Advanced molecular tools for detection and monitoring of invasive carp
Environmental DNA (eDNA) and related molecular methods are important tools for helping to detect and monitor invasive carp presence in the Mississippi River and Great Lakes basins. The use of eDNA has become a common method for detecting presence of invasive carp in areas of low density and uncertain presence. Furthermore, eDNA can be used to identify activities such as spawning. However, an eDNA detection is more uncertain than a capture of a live fish and requires rigorous laboratory quality control. An important aspect of our work is to help develop standards and tools for eDNA detection as well as better understanding the factors influencing eDNA detection of invasive carp. Our research has a direct application to management activities that can benefit from a monitoring tool that can detect invasive carp in aquatic systems that are otherwise difficult to survey using traditional techniques.
Our major objectives for this project are:
- Invasive front monitoring and interpretation
- We conducted eDNA monitoring for bighead and silver carp across the Upper Mississippi River (UMR) from 2014-2023. Samples were collected across several pools, with locations standardized across each year. However, due to the current presence of bigheaded carps up through Pool 5A after the 2023 floods (Fritts et al. 2024), we shifted our efforts to develop and test approaches that can be used to detect evidence of spawning in the upper pools, which has not yet been documented in Minnesota and Wisconsin waters. To do this, we will be testing environmental RNA (eRNA) approaches that could detect evidence of reproduction or recruitment. The advantage of eRNA is that RNA is only produced in living organisms when a gene is expressed. We will identify specific genes that are expressed during spawning or in juvenile fish, but are not in non-spawning adults. Presence of RNA from these genes would indicated potential reproduction. We are also testing eDNA approaches for detecting black carp at their invasion front in Illinois and Missouri. Finally, we have conducted joint studies with other agencies, such as the U.S. Fish and Wildlife Service to optimize methods and provide context for rare carp eDNA detections through their monitoring program.
- eDNA support for management actions
- We are using eDNA detection to help evaluate the success of natural resource management actions for invasive carp. For example, we used eDNA before and after mass carp removal events to assess whether eDNA carp detections have decreased. We have also used eDNA as a monitoring tool for UGSS grass carp attractant (bait) research to help monitor fish aggregations for more efficient removal.
- Ecology of eDNA
- Understanding the sources, transport, and fate of eDNA is crucial for interpretation of eDNA monitoring results. We are defining species-specific eDNA shedding and degradation rates for invasive carp in laboratory studies, and quantifying transport of eDNA in manipulative field experiments.
- Standardization of eDNA practices
- Development of standard practices for eDNA sampling, preservation, analysis, and interpretation are key for technology transfer and familiarizing the technique among natural resource managers. We are working with multiple partners, including the Non-indigenous Aquatic Species database, CSA Group, the Genome Canada iTrackDNA project, the USGS Readi-Net initiative, and the International eDNA Standards Task Force.
References:
Fritts, M., Gibson-Reinemer, D., Appel, D. et al. Flooding and dam operations facilitate rapid upstream migrations of native and invasive fish species on a regulated large river. Sci Rep 14, 20609 (2024). https://doi.org/10.1038/s41598-024-70076-4
Environmental DNA (eDNA) and related molecular methods are important tools for helping to detect and monitor invasive carp presence in the Mississippi River and Great Lakes basins. The use of eDNA has become a common method for detecting presence of invasive carp in areas of low density and uncertain presence. Furthermore, eDNA can be used to identify activities such as spawning. However, an eDNA detection is more uncertain than a capture of a live fish and requires rigorous laboratory quality control. An important aspect of our work is to help develop standards and tools for eDNA detection as well as better understanding the factors influencing eDNA detection of invasive carp. Our research has a direct application to management activities that can benefit from a monitoring tool that can detect invasive carp in aquatic systems that are otherwise difficult to survey using traditional techniques.
Our major objectives for this project are:
- Invasive front monitoring and interpretation
- We conducted eDNA monitoring for bighead and silver carp across the Upper Mississippi River (UMR) from 2014-2023. Samples were collected across several pools, with locations standardized across each year. However, due to the current presence of bigheaded carps up through Pool 5A after the 2023 floods (Fritts et al. 2024), we shifted our efforts to develop and test approaches that can be used to detect evidence of spawning in the upper pools, which has not yet been documented in Minnesota and Wisconsin waters. To do this, we will be testing environmental RNA (eRNA) approaches that could detect evidence of reproduction or recruitment. The advantage of eRNA is that RNA is only produced in living organisms when a gene is expressed. We will identify specific genes that are expressed during spawning or in juvenile fish, but are not in non-spawning adults. Presence of RNA from these genes would indicated potential reproduction. We are also testing eDNA approaches for detecting black carp at their invasion front in Illinois and Missouri. Finally, we have conducted joint studies with other agencies, such as the U.S. Fish and Wildlife Service to optimize methods and provide context for rare carp eDNA detections through their monitoring program.
- eDNA support for management actions
- We are using eDNA detection to help evaluate the success of natural resource management actions for invasive carp. For example, we used eDNA before and after mass carp removal events to assess whether eDNA carp detections have decreased. We have also used eDNA as a monitoring tool for UGSS grass carp attractant (bait) research to help monitor fish aggregations for more efficient removal.
- Ecology of eDNA
- Understanding the sources, transport, and fate of eDNA is crucial for interpretation of eDNA monitoring results. We are defining species-specific eDNA shedding and degradation rates for invasive carp in laboratory studies, and quantifying transport of eDNA in manipulative field experiments.
- Standardization of eDNA practices
- Development of standard practices for eDNA sampling, preservation, analysis, and interpretation are key for technology transfer and familiarizing the technique among natural resource managers. We are working with multiple partners, including the Non-indigenous Aquatic Species database, CSA Group, the Genome Canada iTrackDNA project, the USGS Readi-Net initiative, and the International eDNA Standards Task Force.
References:
Fritts, M., Gibson-Reinemer, D., Appel, D. et al. Flooding and dam operations facilitate rapid upstream migrations of native and invasive fish species on a regulated large river. Sci Rep 14, 20609 (2024). https://doi.org/10.1038/s41598-024-70076-4