All About eDNA

If you're a biology student, you've likely discussed the myriad of genetic materials involved in the life cycles of countless types of organisms. mRNA, tRNA, nuclear DNA, mitochondrial DNA are just some of the many kinds of ribonucleic acid that help the world go around, however, one that is likely unfamiliar is eDNA. eDNA, or environmental DNA, is a term used to describe DNA found outside of an organism in an ecosystem. As animals shed, secrete fluids, excrete, and other body functions they almost leave behind a footprint of themselves in the form of eDNA. By collecting this eDNA from the environment, scientists can deduce a variety things about the environment it was collected in. 

An example of how eDNA is collected and used 

Previously, the only way to take count of the number of members of a species in an environment were methods like camera traps and field surveying, but eDNA provides a new method which doesn't require a physical sighting of the animal. Scientists use a complex methods of sample collection and analysis in order to deduce what animals might have been to a given locations. This is most helpful in dense or hard to reach environments like deep rainforests where relying on spotting is difficult and unreliable. eDNA sample collection can quickly provide a wealth of data about these locations, saving time, money and potentially lives. eDNA sampling cannot replace physical spotting yet, but it is nonetheless promising as a future avenue for studying environments. 

Sources: 

https://www.conservation.org/blog/what-on-earth-is-edna

https://www.nature.com/articles/s44358-025-00044-x

Paw-prints and Genetic Clues

 

    In January of this year, a new research article was published about taking samples from the tracks of animals to study them. More specifically, in this case, it is the bobcat. These big cats are hard to observe since they are not commonly seen during the daytime, especially out in the open where it would be the easiest to observe them. The study presented shows that it is possible to collect viable DNA just from the tracks these hard-to-observe animals leave. This DNA was able to provide information about the animal's ancestry as well as the animal's unique microbial communities. They are calling this environmental DNA or eDNA when collected. 

    This is a huge break in the ways of observing animals, especially those who are not easily observable in the daytime and not often in open areas. This allows researchers to collect data from an animal without causing any interference and also very safely. Collecting eDNA is something important for collecting continuous information on more uncommon animals, even the rare ones! Having this option allows for an easy collection and much less stress for everyone involved. This will change the future of data collection for uncommon animals.

                                        

Resources:

(News Article): https://wildlife.org/bobcat-prints-lead-to-genetic-clues-about-the-species/

(Scientific Article): https://www.sciencedirect.com/science/article/abs/pii/S0006320723004160?via%3Dihub

(Alternative Link): https://www.arlingtontx.gov/city_hall/departments/animal_services/urban_wildlife/urban_wildlife_animals/bobcat

Identifying Species through Swabbing eDNA

A study was done by swabbing two dozen leaves in a tropical forest in Uganda, and it turned out to result in identifying 52 animals in that area. The swab picked up DNA from the environment shed from 52 animals. DNA is not just found inside a cell, it is found all over. So by analyzing environmental DNA, or eDNA, the species can be revealed. Another study was done at the University of Greifswald in Germany with flies. The eDNA is picked up from flies that contains DNA from dead animals and feces. This study was done with another biologist who collected eDNA from the air. Both of the results were compared. The eDNA resulted in many birds and mammals that were known to live in the park. Another researcher has been working on the same type of study and mentioned that he had bird species found in the eDNA that he hadn’t seen before. Sampling eDNA is crucial especially with biodiversity declining and seeing many more species becoming extinct. 

These studies are the answer to a new way to monitor biodiversity in any ecosystem. More than 99% of all species that have lived on Earth have gone extinct. The number of species will degrade as time goes on due to the human population. If scientists can use this information and use this type of study on a larger scale, there can be new results and findings on any species in any area. And with these results, scientists and researchers can find a way to act accordingly and help species and the ecosystem as a whole. The tools required for this study are definitely more convenient since they are only swabs compared to other devices which is another good reason why this is a more approachable technique.

Sources:

https://www.worldwildlife.org/magazine/issues/summer-2022/articles/how-scientists-use-edna-to-monitor-biodiversity#:~:text=Water—like%20soil%2C%20air%2C,an%20ecosystem%20and%20its%20species.

https://www.sciencenews.org/article/environmental-dna-leaf-swab-technique-biodiversity

With Environmental DNA, Small Water Samples Can Find Really Big Animals

In an article posted by SciTechDaily, a team of scientists from California State University (CUNY), the Wildlife Conservation Society (WCS), and Columbia University used an emerging genetic tool to detect whales and dolphins in the New York Bight. This technique searched for environmental DNA (eDNA), or trace amounts of genetic material left behind by wildlife in the water. The results of this study were published in the journal Frontiers.

The scientists said that eDNA can be used to support other efforts to locate whales and dolphins, such as visual observations and acoustic monitoring. According to the study’s lead author, Dr. Elizabeth Alter, “Determining how cetaceans and other threatened marine animals use coastal habitats is critical to their effective conservation. By generating eDNA data in parallel with survey data, it will be possible to gain a clearer understanding of how this tool can be used in management…”

This technique also detected baitfish present in the area preyed on by whales and dolphins in addition to finding the mammals themselves. The authors claim that in the future, as technology improves, this technique could eventually be used to identify individual animals. Because eDNA drops to lower levels over time, the authors also state that additional research is needed to better understand how behavior and oceanic conditions contribute to the longevity of eDNA signals.

Though there are some signs of promising recovery for many whale populations, whales continue to face a range of modern-day threats such as ship strikes, ocean noise, entanglement with nets, and a general loss of habitat. For example, there are currently plans to scale up massive renewable energy projects to meet energy demands in the United States, including a wind energy auction for more than 488,000 acres in the New York Bight. The use of emerging techniques such as eDNA can provide a new perspective on the current status of whale populations and their prey in and around lease areas as offshore wind operations scale up along the east coast. The WCS has also extended these eDNA techniques to detect critically endangered wildlife such as Swinhoe’s softshell turtle, in the Bolivian Amazon, and in some of the most rugged areas on the planet including Mt. Everest.

Related article: https://www.forbes.com/sites/grrlscientist/2018/05/18/the-power-of-environmental-dna-for-monitoring-whales/?sh=64ccf93f264c

Using Environmental DNA Sequencing to Study Aquatic Biodiversity in the Amazon

An article from phys.org shows how an expedition at the Javari River Basin have used environmental DNA (eDNA) sequencing to investigate fish diversity in the Amazon. The expedition team was looking to see if it was feasible to study diversity using this method instead of using traditional methods that rely on nets and other fishing gear which can negatively impact the environment. Using eDNA would help reduce environmental impact and to find all the fish species living their without catching and killing them.

This method involves extracting molecules of DNA that is present in water samples and identifying the species to which the DNA belongs to by using genetic markers. The marker most often used is the 12S mitochondrialRNA gene. To find the small molecules, such as excrement and animal parts, in the water samples, the researchers used DNA extraction kits designed to analyze blood and tissue. The team spent 18 days on the Javari River and collected water samples at three of 46 locations where they collected fish using traditional methods as reference to see if the eDNA testing was accurate. They were able to collect a total of 443 species including 60 that were undiscovered using eDNA. Using traditional methods at these three sites resulted in only 201 species collected.

The article does state the limitations of eDNA. For instance, only 58 out of the 201 species caught were identified with precision at the species levels when using eDNA analysis. This is because 12S is a slowly evolving piece of genetic code and is not sufficient enough to identify specimens at the species level because many of the species in the Amazon diverged quite recently in evolutionary terms. For example, two eels that diverged recently, Electrophorus viltai and E.electricus, would be difficult to identify with just the 12S marker. Perhaps more than one marker is going to have to be used to identify specimens up to the species level. The researcher do expect for the technique to improve over the years so that DNA sampling can be used to identify species accurately without the use of traditional methods.

DNA was Discovered in the Air with Mole Rats

DNA from mammals was discovered in the air, just like in water. This invisible environmental DNA can be found useful in many ways, especially in fields like forensic science, public health, and ecological settings. Researchers in the UK are who discovered this. A scientist, Elizabeth Clare has been studying the genetic footprint left by organisms in the water. This is to help get a better understanding of the organisms that are frequenting certain areas. This has also proven very useful in monitoring endangered species, like the white shark. This is proven to be more effective than the traditional tracking methods.

In water settings, scientists have also been introducing new eDNA into territories, to study how the organisms in the area react. This has also been done on terrestrial organisms as well, but the samples have only ever come from water.

To discover the eDNA in the air, Clare and her team used a pump to draw air through a 45-22 micrometer filter to a housing colony of mole rats. They also did multiple samples with time being one factor, seeing if the longer it ran the more sample it collected as well as where they took the sample. One was in the burrows created by the mole rats and the other was at the top of the larger room. This eas the only thing that led to significant difference was the burrow size vs the large room in yield amount of sample collected, the burrow led to more sample due to being more condensed area. It seemed time and filter size did not have an effect.

The problem these scientists now face is contamination. In the negative control, human DNA was found in there, which would suggest it came from the scientists. This can then conclude that the mole-rat samples are also contaminated with human DNA. Other scientists have done studies similar to plant's eDNA and could use techniques that they used such as blocking probes during sequencing. This will not allow for DNA from humans to amplify. Other suggestions include using suits with respirators, also applying dust traps weeks in advance as well.

This research could leave to forensic science application. Being able to determine who was in the room, can help find a convict a guilty suspect. As well, it can be used in public health. Now, these advancements are far away, as it was just discovered being able to extract eDNA out of the air. Soon I think this will be very useful in getting even more accurate crime convections. And protecting public health. It will also be interesting to see how long eDNA lasts in the air after an organism has moved away.

https://www.the-scientist.com/news-opinion/environmental-dna-can-be-pulled-from-the-air-68645

https://www.the-scientist.com/notebook/researchers-track-sharks-and-whales-using-dna-in-seawater-samples-65236

https://peerj.com/articles/11030/

DNA Amplification Used for Conservation

There is an expansive range of wildlife conservation methods around the world, with specific techniques employed in different habitats. Sometimes the methods used depends on the target species. However, when the animal is elusive or increasingly hard to find due to overexploited populations, scientists find themselves innovating even more techniques to monitor threatened and endangered species. This can be seen through the new method of amplifying DNA from degraded or contaminated genetic samples. Researchers from the National Centre for Biological Sciences at the Tata Institute of Fundamental Research lead a study which acquired small amounts of such DNA from unconventional sources. The scientists were able to successfully amplify tiny amounts of DNA from tiger feces, as well as the whiskers and saliva found on their prey. Other instances of such methods being used are more and more prevalent. One example of this was when the location of an endangered eel species was identified with just one liter of water from different areas from a Japanese river. By utilizing the DNA left behind by these animals in their surroundings, conservationists can glean valuable information such as their location, the population's genetic diversity- thereby leading to more effective management initiatives. 

Environmental DNA Leads to New Population Studies of Whale Sharks

There are a wide variety of methods for tracking and studying populations of animals, from satellite tagging to aerial surveys to tissue samples. However, a new effective means of studying rare marine animals has arisen, and was recently used to study whale shark populations. Seawater environmental DNA (eDNA), or DNA collected in thesurrounding seawater, was used to predict population sizes and relations amongwhale sharks. Scientists from Denmark and Qatar collected water samples and then used DNA sequencing machines to decode the mitochondrial DNA found in the samples. The amount of DNA and the differences between them can be used to determine population sizes and to distinguish between related and unrelated whale sharks. The scientists then compared the DNA from the water samples to DNA previously taken from whale shark tissue samples, and used them to match haplotypes together.

This study took 20 seawater samples off of the coast of Qatar to identify whale shark populations. It discovered that whale sharks will group together between the Arabian Gulf and Indo-Pacific region, but will not group with Atlantic whale sharks. Sharks in the Arabian Gulf and Indo-Pacific region were more closely related due to similar genes, while Atlantic whale sharks had vastly different genes from the ones found around Qatar. The scientists also collected eDNA from mackeral tuna, and discovered that the amount of mackeral tuna eDNA in seawater was proportionate to the amount of whale shark eDNA. The more tuna there are, the more whale sharks that will be present, while fewer tuna results in fewer whale sharks. This indicates that the whale sharks likely feed on the spawn of mackeral tuna.

Though the methods of estimating population size are far from perfect, it is a good start. The predicted range of population size of whale sharks is very large, and ocean currents can move the eDNA to different locations. However, this method of study is beneficial to both humans and whale sharks, as it avoids the stress and potential damage towards whale sharks from tagging and tissue samples all while still allowing scientists to study population sizes. With the continuing advancement of technology and study techniques, the population size range can be narrowed down further and further until it reaches greater accuracy with little variation.

http://www.nature.com/articles/s41559-016-0004

http://www.latimes.com/science/sciencenow/la-sci-sn-shark-seawater-dna-20161121-story.html

DNA collections from seawater

Whale sharks are the world's largest species and often very hard to locate since they live so far from shore. Recently, researches have been able to extract their DNA from environmental DNA-eDNA- in the ocean to understand more about this mysterious species. 

In 2007, there was a sighting of 100 whale sharks at a oil field, approximately 80 kilometers off the coast of Qatar; these became a very popular sight to study this endangered species. A group of researchers came from the Natural Museum of Denmark at the University of Copenhagan, and began to collect samples of the seawater from this sight. The water collected had many materials and cells from the whale sharks. They isolated the cells, extracted and sequenced the DNA, and assigned these DNA to whale sharks; they were good indicators that whale sharks had passed through those waters and interacted in that area. The DNA they sequenced, was then used to estimate the number of reproductive female whale sharks which was approximately 71,000. It is quite amazing that eDNA can be used to estimate such large numbers. This DNA can be used to learn so much about a species, we know so little about. 

http://www.worldwildlife.org/species/whale-shark