Opportunity Information: Apply for NPS NOIP18AC00009
The grant opportunity "Identify Factors Driving Clostridium botulinum Activities in Sleeping Bear Dunes National Lakeshore Coastal Ecosystems" is a National Park Service (NPS) cooperative agreement designed to tackle a persistent and damaging environmental health problem at Sleeping Bear Dunes National Lakeshore (SLBE) in Michigan: recurring outbreaks of type E avian botulism that have been happening since 2006. Over many years, SLBE and partner researchers have invested heavily in tracking bird deaths, studying nearshore conditions, mapping food web pathways, and improving public communication around outbreak risks. Even with that effort, one major gap has remained: the park and its research partners have not been able to reliably pin down what environmental and biological conditions actually trigger Clostridium botulinum to become active and produce botulinum toxin. The central goal of this project is to close that gap by applying newer microbiology tools and experimental approaches that can move beyond simply detecting the organism or its toxin gene and instead measure when the toxin machinery is actively turned on.
Structurally, this is a discretionary funding opportunity issued by the U.S. Department of the Interior, National Park Service, using a Cooperative Agreement as the funding instrument. The project is set up as a partnership between NPS and the Regents of the University of Michigan, with an emphasis on joint planning, shared datasets, collaborative interpretation, and coordinated outreach. The work fits within environmental research and science and technology research and development (CFDA 15.944). Eligibility is aimed at public and state-controlled institutions of higher education, and the opportunity anticipated a single award with a maximum federal amount of up to $500,000. The posting date was October 19, 2017, with an original closing date of November 2, 2017.
The project has three big objectives that shape all proposed activities. First, it aims to build a sustained, collaborative research program focused on microbiological issues affecting the park, with type E botulism as the priority. Second, it is explicitly designed to create hands-on training opportunities for students, including field-based research experiences in a national park setting. Third, it seeks to increase NPS capacity so the park can do more of this analysis internally over time, rather than relying entirely on outside labs and external experts whenever an outbreak occurs or monitoring questions arise.
The technical heart of the work is a set of five tasks that move from method development to experimentation to operational capacity-building. Task 1 focuses on upgrading molecular detection methods. Prior efforts at SLBE used quantitative PCR (qPCR) to detect and measure the abundance of the gene associated with the botulinum neurotoxin (BoNT). That approach was useful for showing where the gene exists (in sediments, mussels, bird tissue, and the macroalga Cladophora), but it could not answer the more urgent management question: is the toxin gene being actively expressed right now? To solve that, the project proposes adding RNA-based measurements using reverse transcription qPCR (RT-qPCR). RNA assays allow researchers to estimate gene expression, which is a closer proxy for toxin production than DNA presence alone. The plan also keeps DNA testing in place so expression can be normalized against gene abundance, improving comparisons across samples and conditions. Samples to develop and validate these assays were to be collected through a University of Michigan field microbiology course and through ongoing nearshore sampling with an established research partner.
Task 2 shifts into controlled laboratory experimentation at the University of Michigan. Using field-collected samples, the team would run experiments to test how nutrient conditions and temperature influence the growth and activity of toxin-producing C. botulinum. This is important because nearshore ecosystems can experience changing nutrient inputs and warming conditions, both of which may affect bacterial behavior. The experiments also include characterizing the broader microbial community, not just C. botulinum in isolation. That piece reflects the idea that toxin production might be shaped by interactions among microbes, such as competition, facilitation, or changes in community structure that either suppress or enable C. botulinum activity.
Task 3 brings hypothesis testing into real-world SLBE settings through field experiments. The project proposes field work aimed at understanding how C. botulinum gene abundance and expression respond to specific ecosystem conditions. A key anchor for this effort is an existing experiment at the Good Harbor reef site involving the removal of dreissenid mussels (invasive mussels known to strongly alter Great Lakes nearshore food webs and nutrient cycling). Researchers would collect mixed biological material scraped from rocks, preserve it for DNA and RNA analysis, and in some cases separate it into categories such as mussels, invertebrates, and Cladophora to see where gene presence and expression are concentrated. Water samples collected about one meter above the lake bottom would also be analyzed. The project leaves room for additional field experiments as time and funding allow, including work in beach habitats that may be relevant to the park's federally endangered Piping Plover population, reflecting concern about broader wildlife exposure and habitat management.
Task 4 is oriented toward management needs, specifically the search for early warning indicators of outbreaks. The practical problem for SLBE is not only understanding why outbreaks happen, but being able to anticipate them in time to reduce wildlife exposure and public risk. The project proposes frequent sampling (about weekly) at beach sites already monitored for recreational health, along with routine sampling of sediments and Cladophora in nearshore depositional areas. The idea is to look for microbial community signals that appear before or alongside increased expression of the toxin gene, similar to how some studies have identified microbial indicators that precede harmful algal blooms. If reliable indicators can be found, SLBE could potentially use them as a forecast tool to trigger targeted monitoring, visitor messaging, or mitigation actions sooner.
Task 5 focuses on building SLBE's in-house technical ability to run botulism-related analyses. SLBE has a refurbished microbiology lab and qPCR capabilities that could support some of this work, but staff training and workflow development are necessary to make it routine and dependable. Under this task, the university team would train SLBE staff in processing and analyzing field samples for C. botulinum and possibly for other microbial indicators tied to botulism risk. This component is meant to leave the park with lasting capacity, reducing turnaround time for results and improving the park's ability to respond during outbreaks.
The agreement also clearly defines roles. The University of Michigan, as the recipient, commits to developing the DNA/RNA assays, running the lab and field experiments, searching for microbial precursors and indicators, and helping SLBE build internal analytical capacity. The National Park Service commits to supporting project development and coordination, providing technical help during field work, assisting with site selection and sample collection, orienting researchers to park resources and lab facilities, and integrating the research with broader park education and outreach efforts. Both parties commit to regular communication, data sharing, joint analysis and reporting, and co-developing outreach materials so findings can inform both scientific understanding and practical park management.
Overall, this opportunity is best understood as a targeted applied research partnership: it funds the development of better detection tools, uses those tools to test specific environmental and biological drivers of type E botulism in a Great Lakes nearshore system, and aims to translate results into earlier warning capability and stronger on-the-ground capacity at Sleeping Bear Dunes National Lakeshore.Apply for NPS NOIP18AC00009
- The Department of the Interior, National Park Service in the environment, natural resources, science and technology and other research and development sector is offering a public funding opportunity titled "Identify Factors Driving Clostridium botulinum Activities in Sleeping Bear Dunes National Lakeshore Coastal Ecosystems" and is now available to receive applicants.
- Interested and eligible applicants and submit their applications by referencing the CFDA number(s): 15.944.
- This funding opportunity was created on Oct 19, 2017.
- Applicants must submit their applications by Nov 02, 2017. (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 $500,000.00 in funding.
- The number of recipients for this funding is limited to 1 candidate(s).
- Eligible applicants include: Public and State controlled institutions of higher education.
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Frequently Asked Questions (FAQs)
What is the title of this grant opportunity?
The opportunity is titled "Identify Factors Driving Clostridium botulinum Activities in Sleeping Bear Dunes National Lakeshore Coastal Ecosystems."
Which agency is offering this funding?
This is a discretionary funding opportunity from the U.S. Department of the Interior, National Park Service (NPS).
What type of funding instrument is being used?
The award is structured as a Cooperative Agreement, emphasizing substantial involvement and collaboration between NPS and the recipient.
What problem is this project trying to solve?
The project targets recurring outbreaks of type E avian botulism at Sleeping Bear Dunes National Lakeshore (SLBE) in Michigan, which have been occurring since 2006. A key unresolved gap is identifying the environmental and biological conditions that trigger Clostridium botulinum to become active and produce botulinum toxin.
Why is there a need for new methods if the park has already done monitoring and research?
SLBE and partners have tracked bird deaths, studied nearshore conditions, mapped food web pathways, and improved public communication for years. However, prior work could not reliably determine when C. botulinum is actively expressing toxin-related machinery (a step closer to actual toxin production), rather than merely being present in the environment.
Where will the project take place?
The work is focused on Sleeping Bear Dunes National Lakeshore (SLBE) coastal and nearshore ecosystems in Michigan, with laboratory experimentation conducted at the University of Michigan.
Who is the planned project partner/recipient?
The cooperative agreement is set up as a partnership between NPS and the Regents of the University of Michigan, with joint planning, shared datasets, collaborative interpretation, and coordinated outreach.
What is the CFDA program listing for this opportunity?
The opportunity is associated with CFDA 15.944 and is described as fitting within environmental research and science and technology research and development.
Who is eligible to apply based on the description provided?
Eligibility is aimed at public and state-controlled institutions of higher education.
Is this expected to be a single award or multiple awards?
The opportunity anticipated a single award.
What is the maximum federal funding amount?
The maximum federal amount is up to $500,000.
When was the opportunity posted and when did it close?
The posting date was October 19, 2017, and the original closing date was November 2, 2017.
What are the main objectives of the project?
The project is organized around three major objectives: (1) build a sustained, collaborative research program focused on microbiological issues affecting SLBE, with type E botulism as the priority; (2) create hands-on training opportunities for students, including field-based research experiences in a national park setting; and (3) increase NPS capacity so SLBE can conduct more analysis internally over time.
What is the central scientific gap the project is designed to address?
The central gap is the inability to reliably determine what conditions trigger C. botulinum to become active and produce toxin. The project aims to move beyond simply detecting the organism or its toxin gene and instead measure when toxin-related genetic activity is turned on.
How does the project plan to improve detection beyond prior approaches?
Earlier SLBE work used quantitative PCR (qPCR) to detect and quantify the abundance of the botulinum neurotoxin (BoNT) gene in materials like sediments, mussels, bird tissue, and the macroalga Cladophora. This project adds RNA-based measurements using reverse transcription qPCR (RT-qPCR) to estimate gene expression, which is a closer proxy for active toxin production than DNA presence alone. DNA testing is retained so expression can be normalized against gene abundance.
What is included in Task 1?
Task 1 focuses on upgrading molecular detection methods by developing and validating RT-qPCR assays for RNA (gene expression) while continuing DNA testing for normalization. Samples for method development and validation are to be collected through a University of Michigan field microbiology course and ongoing nearshore sampling with an established research partner.
What is included in Task 2?
Task 2 consists of controlled laboratory experiments at the University of Michigan. Using field-collected samples, the team will test how nutrient conditions and temperature influence growth and activity of toxin-producing C. botulinum. This task also includes characterizing the broader microbial community, reflecting the idea that microbial interactions may influence toxin production.
What is included in Task 3?
Task 3 involves field experiments at SLBE to test hypotheses in real-world conditions and understand how C. botulinum gene abundance and expression respond to ecosystem conditions. A key element is an existing Good Harbor reef experiment involving removal of dreissenid mussels. The plan includes collecting mixed biological material scraped from rocks (preserved for DNA/RNA), optionally separating it into categories such as mussels, invertebrates, and Cladophora, and analyzing water samples collected about one meter above the lake bottom. The task also leaves room for additional field experiments, including beach habitat work relevant to the federally endangered Piping Plover.
What is included in Task 4?
Task 4 is aimed at identifying early warning indicators for outbreaks. It proposes frequent (about weekly) sampling at beach sites already monitored for recreational health, along with routine sampling of sediments and Cladophora in nearshore depositional areas. The goal is to look for microbial community signals that appear before or alongside increased expression of the toxin gene, potentially enabling earlier forecasting and response actions.
What is included in Task 5?
Task 5 focuses on building SLBE's in-house capacity to run botulism-related analyses. SLBE has a refurbished microbiology lab and qPCR capabilities, but staff training and workflow development are needed to make analysis routine and dependable. Under this task, the University of Michigan team would train SLBE staff in processing and analyzing field samples for C. botulinum and potentially other microbial indicators tied to botulism risk.
How does the project connect research to practical park management needs?
The project is designed as applied research that can inform real decisions, especially by (1) measuring toxin-gene expression rather than only DNA presence, (2) testing likely drivers such as nutrients and temperature, (3) evaluating field conditions including the influence of invasive dreissenid mussels and nearshore habitats, (4) seeking early warning microbial indicators for forecasting outbreaks, and (5) training SLBE staff to reduce reliance on outside labs and speed up response during outbreak events.
What role will students play in the project?
Student training is an explicit objective. The project includes hands-on training opportunities and field-based experiences in a national park setting, including sample collection through a University of Michigan field microbiology course.
What are the responsibilities of the University of Michigan under the agreement?
As described, the University of Michigan (recipient) is responsible for developing DNA/RNA assays, running laboratory and field experiments, searching for microbial precursors/indicators, and helping SLBE build internal analytical capacity.
What are the responsibilities of the National Park Service under the agreement?
NPS commits to supporting project development and coordination, providing technical help during field work, assisting with site selection and sample collection, orienting researchers to park resources and lab facilities, and integrating research with park education and outreach.
How will the partners work together during the project?
Both parties commit to regular communication, data sharing, joint analysis and reporting, and co-developing outreach materials so the findings can inform scientific understanding and park management.
What kinds of samples and habitats are mentioned in the project approach?
The description references sampling and analysis of sediments, dreissenid mussels, bird tissue (from earlier work), Cladophora, mixed biological material scraped from rocks, and water collected about one meter above the lake bottom. It also mentions beach sites monitored for recreational health and nearshore depositional areas.
Why are dreissenid mussels specifically mentioned?
Dreissenid mussels are described as invasive mussels that strongly alter Great Lakes nearshore food webs and nutrient cycling. The project builds on an existing Good Harbor reef experiment involving mussel removal to examine how those ecosystem changes relate to C. botulinum gene abundance and expression.
How could the results improve outbreak response at SLBE?
If the project identifies conditions that trigger activity and finds reliable microbial early warning indicators, SLBE could potentially anticipate outbreaks sooner and use that information to trigger targeted monitoring, visitor messaging, or mitigation actions. Task 5 also aims to reduce turnaround time by enabling more in-house analysis.
Is outreach or public communication part of the project?
Yes. The cooperative agreement emphasizes coordinated outreach and co-development of outreach materials, and NPS will integrate the research with broader park education and outreach efforts.
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