Jon Amberg
Science and Products
Developing RNA Interference to Control Zebra Mussels
We aim to develop a control tool for eliminating zebra mussels that exploits natural gene regulation mechanisms (RNA-induced gene silencing; RNAi) to be specific to zebra mussels without non-target effects. In addition to the nuisance they pose, Pimentel et al. estimated that zebra mussels cost the U.S. economy over $1 billion annually. Zebra mussels are among the International Union...
BOR environmental DNA sampling for invasive mussels at USGS gages
As part of an ongoing project funded by the Bureau of Reclamation and lead by the Idaho Water Sciences Center (IDWSC) and Northern Rocky Mountain Research Center (NOROCK), the Upper Midwest Environmental Sciences Center (UMESC) will analyze environmental DNA samples collected at gage stations directly downstream of multiple reservoirs throughout the Columbia River Basin. The goal of this...
Field Evaluation of Microparticles
With this study, we will validate the use of microparticles to selectively deliver a control agent to feral bigheaded carps. Prior controlled studies conducted in ponds at the Columbia Environmental Research Center (CERC) in Columbia, Missouri indicated that microparticles could be used to deliver antimycin to bigheaded carps while not impacting non-target species like Largemouth Bass and...
Flocks of a feather dock together: Using Docker and HTCondor to link high-throughput computing across the USGS
USGS scientists often face computationally intensive tasks that require high-throughput computing capabilities. Several USGS facilities use HTCondor to run their computational pools but are not necessarily connected to the larger USGS pool. This project demonstrated how to connect HTCondor pools by flocking, or coordinating, within the USGS. In addition to flocking the Upper Midwest...
Increasing Efficiency and Throughput of eDNA
The results from this study will provide protocols for the collection, processing and analysis of environmental deoxyribonucleic acids (eDNA) samples for monitoring aquatic invasive species like Asian carp. These protocols have the potential to be used by fishery management agencies to monitor aquatic invasive species throughout the United States.
Correlating seasonal trends and occupancy of bigheaded carp eDNA to land use and stream characteristics
The results of this study will advance our understanding of environmental DNA (eDNA) and how eDNA signatures change as fish behavior changes over the course of the open water season. This will further develop eDNA as an easy sampling method to collect information about invading populations or cryptic species that are difficult to capture so that resource managers can be given better...
Relationship between fish presence and abundance in Arizona standing waters measured through standard techniques and environmental DNA
The unpredictability of DNA degradation in the environment has plagued the ability of scientists to interpret environmental DNA (eDNA) data since the technique has been used for early detection of aquatic invasive species (AIS) such as silver and bighead carps (Hypophthalmichthys molitrix and Hypophthalmichthys nobilis) throughout the Chicago Area Waterway System (CAWS), Des Plaines River,...
Hunting Invasive Species with HTCondor: High Throughput Computing for Big Data and Next Generation Sequencing
Large amounts of data are being generated that require hours, days, or even weeks to analyze using traditional computing resources. Innovative solutions must be implemented to analyze the data in a reasonable timeframe. The program HTCondor (https://research.cs.wisc.edu/htcondor/) takes advantage of the processing capacity of individual...
Adding invasive species bio-surveillance to the U.S. Geological Survey streamgage network
The costs of invasive species in the United States alone are estimated to exceed US$100 billion per year so a critical tactic in minimizing the costs of invasive species is the development of effective, early-detection systems. To this end, we evaluated the efficacy of adding environmental (e)DNA surveillance to the U.S. Geological Survey (USGS)...
Sepulveda, Adam J.; Schmidt, Christian; Amberg, Jon J.; Hutchins, Patrick R.; Stratton, Christian; Mebane, Christopher A.; Laramie, Matthew; Pilliod, David Refinement of eDNA as an early monitoring tool at the landscape-level: Study design considerations
Natural resource managers use data on the spatial range of species to guide management decisions. These data come from survey or monitoring efforts that use a wide variety of tools. Environmental DNA (eDNA) is a surveillance tool that uses genetic markers for detecting species and holds potential as a tool for large-scale monitoring programs....
Mize, Erica L.; Erickson, Richard A.; Merkes, Christopher M.; Berndt, N.; Bockrath, K.D.; Credico, J.; Grueneis, N.; Merry, J.; Mosel, Kyle; Tuttle-Lau, M.T.; Von Ruden, K.; Amberg, Jon J.; Baerwaldt, K.; Finney, S.T.; Monroe, E.M. Development of a quantitative PCR method for screening ichthyoplankton samples for bigheaded carps
Monitoring ichthyoplankton is useful for identifying reproductive fronts and spawning locations of bigheaded carps (Hypophthalmichthys spp.). Unfortunately, sorting and identifying ichthyoplankton to monitor for bigheaded carp reproduction is time consuming and expensive. Traditional methods require frequent egg-larvae sampling, sorting of all...
Fritts, Andrea; Knights, Brent C.; Larson, James H.; Amberg, Jon J.; Merkes, Christopher M.; Tajjioui, Tariq; Butler, Steven E.; Diana, Matthew J.; Wahl, David H.; Weber, Michael J.; Waters, John D. Environmental DNA as a tool to help inform zebra mussel, Dreissena polymorpha, management in inland lakes
Zebra mussels (Dreissena polymorpha) are an aquatic invasive species that plague much of North America and are difficult to impossible to eradicate once they become established. Therefore, prevention and monitoring are key elements in the control of these organisms. Traditional microscopy is commonly used in monitoring but requires the presence of...
Amberg, Jon J.; Merkes, Christopher M.; Stott, Wendylee; Rees, Christopher B.; Erickson, Richard A. Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA
Environmental DNA (eDNA) samples that are collected from remote locations depend on rapid stabilization of the DNA. The degradation of eDNA in water samples is minimized when samples are stored at ≤ 4 °C. Developing a preservation technique to maintain eDNA integrity at room temperature would allow a wider range of locations to be sampled. We...
Ladell, Bridget A.; Walleser, Liza R.; McCalla, S. Grace; Erickson, Richard A.; Amberg, Jon J. Assessment of carbon dioxide piscicide treatments
Few chemicals are approved to control or eradicate nuisance fish populations in the United States. Carbon dioxide (CO2) is currently being developed and studied as a new piscicide option for nonselective population control. This study evaluated dry ice (solid state CO2) as a simple CO2 delivery method during winter piscicide applications....
Cupp, Aaron R.; Smerud, Justin R.; Tix, John A.; Rivera, Jose M.; Kageyama, Stacie A.; Merkes, Christopher M.; Erickson, Richard A.; Amberg, Jon J.; Gaikowski, Mark P. Correlating sea lamprey density with environmental DNA detections in the lab
Invasive sea lamprey (Petromyzon marinus Linnaeus, 1758) are currently managed by the Great Lakes Fishery Commission in an effort to reduce pest populations below levels that cause ecological damage. One technique to improve stream population assessments could be molecular surveillance in the form of environmental DNA (eDNA) monitoring. We...
Schloesser, Nicholas A.; Merkes, Christopher M.; Rees, Christopher B.; Amberg, Jon J.; Steeves, Todd B.; Docker, Margaret F. Field evaluation of carbon dioxide as a fish deterrent at a water management structure along the Illinois River
Construction of a water management structure (WMS) in the levee surrounding The Nature Conservancy’s Emiquon Preserve (Havana, Illinois, USA) created a new hydrological connection and potential aquatic invasive species pathway between the Illinois River and a large conservation wetland complex. Site managers need a control tool that deters the...
Cupp, Aaron R.; Smerud, Justin R.; Tix, John A.; Schleis, Susan M.; Fredricks, Kim T.; Erickson, Richard A.; Amberg, Jon J.; Morrow, William S.; Koebel, Carolyn M.; Murphy, Elizabeth A.; Vishy, Chad; Blodgett, K. Douglas The complete mitochondrial genome of Hine’s emerald dragonfly (Somatochlora hineana Williamson) via NGS sequencing
Here, we report the complete mitochondrial genome of the endangered Hine’s emerald dragonfly (HED), Somatochlora hineana Williamson. Data were generated via next generation sequencing (NGS) and assembled using a mitochondrial baiting and iterative mapping approach. The full length circular genome is 15,705 bp with 26.6% GC content. It...
Jackson, Craig; McCalla, S. Grace; Amberg, Jon J.; Soluk, Daniel; Britten, Hugh Assessing the efficacy of corn-based bait containing antimycin-a to control common carp populations using laboratory and pond experiments
Strategic use of oral toxicants could allow for practical and sustainable control schemes for the invasive common carp (Cyprinus carpio, or ‘carp’) if a toxicant selectively targeted carp and not native species. In this study, we incorporated antimycin-a (ANT-A), a known fish toxicant, into a corn-based bait and conducted a series of...
Poole, Joshua R.; Sauey, Blake W.; Amberg, Jon J.; Bajer, Przemyslaw G. Profiles of digestive enzymes of two competing planktivores, silver carp and gizzard shad, differ
Typically, studies in digestive physiology in fish focus on a few enzymes and provide insight into the specific processes of the enzyme in a targeted species. Comparative studies assessing a wide number of digestive enzymes on fishes that compete for food resources are lacking, especially in the context of an introduced species. It is generally...
Amberg, Jon J.; Jensen, Nathan R.; Erickson, Richard A.; Sauey, Blake W.; Jackson, Craig Using dissolved carbon dioxide to alter the behavior of invasive round goby
Fisheries managers need effective methods to limit the spread of invasive round goby Neogobius melanostomus in North America. Elevating carbon dioxide (CO2) in water at pinch points of rivers (e.g., inside locks) is one approach showing potential to deter the passage of invasive fishes, such as bigheaded carps Hypophthalmichthys...
Cupp, Aaron R.; Tix, John A.; Smerud, Justin R.; Erickson, Richard A.; Fredricks, Kim T.; Amberg, Jon J.; Suski, Cory D.; Wakeman, Robert