Cooperative Agreement for CESU-affiliated Partner with North Atlantic Coast CESU Cooperative Ecosystem Studies Unit | G23AS00402

FAQs: USGS Great Lakes Science Center Cooperative Agreement (G23AS00402)

What is this funding opportunity?

This is a US Geological Survey (USGS) Great Lakes Science Center cooperative agreement (opportunity number G23AS00402) supporting applied research and development to improve control options for invasive aquatic and wetland plants in the Great Lakes region using modern genomics.

What is the main purpose of the project?

The purpose is to move beyond broad, non-specific invasive plant control methods by building the genetic knowledge needed to design more species-specific, gene-based interventions. The project is designed to generate actionable genetic targets that resource managers could use to prioritize and deploy more precise control strategies.

Which invasive plant species are the focus of this opportunity?

The opportunity targets two non-native invasive plants that are major management concerns in the Great Lakes region:

• Phragmites australis ssp. australis (common reed)
• Hydrocharis morsus-ranae (European frog-bit)

Why focus on genomics for invasive plant control?

USGS describes a need to build genetic knowledge that can enable species-specific interventions. The intent is to identify genes and biological pathways connected to invasive traits (such as rapid growth, reproduction, persistence, stress tolerance, and spread), which can then inform targeted control concepts rather than relying only on broad control approaches.

What is the specific knowledge gap this project is trying to address?

A key gap is that comparable genomic resources are not yet available for European frog-bit (Hydrocharis morsus-ranae). In addition, genetic studies have not adequately examined which environmental signals and stressors trigger or amplify these invasive plants development, stress tolerance, and increased aggressiveness, especially under Great Lakes climate conditions projected for the future.

How does existing research support this work?

USGS notes that prior investments have already produced foundational genomic and transcriptomic resources for Phragmites. That provides a head start for identifying control targets in Phragmites. In contrast, European frog-bit lacks similar resources, so the opportunity emphasizes building those missing foundational datasets.

What are the technical aims of the project?

The work is organized into three technical aims that build toward functional genomics and systems biology-style predictions linking genes to invasive traits:

• Aim 1: Characterize the genome of Hydrocharis morsus-ranae and use comparative genomics to identify genes linked to invasive potential and critical growth processes.
• Aim 2: Use comparative transcriptomics to identify genes uniquely expressed or highly expressed during critical developmental stages of Hydrocharis morsus-ranae.
• Aim 3: Develop potential RNA interference (RNAi) based genetic tools targeting candidate genes in both Phragmites australis ssp. australis and Hydrocharis morsus-ranae.

What does Aim 1 (genome characterization and comparative genomics) involve?

Aim 1 involves generating and analyzing genomic information for European frog-bit and comparing it with related species or existing datasets. The goal is to pinpoint genetic features that may contribute to traits supporting invasiveness, such as rapid growth, reproduction, persistence, or other critical growth processes.

What does Aim 2 (comparative transcriptomics) involve?

Aim 2 focuses on gene activity rather than the DNA sequence alone. It uses comparative transcriptomics to identify genes that are uniquely expressed or highly expressed during critical developmental stages of European frog-bit. This is intended to show when and where key genes are switched on across the life cycle, helping narrow down promising intervention points.

What does Aim 3 (RNAi tool development) involve?

Aim 3 is the translational component. It involves developing potential RNA interference (RNAi) based genetic tools that target candidate genes in both Phragmites and European frog-bit. RNAi approaches generally aim to reduce or silence expression of specific genes, which could disrupt growth, reproduction, or stress responses if appropriate targets are selected.

What kind of control approach is USGS trying to enable?

The stated payoff is the potential to deliver a new type of invasive plant treatment that is described as both species-specific and transient. In this framing, species-specific means designed to affect only the target species, and transient means designed not to persist across multiple plant generations.

Why does the opportunity emphasize "species-specific and transient" treatments?

That emphasis signals an intent to reduce non-target impacts and long-term ecological side effects compared with some conventional controls, while still producing a practical management tool that could be used by resource managers.

How is climate relevance reflected in the project rationale?

The opportunity notes that existing genetic studies have not adequately examined which environmental signals and stressors drive development, stress tolerance, and aggressive spread, particularly under climate conditions projected for the Great Lakes. Closing that gap is part of the motivation for identifying genes tied to invasive traits under relevant environmental conditions.

Is this basic research or applied research?

Based on the description, it is targeted, mission-driven applied research and development. It funds creation of missing genomic and transcriptomic resources (especially for European frog-bit), leverages existing resources for Phragmites, and pushes toward RNAi-based proof-of-concept tools that could expand the invasive plant management toolbox in the Great Lakes.

What type of funding instrument is being used?

The opportunity uses a cooperative agreement. This typically implies substantial agency involvement during the project, such as coordination with USGS scientists, shared planning, and iterative review of methods and findings.

Who is eligible to apply?

Eligibility is limited to organizations that are active participating partners in the North Atlantic Coast Cooperative Ecosystem Studies Unit (CESU).

Which program and assistance listing is associated with this opportunity?

The opportunity is a discretionary financial assistance award under the CESU program and is associated with CFDA 15.808.

What is the activity category for this opportunity?

The activity category is Science and Technology and other Research and Development.

What is the maximum award amount (award ceiling)?

The posted award ceiling is $167,580.

What are the key dates listed for the opportunity?

The creation date listed is 2023-06-13, and the original closing date listed is 2023-07-21.

Which USGS center is associated with the opportunity?

The opportunity is associated with the USGS Great Lakes Science Center.

What outcomes are expected to be useful for resource managers?

The opportunity frames the intended outcomes as actionable genetic targets and the development of potential RNAi-based genetic tools. The broader intended payoff is to provide more precise control strategies for the two target invasive plants, with potential relevance to other high-priority invasive plants.

Does the opportunity include both species equally in all aims?

No. Aims 1 and 2 are focused on Hydrocharis morsus-ranae (European frog-bit), particularly because it lacks comparable genomic resources. Aim 3 targets candidate genes in both Phragmites australis ssp. australis and Hydrocharis morsus-ranae.

What makes European frog-bit a special emphasis in this opportunity?

European frog-bit is highlighted because comparable genomic resources are not yet available for it, creating a key knowledge gap that this project is intended to fill through genome characterization and transcriptomic analysis.

What makes Phragmites a good candidate for faster progress on genetic targets?

USGS notes that foundational genomic and transcriptomic resources already exist for Phragmites due to prior investments, creating a head start for identifying and evaluating potential control targets in that species.

What is meant by "functional genomics and systems biology style predictions" in this context?

In this opportunity, it refers to an approach that connects genes (and their expression patterns) to invasive traits by building toward predictive understanding of which genes and pathways contribute to growth, development, stress tolerance, and spread. The three aims are described as building toward that kind of gene-to-trait linkage.