of her work is to help groups implement successful on-the-ground environmental projects. To do this, she draws on extensive field and community-based experience.

Asian Development Bank (ADB)

The Asian Development Bank is committed to achieving a prosperous, inclusive, resilient, and sustainable Asia and the Pacific, while sustaining its efforts to eradicate extreme poverty. Established in 1966, it is owned by 68 members—49 from the region. Its main instruments for helping its developing member countries are policy dialogue, loans, equity investments, guarantees, grants, and technical assistance.

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