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Persistence of Environmental DNA (eDNA) in Experimental Mesocosms

Ottosson, Theophine (2021) BIOM02 20202
Degree Projects in Biology
Abstract
The application of environmental DNA (eDNA) in ecological research has experienced immense growth in recent years, especially in aquatic research. The technique of eDNA relies on capturing fragments of DNA recovered from environmental samples to infer species presence, making the collection of eDNA an attractive tool due to its non-invasiveness. Improved knowledge on persistence of eDNA degradation and decay is important for biological use of eDNA allowing access to the absence, presence, abundance, and location of target organism. Here, we designed a mesocosm experiment to investigate how long fish eDNA will persist in a water sample after collection from Müggelsee lake. We also investigated if biofilms within the mesocosms absorb fish... (More)
The application of environmental DNA (eDNA) in ecological research has experienced immense growth in recent years, especially in aquatic research. The technique of eDNA relies on capturing fragments of DNA recovered from environmental samples to infer species presence, making the collection of eDNA an attractive tool due to its non-invasiveness. Improved knowledge on persistence of eDNA degradation and decay is important for biological use of eDNA allowing access to the absence, presence, abundance, and location of target organism. Here, we designed a mesocosm experiment to investigate how long fish eDNA will persist in a water sample after collection from Müggelsee lake. We also investigated if biofilms within the mesocosms absorb fish eDNA and the effect of temperature on the persistence of eDNA. The experiment focused on perch (Perca fluviatilis) and pike (Esox lucius). Perch and pike eDNA was quantified via quantitative PCR (qPCR) using primers designed to be species-specific. qPCR result of pike did not show any amplification. We found no relationship between the presence of perch eDNA and time, however, we found that after sampling from the lake, our ability to detect perch eDNA drastically reduced over time and only appeared in two heated mesocosms after 24 hours. Our result also showed that we were more likely to detect perch eDNA in biofilm and filtered water samples 48 hours after Müggelsee lake water was added to the mesocosm. Contrary to our hypothesis that temperature will influence the decay of fish eDNA we found no association between temperature and the presence of eDNA. This study indicates that fish, here perch, eDNA from Müggelsee lake did not persist for long in the mesocosm, in agreement with previous studies on eDNA persistence. Short persistence time of eDNA in aquatic environment can allow for a near real-time monitoring. (Less)
Popular Abstract
Environmental DNA Decay

Environmental DNA (eDNA) refers to DNA that can be extracted and analysed from samples such as, water, sediment, and air. Furthermore, it is a non-invasive method of sampling because organisms can be detected without the need for capturing or visually identifying the organism. However, knowledge on the time it takes for eDNA to degrade and disappear from the environment is important for biological use of eDNA and provides absence, presence, abundance, and location of target organism. To investigate how long fish eDNA will persist in lake environment, we designed an outdoor experiment using large tanks of lake water to create tiny lakes, containing the smallest members of the lake community including, microscopic... (More)
Environmental DNA Decay

Environmental DNA (eDNA) refers to DNA that can be extracted and analysed from samples such as, water, sediment, and air. Furthermore, it is a non-invasive method of sampling because organisms can be detected without the need for capturing or visually identifying the organism. However, knowledge on the time it takes for eDNA to degrade and disappear from the environment is important for biological use of eDNA and provides absence, presence, abundance, and location of target organism. To investigate how long fish eDNA will persist in lake environment, we designed an outdoor experiment using large tanks of lake water to create tiny lakes, containing the smallest members of the lake community including, microscopic algae, animals, and bacteria (we call these tiny lakes ‘mesocosms’). The experiment focused on perch (Perca fluviatilis) and pike (Esox lucius).

To understand how long fish (perch and pike) eDNA will persist in the mesocosms after water was collected from a lake and how temperature affects the rate of fish eDNA decay, water samples were collected and filtered at six intervals from the same tanks (24 h, 48 h, 72 h, 96 h, 120 h and 144 h). At the same time, swabs were taken from the inside of the tanks to check if eDNA from fish can be recovered from the naturally formed biofilm. Biofilms are a community of microorganisms, that stick to each other and often to a surface such as rocks or in this case, the inside of the tanks. To measure eDNA in the experimental lakes, the water samples were filtered to remove the eDNA from the water. Secondly, the eDNA was extracted from the filter in the laboratory using series of solutions and buffers to clean and preserve the eDNA. Lastly, short sections of fish eDNA were targeted and many copies were produced and then quantified in real-time using quantitative polymerase chain reaction (qPCR).

We found that the length of time that fish eDNA remains in the experimental lake environment is extremely short, regardless of the temperature of the lakes. Furthermore, we were more likely to detect fish eDNA in the tank biofilms than in the filtered water samples, up to 48 hours after lake water was added to the tanks. Short persistence time of eDNA in aquatic environment allows for close monitoring of species; for example rare or newly introduced species. Fish eDNA was recovered in biofilm after it had degraded from the tank water, this suggests that there is need to consider extracting eDNA from biofilm alongside filtering eDNA from water when investigating for example the presence or absence of a species, rare or potentially invasive, or quantifying how long a target species will persist in an experiment. Furthermore, we found that filtering larger volumes of water yields more eDNA. This emphasizes the importance of water volumes for eDNA studies.

Overall, this study indicates that fish eDNA degrades rapidly and has low persistence in lake environments. For future research, we recommend that more samples are collected over shorter timescales (e.g. every 6 – 12 hours over 72 hours) to enable a better understanding of fish eDNA persistence in lake environments.


Master’s Degree Project in Biology, 30 credits, 2021
Department of Biology, Lund University
Advisor: Georgina Brennan
CEC, Aquatic Ecology, Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Ottosson, Theophine
supervisor
organization
course
BIOM02 20202
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
9039534
date added to LUP
2021-02-04 15:00:08
date last changed
2021-02-04 15:00:08
@misc{9039534,
  abstract     = {The application of environmental DNA (eDNA) in ecological research has experienced immense growth in recent years, especially in aquatic research. The technique of eDNA relies on capturing fragments of DNA recovered from environmental samples to infer species presence, making the collection of eDNA an attractive tool due to its non-invasiveness. Improved knowledge on persistence of eDNA degradation and decay is important for biological use of eDNA allowing access to the absence, presence, abundance, and location of target organism. Here, we designed a mesocosm experiment to investigate how long fish eDNA will persist in a water sample after collection from Müggelsee lake. We also investigated if biofilms within the mesocosms absorb fish eDNA and the effect of temperature on the persistence of eDNA. The experiment focused on perch (Perca fluviatilis) and pike (Esox lucius). Perch and pike eDNA was quantified via quantitative PCR (qPCR) using primers designed to be species-specific. qPCR result of pike did not show any amplification. We found no relationship between the presence of perch eDNA and time, however, we found that after sampling from the lake, our ability to detect perch eDNA drastically reduced over time and only appeared in two heated mesocosms after 24 hours. Our result also showed that we were more likely to detect perch eDNA in biofilm and filtered water samples 48 hours after Müggelsee lake water was added to the mesocosm. Contrary to our hypothesis that temperature will influence the decay of fish eDNA we found no association between temperature and the presence of eDNA. This study indicates that fish, here perch, eDNA from Müggelsee lake did not persist for long in the mesocosm, in agreement with previous studies on eDNA persistence. Short persistence time of eDNA in aquatic environment can allow for a near real-time monitoring.},
  author       = {Ottosson, Theophine},
  language     = {eng},
  note         = {Student Paper},
  title        = {Persistence of Environmental DNA (eDNA) in Experimental Mesocosms},
  year         = {2021},
}