Airborne eDNA research offers clues about species presence in the wind
By: George Watson
Everyone knows when humans scratch an itch or rub bare skin, microscopic skin cells are sloughed off into the air. But while those skin cells may not be alive in the truest sense, they're not exactly dead, either. Contained in those “dead” skin cells is deoxyribonucleic acid, or DNA, the molecule that carries the genetic information found in all living things. In general terms, researchers call this genetic material that has been shed into the air from a host environmental DNA, or eDNA.
But eDNA is not limited to just humans shedding skin. All living organisms found on planet Earth shed similar materials into the environment in the form of cells, body fluids, pollen and seeds. It is here that a doctoral student in Texas Tech's Department of Natural Resources Management focused his dissertation – to determine whether this genetic material, the eDNA, can be collected and analyzed to learn more about what constitutes a local plant community.
As it turns out, it can. “Our work with airborne eDNA represents the first projects aimed at the detection of plant environmental DNA from airborne samples,” said Mark Johnson, the doctoral student in charge of the research. “There have been a variety of studies that examine plant pollen in the air with genetic methods. However, these studies focus only on pollen and the species that release pollen. We are illustrating that airborne eDNA can be used to detect any plant species in the environment throughout the year. My work has focused on initially determining if airborne eDNA can be used to detect species without pollen and how best to collect this information.”
Recently, Johnson and NRM associate professors Robert Cox,Blake Grisham and Matthew Barnes, along with U.S. Fish and Wildlife Service wildlife biologist Duane Lucia, completed a research project where eDNA was collected. The honey mesquite restoration project involved removing trees that had taken over the Texas Tech Native Rangeland facility adjacent to Texas Tech's Rawls Golf Course in northwest Lubbock.
Their results, published by Frontiers in Environmental Science, showed human interaction with the plants on the rangeland had a significant impact on the amount of airborne eDNA collected, and not just from the honey mesquite that was dug up and removed but also from a grass species surrounding the area.
“First, the honey mesquite experienced a massive increase in the amount of airborne eDNA,” Johnson said. “More surprisingly, we detected a significant increase in the amount of eDNA from the grass genus Bouteloua. This was unexpected because this group was not the target of the restoration. This meant that human activity was not only affecting the most obvious species but less targeted species in the environment.”
This new discovery could give future rangeland managers tremendous insight into how both human activity and natural causes can result in widespread distribution of native and invasive wildlife species and how best to treat and mitigate that spread if necessary.
Defining eDNA: Barnes said the term “environmental DNA” differs slightly depending on the researcher being asked. For him, eDNA involves genetic material that can be collected in bulk environmental samples, and not just in the air. Water and soil also can also carry eDNA. He added eDNA differs from other genetic sampling methods in that it is non-targeted compared to the deployment of fur traps or the collection of scat, or animal feces.
“A useful analogy to describe how eDNA is used in our work is to think about a detective at a crime scene who collects a discarded cigarette butt and swabs it for DNA,” Barnes said. “After analysis, the detective may use the DNA found on the cigarette butt as evidence to place the suspect at the crime scene. By looking for fish eDNA in the water or plant eDNA in the air, we are looking for clues about what animals and plants are in the area.”
Johnson said the genetic material shed into the environment by a host is very broad and can include anything from skin cells and leaf fragments to pollen and sweat. Most people are aware of pollen, either through their knowledge of how plants reproduce or by how much they suffer through allergy season when pollination is in full blast.
But pollen differs from eDNA in that pollen is a part of airborne eDNA. A simple way to think of it is that all pollen is eDNA, but not all eDNA is pollen. Current research, Barnes said, is attempting to learn more about the overall composition of airborne eDNA. “Plant eDNA consists of pollen but also flower fragments, leaf fragments and possibly free-floating DNA,” Johnson said. “This is an important distinction because it means we can detect species that may not release large amounts of pollen or detect a species during seasons they are not reproducing. On the flip side, if we are interested in an invasive species that releases a lot of pollen, we can use that pollen to our advantage to detect that species.”
Just like the wind and dust in the air pick up pollen and carry it downwind, the same goes for eDNA, Johnson said. But it's not limited to human activity or the wind, as Johnson noted eDNA also can be carried by species that rely on insects to pollinate as well as airborne seeds that contain eDNA. He said this could help researchers and wildlife managers detect invasive species in a new area before it becomes established.
Collection & Analysis: Barnes said researchers are still learning about everything that can be detected from eDNA samples. While current work involves detecting the presence or absence of specific species, the hope is that they will be able to relate the amount of eDNA in the environment to the population size and activities of specific organisms as well as distinguishing between different varieties of the same species.
Johnson said eDNA allows for a variety of factors and characteristics to be detected in the environment. “The first and most studied characteristic is whether a single species is present in the environment,” he said. “This is typically referred to as species-specific detection and is often used for the detection of invasive or endangered species. However, as technology continues to advance, a new method is being used called metabarcoding. Instead of analyzing samples for eDNA from individual species one by one, metabarcoding enables simultaneous identification of all species' DNA in a sample at once. This advance in technology is allowing researchers to conduct entire community surveys through eDNA samples.”
Collecting eDNA is actually simpler than it sounds, depending on what environment – water, soil, air – the collection is coming from. Airborne eDNA is collected using passive and active traps. Passive traps use wind power to collect material while active traps involve a fan that draws air in.
In this project, Johnson said, researchers used passive dust traps to collect samples, which he said worked best for him in previous research conducted while pursuing his master's degree, also at Texas Tech. These traps involve a small sail that keeps the opening of the collector pointed toward the wind, and when the wind blows through the collector, eDNA and other particles fall into the bottom.
The traps are then washed out every two weeks, and the water is collected containing all material and eDNA that has been deposited. The water is then filtered, all material is collected from the filter, and the materials' eDNA is extracted and stored. Johnson said the eDNA samples can be frozen and stored for long periods, allowing for long-term study.
Researches collected eDNA samples while the Texas Tech student chapter of The Wildlife Society, students from the NRM 4309: Range Wildlife Habitat course and the Texas A&M Forest Service were conducting the mesquite restoration project. Traps were deployed and airborne eDNA was sampled twice before the first restoration treatment, once afterward and once after a second restoration treatment. The samples were filtered, the eDNA extracted and analyzed for the presence of honey mesquite, Bouteloua grass and general eDNA.
The results were as expected. “We were excited to see patterns in eDNA detection that reflected the restoration activities as we predicted,” Barnes said. “Detections of eDNA from honey mesquite, which is insect-pollinated and not expected to naturally release large plumes of pollen into the wind, increased dramatically during the period in which students were cutting, chipping and hauling honey mesquite around the property. Additionally, we observed plumes of eDNA from a grass species surrounding the activity. Even though grass was not the target of any deliberate management action, we suspect the plumes of grass eDNA resulted from the dramatic increase in traffic associated with the honey mesquite management.”
Putting Knowledge to Use: Now that this project shows eDNA can be detected and analyzed on a large scale, the possibilities going forward are exciting, Johnson and Barnes said. But there also is still a lot to be learned from human interaction and how it affects eDNA release.
“In the short term, hopefully our work inspires more efforts to understand what species – both plants and animals – can be detected in airborne eDNA and on what geographic and temporal scales,” Barnes said. “In the long term, I believe that airborne eDNA could be useful for routine monitoring changes in species composition and activity on large landscape scales. A broad network of airborne eDNA sampling stations could help monitor changes in species presence due to seasonal activity, migration and other unexpected changes, and more labor intensive and expensive research and management requiring boots on the ground could be deployed in response to airborne eDNA clues.”
Johnson said these results could have much wider utility in the long-term, such as helping companies that wish to establish a presence in a certain area to determine how that presence could affect the species there. Then, there are the ecological effects.
“Being able to detect airborne eDNA at such a scale has multiple management implications,” Johnson said. “First, this work opens the door for using airborne eDNA to study how other forms of disturbance – both human and natural, such as fire, floods, deforestation, mowing, etc. – impact species. I think another interesting application of this work would be to understand how a community changes over time after a disturbance with the use of airborne eDNA.”
Ongoing research in this area involves moving from detection of a single species through airborne eDNA to community detection as well as spatial pattern detection, both horizontally across a landscape and vertically into the atmosphere, all with the goal of improving the sensitivity and accuracy of collection efforts.
Johnson would like to continue to explore the next generation of sequencing and metabarcoding to allow for a community survey and detection of multiple species in a landscape community. He also would like to explore how variations in the traps, such as height, deployment times and seasonal changes, impact airborne eDNA and allow for more accurate surveys in the future.
CONTACT: Warren Conway, Bricker Endowed Chair in Wildlife Management and Chairperson, Department of Natural Resources Management, Texas Tech University at (806) 834-6579 or firstname.lastname@example.org
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