Mendenhall Research Fellowship Program

20-2. Development and application of eco-genomic indices and metrics for biodiversity assessments, biomonitoring and biosurveillance at USGS streamgages using robotic samplers


Closing Date: January 6, 2022

This Research Opportunity will be filled depending on the availability of funds. All application materials must be submitted through USAJobs by 11:59 pm, US Eastern Standard Time, on the closing date.

How to Apply

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The USGS has been the Nation’s leader in monitoring hydrologic conditions through its national streamgage network; however, little work has been done to explore how biodiversity assessments, biomonitoring and biosurveillance could be integrated into this network. Autonomous, robotic water sampling technologies present an opportunity to overcome the resource demands associated with biomonitoring. Autonomous robots placed within the streamgage can conduct high frequency sampling, regardless of location, weather or human resource availability. The Monterey Bay Aquarium Research Institute (MBARI) has pioneered a robotic instrument called the Environmental Sample Processor (ESP) that can be programmed to automate water sample filtration and preservation of the captured material, or homogenize it for immediate analyses in situ (Scholin et al. 2017). The USGS and MBARI have collaborated since 2017 to explore how the ESP adds value to environmental (e)DNA-based biosurveillance for invasive species and pathogens at USGS streamgages.

The incumbent will build on these previous efforts by developing, benchmarking and applying novel eco-genomic indices and metrics for biodiversity assessments, biomonitoring, and biosurveillance from eDNA samples collected by ESPs at USGS streamgages. This research will track parallel eco-genomic indices and metric efforts by the European Union’s DNAqua-Net program. However, our efforts will move beyond the snapshot, low frequency sampling that limits most molecular research programs and take advantage of the high frequency sampling enabled by robotic samplers like the ESP. Recently we identified advantages of high frequency robotic sampling,  likely due to the dynamic environments in flowing waters, where eDNA occurrence in the water column is patchy over time and space (Sepulveda et al. 2020, 2021).

The incumbent’s research area will be the Greater Yellowstone Area (GYA) of Idaho, Montana and Wyoming given the availability of eDNA samples already collected by ESPs at multiple USGS streamgages (2018 – present). There exists a need to document GYA baseline conditions of water health and to monitor these waters for deleterious change given the intensification of increasing land-use, recreation and climate stressors. We posit that robotic, molecular sampling technologies are uniquely poised to respond to this need because they can be consistently applied across time and space, thus facilitating like for like comparisons, and samples can be collected at a high enough frequency to capture rare events.

The Fellow is expected to translate research results into a long-term, molecularly informed water quality monitoring plan for agency partners in the Upper Snake River near Jackson, Wyoming. The Fellow will work closely with principle investigators from the USGS Ecosystem and Water Mission areas to ensure that research is cross-disciplinary and fulfilling programmatic priorities. We envision many directions in which the incumbent could develop the project further and describe two of them. The incumbent will not be limited to these directions.

Research opportunity 1: Determine the appropriate spatiotemporal resolution for molecular sampling to inform eco-genomic indices and metrics for biodiversity assessments, biomonitoring, and biosurveillance. Robotic samplers can collect samples at a higher frequency (e.g., sub-daily) than is realistic for manual sampling, but robotic samplers are stationary so are limited to the location of USGS streamgages that were originally located for non-biological purposes like recording water level. Does the higher frequency sampling enabled by robotic samplers provide better or more actionable information and is it worth the added costs, complexities and limitations? We propose a comparison between eco-genomic indices and metrics estimated from higher frequency, robotic data collected at streamgages to regularly collected, lower frequency samples collected by USGS hydrotechnicians at streamgages and to lower frequency, longitudinal river samples. Robotic, regularly collected and longitudinally collected sample sets are available from the Yellowstone River and Snake River. The incumbent can also collect additional robotic and manual samples. This comparison will be used to inform molecular sampling frequency for a long-term, molecular monitoring program in the Upper Snake River subbasin and potentially other river eDNA projects worldwide.

Research opportunity 2: What are the tradeoffs of using the same sample to address different questions (biodiversity vs biomonitoring vs biosurveillance)? A potential advantage of eDNA sampling is that multiple tests can be conducted on a single sample. For example, one aliquot from a sample can be evaluated for DNA of waterborne pathogens that pose human health risks, while additional aliquots can be analyzed for DNA of macroinvertebrates that are associated with water quality. However, for this advantage to be realized, DNA of all taxa of interest must be available for capture when sampling, otherwise results will be biased and lead to false negatives. Indeed, eDNA best practices recommend that time and place are informed by target organism biology. Additionally, optimal workflows for microbial DNA may differ from those used to detect algae and macroorganisms. For example, different DNA extraction methods may be more effective depending on the target taxa, particularly between eukaryotes and prokaryotes (Deiner et al. 2015). We propose that the incumbent develop workflows compatible with biodiversity, biomonitoring and biosurveillance objectives that minimize the tradeoffs between efficiency (i.e., doing as much with one sample as possible) and effectiveness (i.e., low error rates). Available data include archived DNA filters and extracts collected across the Greater Yellowstone Area. The incumbent can also collect additional samples. This evaluation will be used to inform molecular sampling workflows for a long-term, molecular monitoring program in the Upper Snake River subbasin. 

Interested applicants are strongly encouraged to contact the Research Advisor(s) early in the application process to discuss project ideas.

Proposed Duty Station: Bozeman, Montana

Areas of PhD: Molecular ecology, microbiology, bioinformatics or related fields (candidates holding a Ph.D. in other disciplines, but with extensive knowledge and skills relevant to the Research Opportunity may be considered).

Qualifications: Applicants must meet the qualifications for one of the following:  Research Biologist, Research Ecologist, Research Geneticist, Research Microbiologist, Research Statistician, Research Wildlife Biologist.  (This type of research is performed by those who have backgrounds for the occupations stated above.  However, other titles may be applicable depending on the applicant's background, education, and research proposal. The final classification of the position will be made by the Human Resources specialist.)

Human Resources Office Contact:  Audrey Tsujita, 916-278-9395,

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Adam Sepulveda, Ph.D.

Research Zoologist
Northern Rocky Mountain Science Center
Phone: 406-994-7975

Elliott Barnhart

Research Hydrologist (Microbiologist)
Wyoming-Montana Water Science Center
Phone: 406-457-5921