Seed Funding

Project Title: Developing a Nanopore Barcoding Workflow for Identification of Larval Fish in Great Lakes Ichthyoplankton Samples

Key Project Personnel: Maggie Petersen (Great Lakes Environmental Center, Inc.)

About: Ichthyoplankton samples are useful for a wide array of applications and are often used as indicators of fish spawning populations, ecosystem health, and rare or endangered species detection. Accurate identification of larval fish and eggs from ichthyoplankton samples is a valuable tool in ecosystem assessment and can be applied in a variety of ways. Traditionally, larval fish have been manually identified with morphological features, but there is an increasingly limited pool of trained and experienced fish taxonomists capable of performing this work. Larval fish are also collected and analyzed during the certification process for cooling systems which utilize surface waters. Section 316(b) of the Clean Water Act addresses the issue of impingement and entrainment of aquatic life and the standards required for assessment of larval fish and eggs impacted by cooling systems. Several systems in Michigan are approaching recertification deadlines which will require accurate identification of larval fish in ichthyoplankton samples collected outside of their systems.

The aim of this project is to develop a workflow using genetic barcoding to identify individual larval fish from ichthyoplankton samples and compare results to traditional morphological identification. The team will assess the agreement between the two methods, if there is variation in taxonomic resolution between the two methods, and the per sample cost for each method. The study plan will involve the collection of ichthyoplankton samples throughout the Great Lakes, aiming at the highest diversity and abundance possible. Samples will be collected during other GLEC work at sites in Lakes Michigan, Huron, Superior, and Erie using standard methods. All samples will be sorted, isolating all larval fish and eggs, then the team’s staff taxonomists will identify each individual specimen to the lowest taxonomic assignment possible. DNA will be extracted from each, the target amplified, labeled with a unique barcode, and sequenced. Potential primers will target the mitochondrial cytochrome c oxidase subunit I (COI) or the mitochondrial 12S ribosomal RNA markers. Amplicons will be sequenced with Oxford Nanopore MiniION and each assigned a taxonomic identification. Secondary qPCR identification for taxa not resolved to species may be explored to further refine identification.

There is known commercial interest in this service, evidenced by requests the team has received for quotes for larval fish identification for 316(b) compliance. The successful development and deployment of a genetic barcoding method for larval fish and egg identification would be immediately useful for industry. Demonstration of cost-effectiveness would further drive utilization of the method, provided adequate validation was performed. Additionally, the team has identified interest from other partners in genetic larval fish identification for other applications, including fisheries management, ecosystem assessment, and conservation. The Grand Traverse Band of Ottawa and Chippewa Indians have expressed interest in the application, especially for assessment of the Coregonus genus, which could open avenues for additional research funding through systems such as the GLRI Distinct Tribal Program.

Project Title: Implications of record flooding on juvenile Lake Sturgeon habitat in the Manistee River

Key Project Personnel – PIs: Carl Ruetz and Sean Woznicki (GVSU-AWRI); Project partners: Jason Fischer (USFWS)and Corey Jerome (Little River Band of Ottawa Indians)

About: Historic flooding occurred in April 2026 on the Muskegon and Manistee rivers, likely altering the river channel geomorphology and habitat structure for biota. Coincidentally, GVSU-AWRI has ongoing research quantifying juvenile Lake Sturgeon (Acipenser fulvescens) habitat selection in these rivers. The Lake Sturgeon is a state threatened species due to habitat loss and overharvest. Juveniles–a life stage of considerable conservation interest–require specific river conditions with respect to depths, velocities, and substrate types. In 2025, the team performed comprehensive data collection and modeling to map juvenile Lake Sturgeon habitat use under record low-flow conditions (i.e., bathymetric mapping, substrate mapping, 1-D hydraulic modeling, and fish telemetry). The timing of the 2025 surveys and the 2026 flood provide a unique opportunity to understand the implications of extreme events on fish habitat selection. Repeating data collection will allow the team to explore additional questions focused on how juvenile Lake Sturgeon habitat availability changes following extreme floods that are increasing in frequency. The team will estimate the quantity and quality of habitat under two river states to address two research questions: (1) Did the flood create or destroy habitat? (2) How did the spatial distribution of habitat change? The approaches that ecologists use to map and model habitat selection (for any fish species) and make conservation decisions using those models typically operate under the implicit assumption of a steady state environment, which is usually reasonable over short time scales (e.g., a few years). Yet recent flooding events challenge the validity of this assumption, even over short time scales, and allow the team to test its importance for fish conservation.

The team will repeat the tasks completed in 2025 to map juvenile Lake Sturgeon habitat on the Manistee River from the river mouth to the first upstream dam (~45 km). The tasks are: (1) measure bathymetry and river velocity profiles at ~300 cross-sections using an acoustic Doppler current profiler (ADCP); (2) map substrate types using sidescan sonar; (3) update the hydraulic model to reflect geomorphological changes. The team will create a 2026 juvenile Lake Sturgeon habitat suitability map and a 2025-to-2026 habitat change map for the river.

The team plans to submit proposals to NSF RAPID (open call) and Great Lakes Fish and Wildlife Restoration Act Grant Program (announcement anticipated in fall 2026) following collection of preliminary data on the Manistee River supported by this grant. These proposals will aim to: (1) extend data collection on the Muskegon River; (2) conduct additional fish telemetry to produce complete pre- and post-flood data on juvenile Lake Sturgeon habitat use; (3) expand hydraulic models to explicitly simulate flooding in two dimensions. The team also will expand this research to consider multiple fishes of conservation interest beyond Lake Sturgeon, evaluating how the above research questions apply to Walleye (native), Lake Whitefish (native), Chinook Salmon (non-native), and Sea Lamprey (invasive) in terms of spawning and rearing habitat. Habitat requirements of these species will be obtained in the scientific literature.

Project Title: Great Lakes Nano- and Microplastics: Advancing Risk Assessment Through Harmonized Monitoring and Ecotoxicology

Key Project Personnel: Melissa Duhaime (Department of Ecology and Evolutionary Biology, University of Michigan)

About: Nano- and microplastics (NMPs) are widespread Great Lakes (GLs) contaminants in aquatic, terrestrial, and atmospheric habitats, as well as in body tissue and organs, with adverse effects. In response, binational lawmakers at federal (US’s Plastic Health Research Act, HR 4903; Canada’s “Zero Plastic Waste” plan) and GL state/provincial-levels (e.g., Ontario Bill 83; MI SB 503/504/505, HB 4766/4768/4767; IL 4269; MN HF 855, SF 1389/2245; NY S1464/A1749; WI Act 43) have enacted or proposed legislation to establish NMPs monitoring, health impacts, and reduction strategies.

However, policy and management experts lack the harmonized NMP occurrence and effect data for this important work, as recently highlighted by two major reports: (1) a GL-focused risk assessment, which identified fundamental misalignments and uncertainties in current Great Lakes NMP data, and (2) the International Joint Commission’s Science Advisory Board report, which stressed the specific need for more benthic NMPs data and exposure assessments to set reliable NMPs risk thresholds for the GLs.

The policy conversations are happening now. In Michigan, state agencies are scrambling to use resources they have for inland water monitoring, but have expressed eagerness (E. Kostelnick, EGLE) to collaborate as the team’s lab fills knowledge gaps in the GLs. Seed funding is requested to enable GL-wide sampling in 2026 to address these gaps and to advance GL NMPs sciences and policy.

The team’s short-term plan (summer 2026) is to join the Lake Guardian for GL-wide sampling to conduct water column and sediment sampling (near- and off-shore; invitation by E. Osantowski, EPA). The team’s long-term plan is to improve and reduce uncertainty in GL NMP risk assessment models and provide identified data needed for policy makers to guide future monitoring, legislation, and research. Samples collected through seed funding will be used to answer (through other funds):

Objective 1: Establish the relationship between quantification, size, and error, to enable more accurate parameterization of habitat-specific probability density functions (PDFs), which are important for bounding uncertainty in risk assessment models, especially for smaller NMPs (<1–30 μm; existing GL studies report only >100-300 μm).

Plan 1: The team will sample water and sediment across diverse habitats using new analytical methods (OPTIR, micro-Raman and CT) to quantify and characterize nano- and microplastics (NMPs; in collaboration with UM chemistry [McNeil] and statistics [Tewari] faculty), determine analytical error, and facilitate harmonized data for modeling NMP distribution and toxicity.

Objective 2: Determine ecotoxicological effects of NMPs on benthic GL indicator species to inform the insufficiently sparse species sensitivity distributions that limit current risk models for GL benthos2.

Plan 2. The team will assess toxic effects of NMPs on benthic worm T. tubifex through lab exposures, evaluating survival, growth, reproduction, and ingestion to inform risk assessment and strengthen collaborative modeling of plastics transport and impacts (in collab. with C. Rochman, U Toronto).

The team was contacted and invited to/will submit a proposal for the post-sampling part of this work by Georgian Bay Forever foundation. The team (Duhaime, McNeil, Tewari) will submit a proposal to the GL Fisheries Commission1 (Jan 2026), whose current RFP requests both MPs exposure/effects and analytical methods development, extending this work. The team will submit a NSF BioOce proposal (Duhaime, Hoffman-RIT) to support hydrodynamic models using these new GL NMPs data. Samples collected in 2026 will be stable to store until additional funds for analysis are secure.