Cooperative Agreement for CESU-affiliated Partner with Chesapeake Watershed Cooperative Ecosystem Studies Unit | G21AS00552

Opportunity Information: Apply for G21AS00552

The U.S. Geological Survey (USGS) is soliciting proposals for a cooperative agreement under the Cooperative Ecosystem Studies Unit (CESU) Program, specifically limited to partners affiliated with the Chesapeake Watershed CESU. The opportunity is focused on science and technology research and development and is intended to support applied molecular ecology work using targeted amplicon sequencing and next-generation sequencing to answer questions across several ecological themes. The funding opportunity number is G21AS00552 (CFDA 15.808), and it was released as a discretionary cooperative agreement, meaning USGS anticipates substantial involvement and collaboration during the project rather than operating strictly as a hands-off grant.

At its core, the project supports a suite of studies that all rely on the same technical approach: extracting DNA from challenging, real-world environmental and biological samples and using genetic barcode markers to amplify and sequence mixed DNA communities in a single run. Example applications mentioned include diet analysis, identification of plant taxa present in honeybee-collected pollen, and molecular investigations relevant to coral reef systems. In each case, the scientific value comes from being able to detect and quantify many contributing organisms from one composite sample, which can outperform traditional microscopy in sensitivity and resolution. The notice also highlights a specific research gap the work aims to address: while PCR-based amplicon diet methods are relatively common and well-developed for carnivores, herbivore diet studies are less represented in the literature because plant material often includes PCR inhibitors and because reference barcode libraries for local plant communities can be incomplete. The USGS is effectively seeking a partner that can help push these methods forward, especially where plant-rich samples make the laboratory and bioinformatics workflow more complex.

Eligibility is restricted to organizations that are active partners in the Chesapeake Watershed CESU network. The project is also framed around staffing expectations: the recipient should provide one postdoctoral researcher or graduate student to serve as the Principal Investigator. Beyond general research capability, USGS is signaling the need for a fairly complete end-to-end skill set, from field sampling through sequencing and downstream analytics. Required or strongly preferred qualifications include demonstrated experience with field collections spanning both plant and aquatic organisms, hands-on familiarity with Illumina MiSeq and next-generation sequencing workflows, and competence in bioinformatics processing and visualization of high-throughput sequence data. The announcement specifically calls out using R and relevant tools (for example FASTQC for quality control, ggplot2 for visualization, and platforms such as CLC Genomics Workbench) to organize, summarize, analyze, and present genomic or genetic datasets. Experience working in Linux environments and handling sequence processing pipelines is described as beneficial but not mandatory, while practical familiarity with sample collection and DNA extraction across a wide variety of sample types is preferred because these projects often hinge on overcoming contamination, inhibition, and variable DNA quality.

Topic familiarity also matters. USGS indicates a preference for applicants who understand issues tied to diet studies, invasive aquatic species, honey bees, or coral systems, reflecting the range of planned applications for the sequencing work. Publication experience is another differentiator: having at least one manuscript as lead author is described as desirable, suggesting the agency wants the project to produce publishable scientific outputs and not just internal data products. Finally, because the CESU model emphasizes collaboration, the notice underscores the value of experience working within dynamic, multidisciplinary teams operating across both field and laboratory settings.

From an administrative standpoint, the award ceiling listed is $240,000, with an original closing date of July 7, 2021, and the opportunity was created on June 7, 2021. While the announcement does not provide detailed deliverable lists in the excerpt, the emphasis on cooperative agreement structure, method development for difficult sample types (especially plant-heavy diets), and robust bioinformatics capacity strongly implies expected outcomes such as validated laboratory protocols, sequencing datasets suitable for ecological inference, and well-documented analytical workflows that can be shared, reproduced, and extended to multiple study systems.

• The Geological Survey in the science and technology and other research and development sector is offering a public funding opportunity titled "Cooperative Agreement for CESU-affiliated Partner with Chesapeake Watershed Cooperative Ecosystem Studies Unit" and is now available to receive applicants.
• Interested and eligible applicants and submit their applications by referencing the CFDA number(s): 15.808.
• This funding opportunity was created on 2021-06-07.
• Applicants must submit their applications by 2021-07-07. (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 $240,000.00 in funding.
• Eligible applicants include: Others.

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