How we can detect pretty much anything - Hélène Morlon and Anna Papadopoulou
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Many scientists, such as those involved in the iBOL initiative, have found a use of this DNA variation. They target specific DNA segments, known as DNA barcodes, to determine the species of an organism through a method known as DNA-barcoding. Similar to how grocery store computers scan barcodes to identify products, biologists can read DNA barcodes to identify species. However, in order to read them, they need to complete a series of steps. First, they extract and purify the whole DNA from the organism’s cells. Then, they target the DNA barcode using specific primers, which are small artificial DNA strands that bind to its edges and initiate its amplification through PCR. This way, multiple copies of the DNA barcode are created, which is a necessary step in order to sequence and read this highly informative segment. The final step relies on the use of DNA databases with barcodes of known species. To do that, scientists compare the DNA barcode of interest with those of other organisms and evaluate how similar they are.
The amount of similarity is decisive for the identification of the organism under study, which is expected to share the same or highly similar DNA barcode with other individuals of the same species. But what if the DNA barcode of an organism substantially differs from those of any other existing species on these databases? There is a chance that a known species is missing from the database, a critical issue that projects like BIOSCAN are trying to tackle by sequencing all living organisms. Alternatively, it might be one of the estimated 7.5 million still undescribed organisms. A new species!
Now, imagine that grocery store computers could scan multiple barcodes at the same time. This would be analogous to DNA-metabarcoding, which can identify multiple species from a single sample, contrary to DNA-barcoding. The procedure is highly similar, but instead of one organism, scientists extract DNA from several species at once (e.g., from an insect trap) and adjust each step to detect multiple DNA barcodes simultaneously. Such approaches are especially useful when studying whole communities of tiny organisms, like the soil arthropod communities of forests investigated by the scientists involved in the iBioGen project.
When the above methods are applied to environmental samples (e.g., water, soil, sediment) instead of tissue samples (i.e., from single or multiple organisms), they target the DNA that organisms shed in the environment, termed eDNA. These eDNA-metabarcoding approaches have some extra steps to optimally isolate DNA from environmental contaminants and an extra challenge: DNA degradation. In normal conditions, eDNA is degrading relatively fast, making it useful only to study the recent past. However, scientists have thought of many creative ways to utilize this source of information. For instance, a research group applied an eDNA approach to monitor the Canada lynx in a Montana forest. By collecting snow that the lynx had potentially stepped on and returning it to its liquid form, they managed to isolate and identify its DNA.
Other scientists amplified DNA from the blood found in leeches’ stomachs to screen rare and elusive mammals in a tropical rainforest of Vietnam, which allowed them to detect the elusive Truong Son muntjac. While in the tropical rainforest eDNA degrades quickly, under the right (cold, dry and anoxic) conditions, eDNA can stay intact for tens of thousands of years! For example, a team of researchers was able to analyze some eDNA traces that had been trapped in the arctic permafrost for 50,000 years, enabling them to make hypotheses about the changes in the distribution of different plant species and their link to the extinction of the woolly mammoths.
The use of DNA as a tool for biodiversity research has opened endless possibilities. More and more applications of DNA-utilizing techniques are expected to enter the field in the future, helping us fill the empty pages in the catalogue of life, further advancing our knowledge of the Earth’s precious biodiversity and contributing to its conservation.
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