Dataset Information

A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems.

ABSTRACT: The use of environmental DNA (eDNA) to determine the presence and distribution of aquatic organisms has become an important tool to monitor and investigate freshwater communities. The successful application of this method in the field, however, is dependent on the effectiveness of positive DNA verification, which is influenced by site-specific environmental parameters. Factors affecting eDNA concentrations in aquatic ecosystems include flow conditions, and the presence of substances that possess DNA-binding properties or inhibitory effects. In this study we investigated the influence of different environmental parameters on the detection success of eDNA using the invasive goby Neogobius melanostomus. In a standardized laboratory setup, different conditions of flow, sediment-properties, and fish density were compared, as well as different potential natural inhibitors such as algae, humic substances, and suspended sediment particles. The presence of sediment was mainly responsible for lower eDNA detection in the water samples, regardless of flow-through or standing water conditions and a delayed release of eDNA was detected in the presence of sediment. Humic substances had the highest inhibitory effect on eDNA detection followed by algae and siliceous sediment particles. The results of our study highlight that a successful application of eDNA methods in field surveys strongly depends on site-specific conditions, such as water flow conditions, sediment composition, and suspended particles. All these factors should be carefully considered when sampling, analyzing, and interpreting eDNA detection results.

SUBMITTER: Stoeckle BC

PROVIDER: S-EPMC5722286 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems.

Stoeckle Bernhard C BC Beggel Sebastian S Cerwenka Alexander F AF Motivans Elena E Kuehn Ralph R Geist Juergen J

PloS one 20171208 12

The use of environmental DNA (eDNA) to determine the presence and distribution of aquatic organisms has become an important tool to monitor and investigate freshwater communities. The successful application of this method in the field, however, is dependent on the effectiveness of positive DNA verification, which is influenced by site-specific environmental parameters. Factors affecting eDNA concentrations in aquatic ecosystems include flow conditions, and the presence of substances that possess ...[more]

PMID: 29220394

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Project description:The industrial use and widespread application of carbon-based nanomaterials have caused a rapid increase in their production over the last decades. However, toxicity of these materials is not fully known and is still being investigated for potential human and ecological health risks. Detecting carbon-based nanomaterials in the environment using current analytical methods is problematic, making environmental fate and transport modeling a practical way to estimate environmental concentrations and assess potential ecological risks. The Water Quality Analysis Simulation Program 8 (WASP8) is a dynamic, spatially resolved fate and transport model for simulating exposure concentrations in surface waters and sediments. Recently, WASP has been updated to incorporate processes for simulating the fate and transport of nanomaterials including heteroaggregation and phototransformation. This study examines the fate and transport of multiwalled carbon nanotubes (MWCNT), graphene oxide (GO) and reduced graphene oxide (rGO) in four aquatic ecosystems in the southeastern United States. Sites include a seepage lake, a coastal plains river, a piedmont river and an unstratified, wetland lake. A hypothetical 50-year release is simulated for each site-nanomaterial pair to analyze nanomaterial distribution between the water column and sediments. For all nanomaterials, 99% of the mass loaded moves though systems of high and low residence times without being heteroaggregated and deposited in the sediments. However, significant accumulation in the sediments does occur over longer periods of time. Results show that GO and rGO had the highest mass fraction in the water column of all four sites. MWCNT were found predominantly in the sediments of the piedmont river and seepage lake but were almost entirely contained in the water column of the coastal plains river and wetland lake. Simulated recovery periods following the release estimate 37+?years for lakes and 1-4?years for rivers to reduce sediment nanomaterial concentrations by 50% suggesting that carbon-based nanomaterials have the potential for long-term ecological effects.

Project description:The environmental DNA (eDNA) method is the practice of collecting environmental samples and analyzing them for the presence of a genetic marker specific to a target species. Little is known about the sensitivity of the eDNA method. Sensitivity is the probability that the target marker will be detected if it is present in the water body. Methods and tools are needed to assess the sensitivity of sampling protocols, design eDNA surveys, and interpret survey results. In this study, the sensitivity of the eDNA method is modeled as a function of ambient target marker concentration. The model accounts for five steps of sample collection and analysis, including: 1) collection of a filtered water sample from the source; 2) extraction of DNA from the filter and isolation in a purified elution; 3) removal of aliquots from the elution for use in the polymerase chain reaction (PCR) assay; 4) PCR; and 5) genetic sequencing. The model is applicable to any target species. For demonstration purposes, the model is parameterized for bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) assuming sampling protocols used in the Chicago Area Waterway System (CAWS). Simulation results show that eDNA surveys have a high false negative rate at low concentrations of the genetic marker. This is attributed to processing of water samples and division of the extraction elution in preparation for the PCR assay. Increases in field survey sensitivity can be achieved by increasing sample volume, sample number, and PCR replicates. Increasing sample volume yields the greatest increase in sensitivity. It is recommended that investigators estimate and communicate the sensitivity of eDNA surveys to help facilitate interpretation of eDNA survey results. In the absence of such information, it is difficult to evaluate the results of surveys in which no water samples test positive for the target marker. It is also recommended that invasive species managers articulate concentration-based sensitivity objectives for eDNA surveys. In the absence of such information, it is difficult to design appropriate sampling protocols. The model provides insights into how sampling protocols can be designed or modified to achieve these sensitivity objectives.

Dataset Information

A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems.

Publications

A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems.

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