Environmental DNA, a giant leap forward in biodiversity assessment

Posted on
18 March 2021

It is perhaps the fundamental drive in human behaviour which we call curiosity that makes us distinct from fellow inhabitants of the earth. Although animal species are curious by nature, human beings seem to be more curious and inquisitive comparatively. Human history, starting from cave dwellers to hunter gatherers and crop cultivators to pastoralists, and later civilizations that chronicle our past is not without this fundamental character that has influenced and shaped our environment and the world at large. It is curiosity that fuels human mind and intellect in pursuit of knowledge. In modern sense, it is the reason for advancement of science and technology that has transformed our way of life.   

Historically, Ancient Greece is considered as the cradle of western philosophy, art, science and mathematics. The philosophical genius of Socrates laid the foundation of Western Philosophy. Pythagoras’s mathematical finding, well-known known as Pythagorean Theorem, defined the fundamental relationship among the three sides of a right angled triangle. In natural science, Aristotle is credited to have made extensive contribution to the development of biology, the science that studies living organisms. His pupil Theophrastus made the first attempt to classify plants by arranging them into groups. He is often considered the father of botany for his work on plants. It was Carl Linnaeus who later established the hierarchical structure of plant classification based on observable characteristics.  His “Species Plantarum” published in 1753 is internationally accepted as the starting point of modern botanical nomenclature. Preceding the classification system based on morphological characters, the study of organic evolution gave rise to phylogenetic system of classification which is based on evolutionary relationship between different groups. Systematics, the study of naming and classifying organisms has developed manifold since then. From morphological systematics to molecular systematics, from phylogenetic classification to DNA sequencing, the technique of studying biological diversity and evolutionary relationships has advanced dramatically. 

Biodiversity assessment in terms of species richness and relative abundance is commonly used to assess the health of ecosystems. A healthy ecosystem has adequate predators, prey, producers and decomposers that keep the ecosystem alive and stable. The right level of biodiversity in an ecosystem enables it to stay healthy and more resilient to external stress like climate change. Biodiversity is considered as an indicator of ecological well-being. Areas with high biodiversity are detrimental for establishing conservation priorities. 

Traditional biodiversity surveys rely on field surveys and identification of species which require specific expertise. Subject specialists are often scattered between different disciplines such as taxonomy, ecology and biogeography to name a few. This has limited wide coverage of biodiversity in environmental decision-making.  Besides, specimen collection is necessary to determine species identity in some cases and this often give rise to ethical concerns. Survey methodologies are variable, often requiring extensive fieldwork and are not devoid of limitations. For instance, a rapid field assessment could give a quick snapshot of biodiversity information of a particular area but would lack ecological analysis for long term conservation perspective. Plot-based random sampling methods appear unbiased and logical, but could miss certain rare species that fall outside the sampling plots. The vastness of biological diversity is awesome to perceive but at the same time challenging to attempt complete enumeration. Perhaps it is for this reason that ecologists and conservation biologists use indicator species to study environmental changes or assess ecosystem health. How indicator species are selected and how reliable are they is a subject for another discussion. 

Environmental DNA (eDNA) research is a growing field of study that could perhaps ease the cumbersome biodiversity survey techniques and prove more efficient both in terms of time and resource. The idea is based on the fact that organisms leave traces of DNA in the blood, waste products, skin or hair in the environment. Environmental DNA can be defined as the genetic material left behind in environmental samples like soil, water, sediments and saltlicks which is not obtained directly from the host. 

Environmental DNA approach is a method of assessing biodiversity using environmental samples from which DNA is extracted and studied using DNA sequencing technique to determine species presence. It is a combination of traditional approach, molecular methods and advanced computational tools. The method used is DNA barcoding and enables species identification using short section of DNA from a specific gene or genes and comparing it with reference library of such DNA sections. An individual DNA sequence can be used to identify an organism to the species level. The principle of operation is similar to supermarket scanners reading Universal Product Code (UPC) barcode labels to identify an item in its stock against its reference database.  Environmental DNA barcoding methods have expanded to enable assessment of whole communities from a single sample through a process called metabarcoding.  Environmental DNA metabarcoding has recently emerged as a non-destructive alternative to traditional sampling for characterizing species assemblages. 

There are several reports of scientific studies using environmental DNA metabarcoding. An interesting aspect of this approach is the ability to identify the diet of carnivorous invertebrates using feces or stomach contents.  A study published in 2013 (Boyer et al., 2013) used metabarcoding of feces to analyze the diet of a carnivorous and critically endangered land snail, uncovering that the snails mostly fed on earthworms that either live in the leaf litter or come to the surface to consume leaf litter at night, suggesting that the snail will eat any earthworm it comes across in the leaf litter. Such knowledge is valuable in making conservation decisions without having to disturb the organisms in their natural environment. Another interesting publication is on the use of environmental DNA to study quantitative patterns of fish biodiversity in large rivers (Pont, D., et al., 2018). Using environmental DNA metabarcoding approach, they sampled 500 km of a major European river (Rhône River) and demonstrated the ability of the technique to qualitatively and quantitatively uncover relative species abundance in a larger space. 
Environmental DNA barcoding approach has a wider application beyond biodiversity assessment. From human health perspective, air quality monitoring by detecting airborne microbes could be useful in determining the presence of disease-causing germs in the air, and help administer appropriate safety or control measures. Fresh water monitoring for invasive aquatic invertebrates and other harmful microbes is another important aspect of environmental DNA barcoding technique. The scope of environment DNA barcoding approach is seemingly limitless, but for all to be detected reference databases would need to be established to include identifiable sequences for all target biodiversity, and advanced facilities will need to be created to house the growing data libraries.
One of the recent developments in environmental DNA studies is the emergence of global biodiversity monitoring network using environmental DNA. Project VigiLife was initiated in 2011 by SpyGen, a French biotechnology company specializing in molecular ecology with the objective of building a worldwide network for monitoring global biodiversity, with the long-term monitoring of thousands of sites around the world. An interesting side of this initiative is the development of a mobile laboratory meeting the highest standards of quality, performance and microbiological safety in the field, with the assembly of equipment in a container. This establishment would enable onsite environmental DNA sampling and analysis saving considerable amount of time and resources spent in transporting samples to laboratories thousands of miles away, let alone time taken for the actual analysis. On the other hand, there could be limitations when it comes to taking it to the field, particularly in places with rugged terrain and limited road access. For developing countries, cost would be another factor besides the need to develop technical expertise to run the lab. The samples need to be free of contaminants and require immediate preservation to avoid degradation emanating from exposure to environmental conditions such as temperature and light. Sample quality in so critical that the slightest presence of contaminants or sample degradation will either disqualify it for analysis or produce results way beyond the actual fact. This calls for adequate expertise, financial resource availability and dedication in using environmental DNA approach for biodiversity assessment. Nevertheless, technological advancement in the application of DNA studies for biodiversity assessment is simply stunning, and it surely is the next generation of biodiversity assessment and monitoring.
Boyer, S., Wratten S.D et. al. (2013). Using Next-Generation Sequencing to Analyse the Diet of a Highly Endangered Land Snail (Powelliphanta augusta) Feeding on Endemic Earthworms. PLoS ONE 8(9): e75962. 
Krista. M. Ruppert et. al. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation 17 (2019)-Elsevier.
Pont, D., Rocle, M., Valentini, A. et al. Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation. Sci Rep 8, 10361 (2018).
P.F. Thomsen, E. Willerslev. Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation 183 (2015) 4–185.
Species Plantarum – Wikipedia

Tandin Wangdi
Program Specialist
WWF Bhutan