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Assessing the properties of RNA degradation in complex environmental water samples Active

By Upper Midwest Environmental Sciences Center May 8, 2017

The unpredictability of nucleic acid 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 nucleic acid that enter the environment.  Live fish is the source of DNA/RNA scientists and managers are most interested in detecting, but nucleic acid 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. 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). Double-stranded RNA, however, only persisted up to 48 hours in soil in one recent study (Dubelman and others, 2014). To date, very little research has been done to characterize the persistence and significance of eRNA from AIS. Having the ability to segregate the source of detected nucleic acids 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 eDNA/eRNA 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 and eRNA detections resulting from live fish presence and those from remnant source deposition will make eDNA/eRNA monitoring programs more effective. 

USGS Scientist labels Invasive carp samples.
Sources/Usage: Public Domain. View Media Details
USGS Scientist labels invasive carp samples.(Public domain.)

 

Objectives

  1. Determine if Invasive carp-specific RNA 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 slurry.
  2. Determine if Invasive carp-specific RNA 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 transcriptomes 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.

Dubelman S, Fischer J, Zapata F, Huizinga K, Jiang C, Uffman J, Levine S, Carson D. 2014. Environmental Fate of Double-Stranded RNA in Agricultural Soils. PLoS ONE 9(3): e93155. doi:10.1371/journal.pone.0093155.

  • Overview

    The unpredictability of nucleic acid 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 nucleic acid that enter the environment.  Live fish is the source of DNA/RNA scientists and managers are most interested in detecting, but nucleic acid 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. 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). Double-stranded RNA, however, only persisted up to 48 hours in soil in one recent study (Dubelman and others, 2014). To date, very little research has been done to characterize the persistence and significance of eRNA from AIS. Having the ability to segregate the source of detected nucleic acids 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 eDNA/eRNA 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 and eRNA detections resulting from live fish presence and those from remnant source deposition will make eDNA/eRNA monitoring programs more effective. 

    USGS Scientist labels Invasive carp samples.
    Sources/Usage: Public Domain. View Media Details
    USGS Scientist labels invasive carp samples.(Public domain.)

     

    Objectives

    1. Determine if Invasive carp-specific RNA 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 slurry.
    2. Determine if Invasive carp-specific RNA 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 transcriptomes 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.

    Dubelman S, Fischer J, Zapata F, Huizinga K, Jiang C, Uffman J, Levine S, Carson D. 2014. Environmental Fate of Double-Stranded RNA in Agricultural Soils. PLoS ONE 9(3): e93155. doi:10.1371/journal.pone.0093155.