Developing a portable LAMP assay for detecting grass and black carp Active
Aquatic invasive species are a significant problem throughout the world. They cause millions of dollars in damages to industry, devastate natural ecosystems, and ruin outdoor recreational areas. Preventing their spread is imperative to preserving our natural resources. One potential pathway invasive fishes can spread is by harvesting and transporting baitfish. Often shipments of baitfish are transported great distances from where they were collected, and thus pose a risk of transporting invasive species into new areas. Because baitfish are typically small minnow species (of the family Cyprinidae) and are transported by the thousands, there is a risk for just a few similarly sized invasive fishes to be included, and it is virtually impossible to visually detect and completely remove unwanted species from the hauling tanks.
Asian carp are a group of aquatic invasive species are of particular concern. Bigheaded carps (Hypophthalmichthys nobilis and H. molitrix) have had a significant and well documented impact on the Mississippi River Basin (Kolar and others, 2007). Grass carp (Ctenopharyngodon idella) and black carp (Myelopharyngodon piceus) are two other Asian carp species that are of growing concern since they have been shown to be reproducing naturally (Chapman and others, 2013; Whitledge and others, 2015). We have developed and validated a portable kit that uses LAMP to detect bigheaded carps in bait tanks (Merkes and others, unpublished data). This kit is currently in use by law enforcement in three states to help stop the spread of bigheaded carps, and the development of another assay to detect grass and black carp would expand their capacity to help stop the spread of these invasive species as well.
In this study, we will develop a new assay to detect black and grass carp, and we will model this effort based on the work done to validate the bigheaded carps portable detection kit.
Objectives
- Develop a LAMP assay to detect grass carp and black carp.
- Determine the minimum density of grass carp that need to be present for the LAMP assay to get positive detection.
- Determine the minimum amount of time that grass carp must be held in transport tanks for the LAMP assay to get positive detection.
- Determine the minimum number of replicates needed to run to gain confidence of positive detection.
References
Bates D, Maechler M, Bolker B, Walker S. (2015) Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software. 67:1, 1-48. doi: 10.18637/jss.v067.i01.
Chapman DC, Davis JJ, Jenkins JA, Kocovsky PM, Miner JG, Farver J, Jackson PR. (2013) First evidence of grass carp recruitment in the Great Lakes Basin. Journal of Great Lakes Research. 39(4): 547-554.
Kolar CS, Chapman DC, Courtenay WR Jr., Housel CM, Williams JD, Jennings DP. (2007) Bigheaded carps: a biological synopsis and environmental risk assessment. American Fisheries Society, Special Publication 33, Bethesda, Maryland.
Merkes CM, Jackson CA, Cronan LD, Erickson RA, Schoenfeld TW, Amberg JJ. (in review) Rapid molecular detection of aquatic invasive species in the field.
R Core Team. (2015) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Whitledge GW, Chapman DC, Jenkins JA, Bailey J, Nicks D. (2015) Evidence of black carp establishment in the Mississippi River. Presented at American Fisheries Society 145th annual meeting in Portland, Oregon on 17-August, 2015. https://afs.confex.com/afs/2015/webprogram/Paper19942.html
- Overview
Aquatic invasive species are a significant problem throughout the world. They cause millions of dollars in damages to industry, devastate natural ecosystems, and ruin outdoor recreational areas. Preventing their spread is imperative to preserving our natural resources. One potential pathway invasive fishes can spread is by harvesting and transporting baitfish. Often shipments of baitfish are transported great distances from where they were collected, and thus pose a risk of transporting invasive species into new areas. Because baitfish are typically small minnow species (of the family Cyprinidae) and are transported by the thousands, there is a risk for just a few similarly sized invasive fishes to be included, and it is virtually impossible to visually detect and completely remove unwanted species from the hauling tanks.
Asian carp are a group of aquatic invasive species are of particular concern. Bigheaded carps (Hypophthalmichthys nobilis and H. molitrix) have had a significant and well documented impact on the Mississippi River Basin (Kolar and others, 2007). Grass carp (Ctenopharyngodon idella) and black carp (Myelopharyngodon piceus) are two other Asian carp species that are of growing concern since they have been shown to be reproducing naturally (Chapman and others, 2013; Whitledge and others, 2015). We have developed and validated a portable kit that uses LAMP to detect bigheaded carps in bait tanks (Merkes and others, unpublished data). This kit is currently in use by law enforcement in three states to help stop the spread of bigheaded carps, and the development of another assay to detect grass and black carp would expand their capacity to help stop the spread of these invasive species as well.
In this study, we will develop a new assay to detect black and grass carp, and we will model this effort based on the work done to validate the bigheaded carps portable detection kit.
Objectives
- Develop a LAMP assay to detect grass carp and black carp.
- Determine the minimum density of grass carp that need to be present for the LAMP assay to get positive detection.
- Determine the minimum amount of time that grass carp must be held in transport tanks for the LAMP assay to get positive detection.
- Determine the minimum number of replicates needed to run to gain confidence of positive detection.
Sources/Usage: Public Domain. View Media DetailsUSGS Scientist Chris Merkes using portable detection kit (Credit: Mike Caucutt. Public domain.) References
Bates D, Maechler M, Bolker B, Walker S. (2015) Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software. 67:1, 1-48. doi: 10.18637/jss.v067.i01.
Chapman DC, Davis JJ, Jenkins JA, Kocovsky PM, Miner JG, Farver J, Jackson PR. (2013) First evidence of grass carp recruitment in the Great Lakes Basin. Journal of Great Lakes Research. 39(4): 547-554.
Kolar CS, Chapman DC, Courtenay WR Jr., Housel CM, Williams JD, Jennings DP. (2007) Bigheaded carps: a biological synopsis and environmental risk assessment. American Fisheries Society, Special Publication 33, Bethesda, Maryland.
Merkes CM, Jackson CA, Cronan LD, Erickson RA, Schoenfeld TW, Amberg JJ. (in review) Rapid molecular detection of aquatic invasive species in the field.
R Core Team. (2015) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Whitledge GW, Chapman DC, Jenkins JA, Bailey J, Nicks D. (2015) Evidence of black carp establishment in the Mississippi River. Presented at American Fisheries Society 145th annual meeting in Portland, Oregon on 17-August, 2015. https://afs.confex.com/afs/2015/webprogram/Paper19942.html