Molecular Tools for Management of Threatened and Endangered Species | W81EWF 22 SOI 0009

Opportunity Information: Apply for W81EWF 22 SOI 0009

The grant opportunity titled Molecular Tools for Management of Threatened and Endangered Species (Funding Opportunity Number W81EWF 22 SOI 0009) is a Department of Defense, U.S. Army Corps of Engineers (ERDC-CERL) effort to apply modern molecular ecology methods to practical conservation and risk-management needs on two military installations: Fort McCoy, Wisconsin and Camp Grayling, Michigan. The project is structured as a cooperative agreement in the science and technology/research and development category (CFDA 12.630), with one anticipated award and a modest budget cap of $64,300. The government is looking for research and technical support that can turn collected (and potentially newly collected) field samples into actionable information for natural resource managers, with the expectation that findings will be useful not just locally on the installations but across the broader ranges of the focal species.

A central theme across the work is using DNA-based tools, especially environmental DNA (eDNA) and metabarcoding, to detect species and characterize communities in ways that can be faster, more sensitive, or more comprehensive than traditional surveys alone. The specific lab methods and whether more sampling is needed are intentionally left somewhat flexible and will be finalized collaboratively with the installation staff, ERDC-CERL, and partner organizations (notably within the CESU network). In practice, that means the awardee should be prepared to coordinate closely with on-the-ground natural resource personnel and adapt the technical plan based on local constraints, seasonal timing, and management priorities.

Task 1 focuses on DNA metabarcoding of freshwater aquatic communities at Fort McCoy, which contains roughly 4,400 acres of wetlands and supports multiple at-risk reptiles and amphibians, including wood turtle and Blanding's turtle, plus several amphibians listed as state endangered or species of special concern. The management problem is straightforward: before you can protect sensitive species or control invasive ones, you need a reliable picture of where they are. Wisconsin also regulates a large number of aquatic invasive species that could threaten these wetlands, so early detection and mapping of occurrences matters. The planned approach is to sample ponds, ephemeral pools, and streams across three seasonal windows (spring, summer, fall). Typical sampling intensity is described as 10 to 30 sites per season, with three 1-liter replicate water samples per site, along with a molecular-grade water control handled at the site to help identify contamination. Water samples are filtered in the field or shortly after collection (0.80 micrometer cellulose nitrate filters), preserved in CTAB buffer, and then processed with an extraction method designed to handle common PCR inhibitors found in natural waters (for example, humic substances). Extracted DNA is quantified (Qubit) and sequenced using a multi-primer, multi-locus metabarcoding strategy aimed at capturing vertebrates, plants, and invertebrates from the same eDNA samples, producing a broad community snapshot that can highlight both imperiled and invasive taxa.

Task 2 addresses human and operational health risk by testing ticks for bacterial and protozoan pathogens at Fort McCoy. The rationale is that military training and natural resources work increase time spent in tick habitat, and ticks are responsible for the vast majority of vector-borne diseases in the United States, including Lyme disease. Field collection uses standard techniques such as cloth dragging and CO2 trap cloths, with sampling locations chosen based on habitat suitability and local input. At each site, the plan calls for five 150-meter transects in habitat likely to harbor ticks (for example, leaf litter in deciduous or mixed forest, or edge habitat between forest and grassland where animal activity is evident). Transects are revisited seasonally. A subset of 50 ticks is then analyzed in an appropriate biosafety setting using DNA extraction and RT-PCR diagnostics. For blacklegged ticks (Ixodes scapularis), the project follows a CDC-style screening approach for a set of major pathogens, including Anaplasma phagocytophilum, Babesia microti, Borrelia burgdorferi sensu stricto (Lyme disease), Borrelia miyamotoi, and Ehrlichia muris euclairensis. The practical deliverable is a clearer picture of pathogen presence and potential exposure risk on the installation, which can inform guidance, surveillance, and mitigation measures.

Task 3 uses metabarcoding in a different way: to evaluate pollinator monitoring and plant-pollinator interactions at Fort McCoy, with special attention to species of conservation concern. Fort McCoy supports federally endangered pollinators like the Karner Blue butterfly and the Rusty Patched Bumblebee, as well as other rare butterflies and skippers listed at the state level. The project compares conventional field surveys against an eDNA approach that attempts to detect pollinators from trace DNA left behind on flowers. Initial emphasis is placed on two butterfly species that have been petitioned for federal listing, the Frosted Elfin and the Regal Fritillary. Traditional surveys are conducted in plots chosen with installation staff based on host plant presence, past survey history, and access, using both random-walk methods and fixed 110 by 10 meter transects. Surveys occur multiple times across the flight season (roughly April through June), and they incorporate standardized recording of effort, weather, and habitat variables, following constraints like those in U.S. Fish and Wildlife Service guidance. When adult butterflies are scarce, surveyors also document eggs, larvae, and signs of larval feeding on host plants. In parallel, flowers are randomly selected in survey areas, identified to species, collected, and preserved for lab work. Pollinator trace eDNA is extracted (modified Qiagen DNeasy workflow), amplified, and sequenced (Illumina at a core facility), and the resulting reads are processed through a reproducible bioinformatics pipeline (metaBEAT) to generate taxonomic assignments. The end goal is to judge how well flower-based eDNA metabarcoding can detect at-risk pollinators and describe which pollinators are visiting which plants, potentially offering a scalable complement to labor-intensive visual surveys.

Task 4 shifts to population genomics for at-risk bats (Myotis species) at Camp Grayling, Michigan, motivated by the severe declines linked to white-nose syndrome since 2006, with some bat populations dropping by more than 90 percent. The scientific premise is that surviving individuals and populations may carry genetic signatures associated with resistance or tolerance, and the northern Midwest has comparatively limited genomic data for these taxa. The work includes field sampling using wing biopsy punches to obtain tissue suitable for genomic analysis, followed by laboratory processing and reporting. While the opportunity description does not specify an exact sequencing platform or genomic method, the intent is clear: generate data that help fill a regional gap and allow comparisons with other studies to support broader, range-wide assessments of vulnerability and persistence. Outputs are expected to feed directly into installation reporting on at-risk species status and, by extension, inform conservation and compliance planning on DoD lands.

Overall, this opportunity is a compact, applied research project that blends field sampling, molecular lab workflows, and bioinformatics to deliver practical intelligence for managing sensitive species and ecological risks on military lands. The emphasis is on demonstrating and operationalizing molecular tools (eDNA metabarcoding, targeted pathogen PCR diagnostics, and bat genomics) in ways that are coordinated with installation managers and can translate into clearer occurrence data, improved monitoring efficiency, and better-informed decisions about habitat management, invasive species threats, and disease exposure.

• The Department of Defense, Dept. of the Army -- Corps of Engineers in the science and technology and other research and development sector is offering a public funding opportunity titled "Molecular Tools for Management of Threatened and Endangered Species" and is now available to receive applicants.
• Interested and eligible applicants and submit their applications by referencing the CFDA number(s): 12.630.
• This funding opportunity was created on Jan 27, 2022.
• Applicants must submit their applications by Feb 25, 2022. (Agency may still review applications by suitable applicants for the remaining/unused allocated funding in 2026.)
• Each selected applicant is eligible to receive up to $64,300.00 in funding.
• The number of recipients for this funding is limited to 1 candidate(s).
• Eligible applicants include: Others (see text field entitled Additional Information on Eligibility for clarification).

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