Unlocking biodiversity with e-DNA metabarcoding

Biodiversity is described by the variety of life on Earth. It is essential for maintaining healthy ecosystems. It provides food, clean water, air, and natural resources while ensuring ecosystem stability. However, we know that biodiversity is under threat due to climate change, pollution, and habitat destruction, leading to rapid species extinction.

Understanding biodiversity is the first step in protecting it. Traditional monitoring methods, such as physically tracking species, are costly and labor-intensive. Fortunately, e-DNA metabarcoding is revolutionizing biodiversity research by enabling scientists to detect species without direct observation. This blog explores how e-DNA metabarcoding works and its role in biodiversity conservation.

Environmental DNA (e-DNA) refers to genetic material that organisms shed into their surroundings through skin, hair, waste, or saliva. This DNA can be collected from soil, water, or air, providing a non-invasive method for detecting species. For example, a water sample from a river may contain traces of DNA from fish, amphibians, or plants, offering insights into ecosystem composition without the need for direct interaction with organisms.

How metabarcoding works

Metabarcoding is a technique that enables scientists to identify multiple species from a single environmental sample. The process involves collecting a sample, extracting DNA, amplifying specific genetic regions using Polymerase Chain Reaction (PCR), sequencing the DNA, and comparing results to existing genetic databases. This approach allows for rapid and accurate biodiversity assessment, making it an efficient alternative to traditional monitoring.

My research focuses on analyzing environmental DNA (e-DNA) from coniferous plant samples to investigate arthropod and fungal diversity within forest and peatland ecosystems. By utilizing genetic material preserved on samples, I aim to study species that might otherwise remain undetected through traditional monitoring methods. This approach allows for a comprehensive understanding of biodiversity in these habitats, capturing both common and rare taxa that interact with the needle surfaces.

A key aspect of my study involves working with an invaluable archive of pine needle samples preserved under dry-frozen conditions for the last 40 years. These samples provide a unique opportunity to examine long-term changes in arthropod and fungal diversity across both spatial and temporal scales. By applying modern DNA sequencing techniques to these historical specimens, I can reconstruct past community compositions and compare them to present-day biodiversity patterns.

The primary research questions I am addressing includes understanding How has the diversity of arthropods and fungi associated with the habitats have changed over the past four decades? and What spatial and temporal patterns of biodiversity shifts can be observed across different forest and peatland regions?

This study is of critical importance for biodiversity conservation. By understanding long-term changes in species composition and diversity, we can identify trends that may be linked to climate change, habitat degradation, pollution, or other ecological pressures. Additionally, recognizing shifts in fungal and arthropod communities is crucial, as these organisms act as bioindicators, providing insight into ecosystem health and stability. The insights gained from this research will help inform conservation strategies, ensuring that forest and peatland ecosystems remain resilient against future environmental challenges. Ultimately, this work contributes to the broader goal of preserving biodiversity and maintaining ecological balance in these vital habitats.

Advantages and challenges of e-DNA metabarcoding

e-DNA metabarcoding offers several advantages: it is non-invasive, cost-effective, and capable of detecting elusive species. It provides a broader picture of biodiversity and enables long-term monitoring to track ecosystem changes. However, the technique also faces challenges, including potential contamination, DNA degradation over time, and gaps in reference databases. Differences in lab methodologies can also affect the consistency of results.

Despite its challenges, e-DNA metabarcoding is transforming biodiversity monitoring. By enabling early detection of endangered species and ecosystem shifts, it supports more effective conservation strategies. As threats to biodiversity continue to rise, investing in this technology can help safeguard the planet’s rich biological diversity for future generations.

Biodiversity is not just an abstract concept—it is the foundation of life. With advanced tools like e-DNA metabarcoding, we can take significant steps toward protecting and preserving the world’s ecosystems.

Acknowledgement:

I would like to thank my Supervisor Dr. Stefan Prost and Co-Supervisors Marko Mutanen and Aleksi Räsänen for their support. I am also thankful to I4WORLD Doctoral Programme and European Union for Co-funding this project.