We can’t protect what we can’t detect
Humans are driving biodiversity loss among all species and ecosystems across the planet, according to a recent study accounting for nearly 100,000 sites across all continents. It’s a distressing finding as biodiversity is key to stabilizing our world as we know it. Diverse ecosystems are generally more resilient to climate change, natural disasters, and disease outbreaks. Genetic diversity in plants and animals is important for food security, and diverse forests, wetlands, and oceans act as carbon sinks, helping mitigate climate breakdown.
But to understand our impact on biodiversity, we must start by cataloguing the organisms around us, which is often easier said than done.
Enter eDNA. Every time a living organism passes through an environment, it sheds genetic material. This might come from its skin, feces, bodily fluids, or upon decomposition. All around us, bits of genetic material sit in the soil, float in the water, drift through the air, or chill in ice.
Scientists first described eDNA in the 1980s after analyzing DNA in soil and marine sediments to detect bacteria. However, it wasn’t until the invention of powerful next-generation sequencing technologies in the early 2000s that eDNA hit the mainstream. One of its first proof-of-principles was when it reliably detected a secretive species of frog in a freshwater environment, even without direct observation.
Being able to tell whether a creature is present without ever needing to lay eyes on it is a game-changer for conservation, pandemic preparedness, and animal and human health, as it decreases the time, resources, and physical effort needed to monitor and protect the organisms around us.
Simply put, we can’t protect what we can’t detect.
Drones and robots in on the act
Since its first real-world use, the field has evolved rapidly. Alongside manual collection, scientists can now gather eDNA samples with drones covered in sticky pads from inaccessible forest canopies or with deep-sea robots from the most inhospitable places on Earth.
Researchers now routinely use eDNA to track changes in biodiversity within ecosystems over time, reveal the presence of invasive or endangered species (the Loch Ness Monster!), or monitor harmful disease-causing organisms potentially devastating to native species or humans.
From the sewers…
While scientists initially applied eDNA to detect human pathogens over a decade ago, the COVID-19 pandemic gave researchers a new focus: accurately predicting the locations and dates where clinical cases might peak.
As coronavirus genomes consist of RNA, not DNA, scientists adapted the technology to pick up SARS-CoV-2 environmental RNA (eRNA) in human wastewater. This revealed that people were shedding SARS-CoV-2 RNA in their stool even before the first cases were reported in an area. The results gave authorities strong early indicators of infection so they could adapt their response accordingly.
To the Poles…
In a somewhat cuter example, researchers recently analyzed ancient 6,000-year-old penguin poo in Antarctica with a modified eDNA approach to detect ancient DNA trapped in sediment. This allowed the paleobiologists to travel back in time to detect other local species, including a range of birds, seals, and invertebrates, and pinpoint how species interactions changed over millennia.
The study also revealed the presence of southern elephant seals some 1,000 years ago, despite them no longer breeding on the Antarctic mainland. Understanding how the species detected in these samples coped with past climate change events could ultimately help us prepare for the future.
To Belgium…
Closer to home, the Belgium-based Flanders Marine Institute (VLIZ) and KU Leuven recently provided funding and expertise to use eDNA to map marine biodiversity across 21 UNESCO World Heritage sites, including the Great Barrier Reef and the Galapagos Islands.
The researchers identified 4,500 marine species, including invasive and endangered species like the rare Commodore black and white dolphin that was found in waters around the sub-Antarctic Kerguelen islands, one of the most isolated places on Earth. The research provides valuable insight into the biodiversity changes in these sensitive environments, allowing authorities to plan and measure the success of current and future protection initiatives.
eDNA in the big data era
While eDNA and its related approaches are undoubtedly powerful, the technology comes with a catch. The amount of data generated is vast, posing challenges for researchers unfamiliar with big data analytics. For instance, the penguin poo study generated 94 billion DNA sequences from 156 sediment samples requiring highly specialist knowledge and advanced algorithms to make sense of the noise. Ecologists collaborated with BGI Research, one of the largest genomics companies in the world, to plan, perform, and analyze experiments.
The sample-gathering process is relatively straightforward, but once scientists have collected an eDNA sample, the DNA undergoes ‘metabarcoding’ where particular regions of DNA are amplified. This allows researchers to simultaneously identify individual or multiple species by sequencing these metabarcodes and comparing any DNA stretches they find to online reference databases housing the genomes of thousands of different species. If they find a significant match, it suggests that the creature is likely present in that environment.
However, the results are only as good as the reference database the data was compared to. If the genome of a species isn’t present in a database or the sequence is of poor quality, no matches will be found. This could mean researchers are led to believe the organism is absent from an environment, even if, in reality, it’s not. With an estimated 20% of approximately 200,000 European species at risk of extinction, scientists must act quickly to generate complete large-scale genome banks to make detection easier.
A bold vision for the future of biodiversity
To tackle this, bold initiatives like the European Reference Genome Atlas and the Earth BioGenome Project (EBP) have ambitious aims. The goal of EBP is ‘to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of ten years’ and to create annotated reference-quality genomes for a staggering 1.8 million named eukaryotic species. It’s a collaboration of over 50 international partners, including France-based ATLASea who are focusing on sequencing 4,500 eukaryotic marine species, around a third of the known marine species in France.
Comprehensive genome libraries have another benefit in the age of AI. Data scientists can use the many billions of data points to train, refine, and implement sophisticated AI models that detect the presence of all species in an eDNA sample at the click of a button. These tools will help biologists and conservationists draw useful conclusions to help protect and manage the biodiversity around us.
Although we aren’t there yet, thanks to eDNA, we’re gradually getting closer to discovering all the hidden organisms in habitats far and wide; knowledge that’s necessary to protect the delicate ecosystems that both humanity and our planet depend on and achieve the One Health vision.
