Proof of concept airborne eDNA testing to detect invasive species in shipping containers Active
Shipping containers that are transported by water vessels traveling between islands and the mainland or other islands can act as a vector for invasive species that are accidentally transported with the cargo. If the vessel carries a lot of cargo, or cargo has areas for different species to hide, inspections can be difficult, time consuming, and expensive, or in the case of non-agricultural products, physical inspections may not occur at all. Many organisms such as plants and invertebrates require a large collection effort and a taxonomic expert to visually distinguish between species, but if adequate genetic information is available, species can be identified using gene-based tools. Recent studies have indicated that airborne environmental DNA (eDNA) can be used to detect nearby species, including within an enclosed space (Bohmann & Lynnggaard 2023; Garrett et al. 2023). Given that shipping containers are shut for long periods of time, researchers can expect airborne eDNA to accumulate to levels that are detectable.
Researchers will test multiple novel airborne samplers to determine if airborne eDNA can be used to rapidly detect the presence of possible invasive species to lessen the time and resources it takes to examine shipping containers. Using multiple types of airborne samplers, researchers will first determine which sampler most effectively accumulates eDNA by placing samplers in shipping containers with three different species (Little fire ant, Queensland longhorn beetle, and Southern house mosquito) as targets. We are initially determining eDNA concentrations by running quantitative polymerase chain reaction (qPCR) using targeted assays. This method allows researchers to amplify and detect target DNA. The second phase is to apply these same air samplers to an actual cargo shipment and use multispecies metabarcoding to identify multiple vertebrate and invertebrate species that may occur within the shipment.
Results from this project will help inform federal, state, and non-government organizations on a new and possibly improved methods for detecting the unintended movement of invasive species, including application to point of use rapid detection for shipment inspectors. This project is a collaborative effort across three USGS science centers (UMESC, PIERC, and FRESC) as well as the U.S. Fish and Wildlife Service and the Hawaii Cooperative Studies Unit at the University of Hawaii at Hilo.
Biological Threats and Invasive Species Research Program
References:
Bohmann, Kristine, and Christina Lynggaard. Transforming Terrestrial Biodiversity Surveys Using Airborne eDNA. Trends in Ecology & Evolution 38, no. 2 (February 1, 2023): 119–21. https://doi.org/10.1016/j.tree.2022.11.006.
Garrett, Nina R., Jonathan Watkins, Nancy B. Simmons, Brock Fenton, Alejandro Maeda-Obregon, Daniel E. Sanchez, Emma M. Froehlich, Faith M. Walker, Joanne E. Littlefair, and Elizabeth L. Clare. Airborne eDNA Documents a Diverse and Ecologically Complex Tropical Bat and Other Mammal Community. Environmental DNA 5, no. 2 (2023): 350–62. https://doi.org/10.1002/edn3.385.
Shipping containers that are transported by water vessels traveling between islands and the mainland or other islands can act as a vector for invasive species that are accidentally transported with the cargo. If the vessel carries a lot of cargo, or cargo has areas for different species to hide, inspections can be difficult, time consuming, and expensive, or in the case of non-agricultural products, physical inspections may not occur at all. Many organisms such as plants and invertebrates require a large collection effort and a taxonomic expert to visually distinguish between species, but if adequate genetic information is available, species can be identified using gene-based tools. Recent studies have indicated that airborne environmental DNA (eDNA) can be used to detect nearby species, including within an enclosed space (Bohmann & Lynnggaard 2023; Garrett et al. 2023). Given that shipping containers are shut for long periods of time, researchers can expect airborne eDNA to accumulate to levels that are detectable.
Researchers will test multiple novel airborne samplers to determine if airborne eDNA can be used to rapidly detect the presence of possible invasive species to lessen the time and resources it takes to examine shipping containers. Using multiple types of airborne samplers, researchers will first determine which sampler most effectively accumulates eDNA by placing samplers in shipping containers with three different species (Little fire ant, Queensland longhorn beetle, and Southern house mosquito) as targets. We are initially determining eDNA concentrations by running quantitative polymerase chain reaction (qPCR) using targeted assays. This method allows researchers to amplify and detect target DNA. The second phase is to apply these same air samplers to an actual cargo shipment and use multispecies metabarcoding to identify multiple vertebrate and invertebrate species that may occur within the shipment.
Results from this project will help inform federal, state, and non-government organizations on a new and possibly improved methods for detecting the unintended movement of invasive species, including application to point of use rapid detection for shipment inspectors. This project is a collaborative effort across three USGS science centers (UMESC, PIERC, and FRESC) as well as the U.S. Fish and Wildlife Service and the Hawaii Cooperative Studies Unit at the University of Hawaii at Hilo.
Biological Threats and Invasive Species Research Program
References:
Bohmann, Kristine, and Christina Lynggaard. Transforming Terrestrial Biodiversity Surveys Using Airborne eDNA. Trends in Ecology & Evolution 38, no. 2 (February 1, 2023): 119–21. https://doi.org/10.1016/j.tree.2022.11.006.
Garrett, Nina R., Jonathan Watkins, Nancy B. Simmons, Brock Fenton, Alejandro Maeda-Obregon, Daniel E. Sanchez, Emma M. Froehlich, Faith M. Walker, Joanne E. Littlefair, and Elizabeth L. Clare. Airborne eDNA Documents a Diverse and Ecologically Complex Tropical Bat and Other Mammal Community. Environmental DNA 5, no. 2 (2023): 350–62. https://doi.org/10.1002/edn3.385.