Are Environmental Swabs The Future of Biomonitoring?
What are environmental swabs and how are they collected?
Environmental swabs involve using a swab to collect DNA material from surfaces in the environment. This allows researchers to obtain DNA samples from vertebrates without directly handling or observing the animals. The swabs are simply rubbed against environmental surfaces like leaves, branches, or tree trunks that animals have contacted. The swabbing motion can last for several minutes to collect sufficient DNA material on the swab tip. The used swabs are then stored in buffer solution to preserve the DNA until analysis. Environmental swabbing provides a quick, easy, and minimally invasive way to gather DNA evidence of local vertebrates.
What can environmental swabs detect?
Swabbing environments like rainforests allows detection of a wide variety of terrestrial vertebrates from the collected DNA. Researchers in Kibale National Park in Uganda detected 52 vertebrate genera from just 24 leaf swabs. This included 26 bird and 24 mammal genera representing species with diverse lifestyles and body sizes. Over half of the detections could be identified to the species level. An average of 7.6 genera were found per leaf swab despite the small sample. Environmental swabs can pick up DNA from elusive, arboreal, and nocturnal species that are rarely observed directly. The technique provides an easy biomonitoring solution to catalog vertebrate diversity and detect rare or cryptic animals.
How does animal DNA get onto environmental surfaces?
There are several ways vertebrate DNA can be transferred to surfaces like leaves and branches. Animals directly contacting the vegetation will leave behind skin cells and hair. Urine and feces may also contain shed DNA. Birds and other predators that consume animals may deposit DNA from their prey. Airborne DNA particles emitted from vertebrates can settle onto environmental surfaces. One study even detected terrestrial vertebrate DNA in rainwash samples, indicating aqueous transport of genetic material. Environmental swabbing takes advantage of these multifaceted DNA transfer pathways to sample the local community. Different surface types like waxy or sticky leaves may be ideal for trapping and accumulating DNA from various sources.
What are the advantages of environmental swabs?
Environmental swabs provide several key advantages over traditional vertebrate survey methods like live trapping, camera traps, or transect surveys. They are quick, inexpensive, and simple to collect without specialized equipment. DNA sampling avoids direct handling of animals needed for observation-based techniques. Large areas can be covered by collecting multiple swab samples which takes just minutes at each location. The preservation buffer protects DNA until processing which provides flexibility. Swabs are easily automated for high-throughput DNA extraction and sequencing using standard molecular biology protocols. Environmental swabbing is also amenable to non-experts, enabling large-scale community science initiatives. Overall, it provides an efficient biomonitoring approach to catalog vertebrate diversity and track ecosystem changes over time.
How does environmental DNA swabbing compare to other techniques?
Vegetation swabbing outperforms other environmental DNA techniques for terrestrial vertebrate detection. Soil DNA sampling yields low vertebrate detection rates. Airborne eDNA capture requires specialized equipment and power supplies. Passive settling of airborne particles is also inefficient. Alternatives like DNA sampling from vertebrate feces or carcasses rely on opportunistic discovery. Swabbing tree trunks or branches can work, but is more time consuming than leaf swabbing. Direct leaf swabbing enables rapid, high-density vertebrate DNA sampling. A recent study in Kibale Park detected 5X more mammal genera using leaf swabs compared to soil samples collected at the same locations. The direct swabbing approach also surpasses rainwash or flower DNA which are more circuitous vertebrate sampling strategies.
What are limitations and open questions with environmental swabbing?
While showing initial promise, environmental DNA swabbing has some limitations and uncertainties that require further research. The persistence of DNA on different surface types is unknown. Environmental conditions like sunlight, heat, and moisture can degrade DNA, so shed DNA likely persists for limited time periods. The specificity of the spatial and temporal information obtained from vertebrate DNA on surfaces needs to be determined. Understanding how far DNA may travel from the source and how long it is retained will better inform ecosystem inferences. The mechanisms transferring DNA to surfaces also need clarification; relative contributions from direct contact, prey, urine, and airborne particles are undefined. Some detections like catfish DNA in rainforest understory are unexplained curiosities. These knowledge gaps will be filled over time as environmental DNA swabbing is further developed and validated.
What is the future outlook for environmental swab biomonitoring?
Environmental swabbing provides an efficient new tool to survey vertebrate diversity and inform conservation efforts. The technique enables inexpensive large-scale monitoring not feasible with standard methods that require direct vertebrate observation or handling. It allows biologists to assess ecosystem composition through genetic evidence of local species. Changes in communities can be tracked over time to guide management strategies. The minimal equipment and expertise required positions environmental swabbing for widespread adoption by conservation organizations and use in community science initiatives. Standardization and best practices will develop with broader deployment. Environmental swabbing has potential to revolutionize terrestrial biomonitoring by generating rapid insights into vertebrate biodiversity and dynamics from the DNA they leave behind in natural environments.
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VOLUME 33, ISSUE 16, PR853-R854, AUGUST 21, 2023. Vertebrate environmental DNA from leaf swabs.