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Relationship between fish presence and abundance in Arizona standing waters measured through standard techniques and environmental DNA Active

By Upper Midwest Environmental Sciences Center May 8, 2017

The unpredictability of DNA degradation in the environment has plagued the ability of scientists to interpret environmental DNA (eDNA) data since the technique has been used for early detection of aquatic invasive species (AIS) such as silver and bighead carps (Hypophthalmichthys molitrix and Hypophthalmichthys nobilis) throughout the Chicago Area Waterway System (CAWS), Des Plaines River, near shore waters of Lake Michigan and Lake Erie, and the Upper Mississippi River. This technique is potentially useful for early Invasive carp detection because it can presumably detect the presence of DNA in water even when fish are not abundant (Jerde and others, 2011).

A positive eDNA sample indicates the presence of Invasive carp DNA but not its source, and there are numerous sources of DNA that enter the environment.  Live fish is the source of DNA scientists and managers are most interested in detecting, but DNA that comes from vectors such as waste from fish-eating birds, barges, dredge operations, waste treatment facilities, dead fish, and discharge pipes near areas containing fish markets can also be significant sources of eDNA. Carcasses, slime, and avian feces have been shown to be capable of contributing detectable DNA to the environment for a month or longer (Merkes and others, 2014). Having the ability to segregate the source of detected DNA found in the environment is a more recent goal during the design of eDNA assays. The CAWS is a dynamic waterway system with a heavy amount of barge and boat traffic, wastewater effluent, and is situated in one of the most frequented flyways of migratory fish-eating birds anywhere in the United States. Just down river is the largest population of silver and bighead carp anywhere in the world. This increases the likelihood that a bird that feeds in carp-infested waters or a boat that travels upriver through carp-infested waters may deposit genetic material in the CAWS resulting in positive DNA detections.

Historical eDNA data from the CAWS is perplexing because there have been many eDNA detections of silver carp, but never a live capture of a fish. Oddly enough, the only capture of a live Invasive carp in these waters has been bighead carp, but there has been only one eDNA detection for bighead carp in three years of intensive monitoring by the U.S. Fish and Wildlife Service. Therefore, discovering ways to differentiate eDNA detections resulting from live fish presence and those from remnant source deposition will make eDNA monitoring programs more effective.

 

UMESC Scientist prepares eDNA sample
Sources/Usage: Public Domain. View Media Details
UMESC Scientist prepares eDNA sample (Public domain.)

 

Objectives

  1. Determine if Invasive carp-specific DNA fragments from tanks containing live fish are different in size compared to fragments from tanks treated with dead fish, fecal material from birds, or Invasive carp-DNA slurry.
  2. Determine if Invasive carp-specific DNA fragments from a tank of live fish stay intact longer than fragments from tanks treated with dead fish, fecal material from birds, or Invasive carp slurry.
  3. Determine if there are common breakage points or specific regions of Invasive carp mitochondrial genomes that are more susceptible to rapid degradation.

References

Jerde CL, Mahon AR, Chadderton WL, Lodge DM. 2011 “Sight-unseen” detection of rare aquatic species using environmental DNA. Conservation Letters 4: 150-157.

Merkes CM, McCalla SG, Jensen NR, Gaikowski MP, Amberg JJ. 2014 Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data. PLOS One 9(11): e113346.

  • Overview

    The unpredictability of DNA degradation in the environment has plagued the ability of scientists to interpret environmental DNA (eDNA) data since the technique has been used for early detection of aquatic invasive species (AIS) such as silver and bighead carps (Hypophthalmichthys molitrix and Hypophthalmichthys nobilis) throughout the Chicago Area Waterway System (CAWS), Des Plaines River, near shore waters of Lake Michigan and Lake Erie, and the Upper Mississippi River. This technique is potentially useful for early Invasive carp detection because it can presumably detect the presence of DNA in water even when fish are not abundant (Jerde and others, 2011).

    A positive eDNA sample indicates the presence of Invasive carp DNA but not its source, and there are numerous sources of DNA that enter the environment.  Live fish is the source of DNA scientists and managers are most interested in detecting, but DNA that comes from vectors such as waste from fish-eating birds, barges, dredge operations, waste treatment facilities, dead fish, and discharge pipes near areas containing fish markets can also be significant sources of eDNA. Carcasses, slime, and avian feces have been shown to be capable of contributing detectable DNA to the environment for a month or longer (Merkes and others, 2014). Having the ability to segregate the source of detected DNA found in the environment is a more recent goal during the design of eDNA assays. The CAWS is a dynamic waterway system with a heavy amount of barge and boat traffic, wastewater effluent, and is situated in one of the most frequented flyways of migratory fish-eating birds anywhere in the United States. Just down river is the largest population of silver and bighead carp anywhere in the world. This increases the likelihood that a bird that feeds in carp-infested waters or a boat that travels upriver through carp-infested waters may deposit genetic material in the CAWS resulting in positive DNA detections.

    Historical eDNA data from the CAWS is perplexing because there have been many eDNA detections of silver carp, but never a live capture of a fish. Oddly enough, the only capture of a live Invasive carp in these waters has been bighead carp, but there has been only one eDNA detection for bighead carp in three years of intensive monitoring by the U.S. Fish and Wildlife Service. Therefore, discovering ways to differentiate eDNA detections resulting from live fish presence and those from remnant source deposition will make eDNA monitoring programs more effective.

     

    UMESC Scientist prepares eDNA sample
    Sources/Usage: Public Domain. View Media Details
    UMESC Scientist prepares eDNA sample (Public domain.)

     

    Objectives

    1. Determine if Invasive carp-specific DNA fragments from tanks containing live fish are different in size compared to fragments from tanks treated with dead fish, fecal material from birds, or Invasive carp-DNA slurry.
    2. Determine if Invasive carp-specific DNA fragments from a tank of live fish stay intact longer than fragments from tanks treated with dead fish, fecal material from birds, or Invasive carp slurry.
    3. Determine if there are common breakage points or specific regions of Invasive carp mitochondrial genomes that are more susceptible to rapid degradation.

    References

    Jerde CL, Mahon AR, Chadderton WL, Lodge DM. 2011 “Sight-unseen” detection of rare aquatic species using environmental DNA. Conservation Letters 4: 150-157.

    Merkes CM, McCalla SG, Jensen NR, Gaikowski MP, Amberg JJ. 2014 Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data. PLOS One 9(11): e113346.