Exploring Biodiversity with Environmental DNA Monitoring
Understanding and monitoring biodiversity is vital for effective ecosystem restoration, conservation and sustainable management. However, traditional methods of biodiversity monitoring often rely on direct observation or invasive sampling, which can be time-consuming, labor-intensive, and disruptive to natural habitats. A new technique called Environmental DNA (eDNA) has emerged as an efficient method for studying and monitoring biodiversity. Camilla Werl, our mangrove project development manager, explains the basics of eDNA and how Vlinder utilizes it in its mangrove reforestation projects.
Introduction to Environmental DNA
Environmental DNA, or eDNA, is a technique used to study and monitor biodiversity in various ecosystems. Unlike traditional methods that involve sampling individual organisms directly, eDNA collects genetic material from the environment, such as soil, water, or air. This non-invasive approach provides an efficient method for detecting and analyzing the presence of species in their natural habitats.
Organisms constantly interact with their surroundings, leaving traces of their genetic material in the form of DNA fragments. These fragments can originate from various sources like shed skin cells, hair, mucus, feces, or other biological excretions. Through careful sampling and extraction, eDNA allows scientists to capture and analyze this genetic material to identify the organisms present in an ecosystem.
The process of eDNA collection typically involves taking environmental samples, such as water or soil, from targeted locations. In the case of Vlinder’s mangrove reforestation projects, only water samples are collected. These samples are often obtained by filtering large volumes of water, enabling the capture of DNA fragments present in the water on filter membranes. The samples are then carefully preserved in sealed bags, properly labeled, and stored in cool, dark conditions to maintain the integrity of the DNA until further analysis.
The analysis of collected eDNA samples is typically outsourced to specialized laboratories and solution providers. These entities employ advanced techniques like polymerase chain reaction (PCR) and metabarcoding. PCR amplifies specific DNA regions, generating millions of copies of the targeted DNA fragments in a rapid manner. On the other hand, metabarcoding utilizes DNA barcoding and universal genetic markers to simultaneously identify the DNA sequences of multiple species present in a sample. By comparing these DNA sequences to comprehensive genetic databases, scientists can accurately identify the organisms that have left their genetic signatures in the sampled environment.
One notable advantage of eDNA monitoring is its cost-effectiveness compared to traditional biodiversity monitoring methods. It allows researchers to survey a wide range of species simultaneously, without the need for direct observation or invasive sampling of individual organisms.
Establishing a sampling procedure
When setting up a sampling procedure, several parameters need to be considered. Vlinder focused on the following factors when choosing a company for eDNA monitoring:
- Costs per kit
- Cost for laboratory work (the pricing for laboratory work may vary depending on the desired taxonomic resolution for accurate species identification)
- Shipping expenses
- Water sampling capacity, which depends on the filters and devices used
- Determining the number of samples required to obtain reliable results, which can be linked to permanent monitoring plots
Additionally, when selecting an eDNA solution provider, it is important to inquire about their database access and the experience they have in studying specific ecosystems (in our case — mangrove forests) and the selected country. A comprehensive and reliable database is crucial for accurate species identification, and expertise in specific ecosystems and countries enhances the reliability and applicability of the eDNA results obtained.
Performing eDNA tests for Papariko, Vlinder’s mangrove reforestation project in Kenya
Based on Vlinder’s experience in Kenya, it is recommended to seek detailed explanations of the sampling procedure and conduct trial sampling. We encountered some challenges during the initial sampling.
For instance, sampling clear water is more efficient as it allows for the filtration of larger volumes through a single filter. In cases where the water is muddy, it is advisable to let it settle in a bucket before pumping it through the filters.
The drying process is critical and should be discussed in detail with the company and the sampling personnel. While most companies provide the necessary equipment, collaboration with the company and sharing a video for double-checking is suggested, especially when selecting pumps for sampling.
Shipping can be challenging, including customs-related issues. To ensure smoother customs clearance, it is advisable to make necessary arrangements in advance.
We would like to thank the Papariko project leader Isabella Masinde for her assistance with doing eDNA tests in Kenya.
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In conclusion, environmental DNA offers a non-invasive and cost-effective approach to biodiversity monitoring by collecting genetic material from various environmental sources. Based on Vlinder’s experience in Kenya, seeking detailed explanations, conducting trial sampling, and considering the provider’s expertise in specific ecosystems and the selected country can enhance the success and reliability of eDNA monitoring. With its ability to provide valuable insights into species presence and distribution, eDNA holds great potential for advancing our understanding and conservation of ecosystems.
