Cooperative Agreement for CESU-affiliated Partner with Californian Cooperative Ecosystem Studies Unit | G21AS00309

Opportunity Information: Apply for G21AS00309

This grant opportunity is a US Geological Survey Western Ecological Research Center (USGS-WERC) cooperative agreement intended specifically for an eligible partner within the Californian Cooperative Ecosystem Studies Unit (CESU) network. The overall aim is to continue building and improving a wildlife immunology and nearshore ecosystem health research program that uses molecular tools, especially gene transcription (transcriptomics), to detect early physiological signs of stress in marine organisms. The work is framed around growing concerns that nearshore marine habitats are being pressured by climate-driven changes (warming waters and expected increases in ocean acidification) as well as expanding industrial and commercial activity such as oil and gas development, tourism, and resource harvesting. While Alaska's remoteness has historically reduced some direct human impacts, the opportunity emphasizes that Alaskan coastal systems are still vulnerable to large-scale climate stressors and to contamination risks as industrial activity increases.

A central motivation for the project comes from lessons learned after the 1989 Exxon Valdez oil spill, which demonstrated that even low, persistent concentrations of hydrocarbons can cause long-lasting harm to exposed species. USGS-WERC notes that its recent work has already detected differences in gene transcription patterns among Alaskan parks and sites, suggesting that both broad regional conditions and local stressors are influencing organism health. Because gene transcription assays can reveal physiological changes before obvious population-level declines occur, they are presented as a practical early warning system for managers responsible for sustaining intertidal resources. Building on prior USGS work, including Bowen et al. (2020, PeerJ), this funding is positioned as the next step to strengthen the genetic and transcriptomic toolkit for monitoring nearshore ecosystem condition.

The indicator species at the heart of the research is the Pacific razor clam (Siliqua patula), chosen because it is ecologically important (as prey for marine animals) and economically important (supporting commercial, sport, and personal-use harvest). The opportunity highlights a striking management and conservation contrast within Alaska: West Cook Inlet (WCI), including the area near Polly Creek, continues to support the state's largest commercial razor clam fishery, averaging around 300,000 pounds harvested annually, and also supports recreational harvest that benefits local economies. In East Cook Inlet (ECI), however, a historically massive sport and personal-use fishery along the beaches between the Kasilof and Anchor rivers collapsed: harvest levels from 2009 to 2012 were reported as substantially below the long-term average from 1977 to 2008, leading to restrictions in 2013 and full closure by 2015, with clam numbers not rebounding to historical levels afterward. This contrast sets up a core scientific and management question: what environmental, contaminant, or physiological differences might help explain why one area remains productive while another has not recovered?

USGS-WERC is seeking a CESU partner that can demonstrate real capability and a publication track record in transcriptomic analyses for Pacific razor clams. The cooperative agreement structure is important here: it is not simply a pass-through grant, but a collaborative effort in which the federal partner (USGS) and the CESU-affiliated institution work closely to produce decision-support products for nearshore conservation and management. The intended users of the outputs include agencies and organizations responsible for coastal stewardship, such as the US Fish and Wildlife Service, the National Park Service, and state and local agencies in California and Alaska, along with nongovernmental organizations. The larger vision is that the methods and tools developed for Alaska can be applied much more broadly, contributing to nearshore ecosystem conservation strategies worldwide.

The research plan is organized into two distinct work elements, and each is expected to result in a peer-reviewed publication and an accompanying data release. While the announcement does not lay out every experimental detail, it makes clear that the project is meant to expand beyond earlier efforts and produce stronger, more actionable molecular indicators of stress and health. A key deliverable across the work is a refined transcriptome-based panel (a set of genes or gene-expression markers) that can be used to assess nearshore ecosystem health. This is intended to move the field from small, preliminary gene sets toward a more informative and reliable diagnostic panel grounded in broader transcriptomic knowledge and, potentially, controlled laboratory exposure studies that help link specific stressors to measurable gene-expression responses.

A major technical gap the project aims to address is how little genetic information currently exists for the Pacific razor clam. The previous study referenced in the opportunity relied on a limited transcript panel of about five genes, largely because the species is underrepresented in public genetic databases compared with other commercially harvested invertebrates. The notice points out that, at the time of writing, GenBank contained only a handful of sequences for Pacific razor clams, essentially representing a single gene, underscoring how thin the reference information is. By contrast, work on the Chinese razor clam (Sinonovacula constricta) has identified genes responsive to stressors like heavy metals, anthropogenic sound, and bacterial challenges, yet even there the proportion of transcripts with strong database matches can be low. The implication is that a deeper look at the Pacific razor clam transcriptome may reveal additional stress-responsive genes, improve interpretation of field patterns, and potentially refine or even change earlier conclusions drawn from a small marker set.

From an administrative standpoint, this is a discretionary funding opportunity from the US Geological Survey under CFDA 15.808, offered as a cooperative agreement through the CESU program. Eligibility is restricted to partners in the Californian CESU. The funding opportunity number is G21AS00309, with an award ceiling of $50,000 and an original closing date of 2021-02-26. The practical expectation is that the selected CESU partner will collaborate closely with USGS-WERC to generate publishable science, publicly releasable datasets, and an improved transcriptomic assessment tool that resource managers can use to detect emerging stress in coastal ecosystems early enough to inform intervention, monitoring priorities, and long-term management decisions.

• 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 Californian 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 2021-02-02.
• Applicants must submit their applications by 2021-02-26. (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 $50,000.00 in funding.
• Eligible applicants include: Others.

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