Seeing Silicon | Cracking the case with eDNA

Right now, ecologists and biologists use physical surveys to study any species on the planet in a patch of land or ocean. Experts walk through dense forests collecting samples. Divers head into deep oceans, to record species. These researchers meticulously set up camera traps, use remote sensing equipment, or other ways to record, take samples and track species in biodiverse systems across the world.

It’s exhausting, needs expertise and sometimes also ends up disturbing the ecosystem that the researcher is studying to protect. Now, a new technique has made it possible to survey ecosystems in a dramatically different way.
Environmental DNA or eDNA is an approach where researchers collect environmental samples such as a scoopful of soil, a pail of water or a handful of air from an ecosystem. “These samples contain genetic material shed by multiple species present in the environment and give us a larger picture of biodiversity changes, habitat degradation and overall environmental health,” says Dr Nelum Wickramasinghe, a post-doctoral researcher with Natural Centre of Biological Sciences (NCBS) in Bangalore who studies species in urban lakes of Bengaluru using eDNA. In her research, Wickramasinghe surveys the biodiversity of various lakes with varying pollution levels to understand the native and introduced biodiversity in these lakes and how pollution affects them.
After all, everything living constantly sheds DNA. A frog sheds cells in a puddle, a tiger sheds hair on a path. A flower leaves its pollen in honey. A fish discards slime in water. Wherever the living goes they leave behind invisible and visible bits of living matter – breath, mucus, slime, hair, spit, faeces, scales and more. Scientists such as Dr Wickramasinghe run a DNA analysis on the environmental samples they collect from an ecosystem and list down everything living that’s been at, exchanged or interacted with the sampled habitat.
The obvious use of this technique is ecological monitoring at a large scale. The method is not intrusive and does not disturb the environment in any way and can be used in remote areas like deep oceans, volcanoes, higher altitudes, or dense forests.
In the Andamans for example, Dr Tejal Vijapure, a postdoctoral researcher with the Centre for Ecological Sciences (CES) at the Indian Institute of Science (IISc) in Bengaluru uses metabarcoding to study the diversity of Andaman coral reefs. “Metabarcoding is an eDNA technique which gives me the liberty to detect and quantify all species occurrence in a sample through a single process and see the diversity of an ecosystem,” she explains. This expedites her aim to develop a database of marine invertebrates in Indian waters.
“eDNA is exciting as the technique. Sampling can be done quickly and it works out less expensive in the long run,” says Dr G Ravikanth, senior fellow, Ashoka Trust for Research in Ecology and the Environment (ATREE), who uses this method to study invasive fish species in Ramsar wetlands. Using eDNA tools, Dr Ravikanth’s lab also combs through Myristica swamps – a type of freshwater swamp forest with the species of Myristica primarily found in South India – looking for endemic amphibians. Though currently the technique is mostly being used to make biodiversity surveys faster and more efficient, in the future, Dr Ravikanth says there are possibilities of it being used in agriculture and elsewhere in sciences too. “We can assess soil biodiversity and compare regenerative agriculture practices to soils where pesticide is used or we can assess honey in a particular area to understand which species of plants a bee has collected nectar from,” he says, adding these are two directions his lab is already thinking about.
A lot is possible when it comes to eDNA. A flip through the digital pages of the technique’s exclusive journal, Environmental DNA, shows the varied ways in which this tool is being experimented with. Scientists in Spain are studying mackerel eDNA to estimate the bycatch species that are caught with this fish in commercial fishing. In Copenhagen, researchers are trying to develop eDNA techniques to be used in geology. Virologists in the USA are using this technique to track viruses in New York and setting up systems to alert them of a potential future pandemic. In China, researchers are increasing their understanding of extinct species by studying eDNA in fossils.
“eDNA research is rapidly evolving with advancements in sequencing and bioinformatics, expanding into subfields such as biosecurity, screening invasion, environmental health, forensics and even paleoecology,” says Dr Mukesh Thakur, scientist, Centre for Forensic Sciences, Zoological Survey of India in Kolkata. Dr Thakur has been running eDNA analysis to monitor the biodiversity of the Ganga River for a couple of years now. Dr Thakur believes the technique shortens the time required for massive environmental impact studies tracking invasive species in an ecosystem, or simply understanding changing migration patterns and biological relationships between multiple species. This allows scientists to alert governments in a timely fashion, detect invasive species early on, or do interventions to prevent or mitigate their spread or ecological impact. Large samples can be analysed quickly, and cheaply and scientists can study not only abundance but also the interaction of species over increasingly broad geographic scales.
The reason eDNA has suddenly become the go-to technique in ecology is also because of technology. The last few years have seen a rapid rise in computational powers. At the same time, DNA sequencing costs have also been reduced. According to National Human Genome Research Institute data, sequencing one megabase of DNA cost nearly $5300 in 2001, and in 2021 it’s at $0.006. It’s possible to get a basic DNA testing lab up to $100,000.
A 2021 study by Pacific Northwest National Laboratory in Washington, USA, found that though initial costs were high, in the long run, eDNA surveys for biomonitoring marine environments were less expensive when compared to traditional methods of surveying such as beach seining and scuba surveys. “While eDNA methodologies can be cost-efficient compared to traditional biodiversity monitoring techniques, setting up eDNA research requires significant initial investment in equipment and skilled personnel,” explains Dr Thakur. This can take up the initial costs. Other than the equipment, you also need skilled people to collect samples the right way, technicians to sequence DNA, and researchers to analyse the data that’s generated and turn it into research. India currently lacks on all fronts, the reason only a handful of labs in India have undertaken this research.
As the field matures, startups have started to mushroom across the world, which specialise in environmental genomics techniques such as Next-Generation Sequencing (NGS), and offer eDNA analysis as consultants. One such Canada-based startup, eDNAtec, offers private assessments of biodiversity in any ecosystem. Their clientele are fishing, oil and gas companies who want to monitor their sustainability measures and conservation efforts. California-based Genidaqs charges around $7000 for metabarcoding of a single sample that includes collection, DNA extraction, sample processing, analysis and a standardized report. Again, their clientele is companies who want to measure their sustainability efforts.
Surveying through the eDNA method has other challenges. “Right now, less than 10 percent of all species have reference DNA barcodes,” says Dr Ravikanth. Without a reference database, researchers might have DNA samples but don’t know the corresponding species it represents. Hopefully, says Dr Ravikanth, in the next decade, this will change as DNA barcodes are developed for a wide variety of taxa. Young researchers such as Dr Vijapure at IISc are building these DNA datasets – sometimes from scratch. “My study is the first deployment of Automated Reef Monitoring Structures in India, which is a standardized methodology for censusing coralline biodiversity,” she says. Her aim: To ramp up the database of the marine invertebrates from the Indian waters in the next few years – so it can be a valuable reference for molecular studies worldwide.
Once scientists have sorted out the DNA database itself, other challenges remain. DNA can live for a long time in the environment. If you detect a species’ DNA, there’s no guarantee that it’s alive or went through the location recently. Sometimes, the DNA might even be of extinct species. In a way, eDNA might be giving too much data, which the researchers have to go through patiently and meticulously to make sense of what’s happening. Researchers still need field surveys to confirm, or research deeper questions like a species’ health, breeding, or status of its habitat. “eDNA might be effective in detecting the presence of species, but it doesn’t tell you how many of those species are present in the environment,” says Dr Thakur. That’s the reason for now, that most researchers feel, eDNA technique will complement rather than replace other data-collecting research techniques like surveys, traps, nets, camera traps, and even citizen science platforms like iNaturalist and eBird.
Over the next decade though, scientists are optimistic about eDNA. The technique will integrate more fully with other types of ecological data, including traditional survey data, remote sensing data, and citizen science data and provide a more comprehensive understanding of ecosystems, says Dr Thakur. “Expect better detection of rare species, more robust and accurate global monitoring networks and even involvement of citizen scientists in collective eDNA samples and contributing to biodiversity research,” he says. In future, interested citizens like me and you might be collecting eDNA around us, and helping scientists conserve and protect our biodiversity systems.
Shweta Taneja is an author and journalist based in the Bay Area. Her fortnightly column will reflect on how emerging tech and science are reshaping society in Silicon Valley and beyond. Find her online with @shwetawrites. The views expressed are personal.