Stirring up the relationship between quantified environmental DNA concentrations and exoskeleton‐shedding invertebrate densities

Environmental DNA, vol. 3, pp. 605–618

Abstract

Abstract The application of eDNA techniques for the detection, monitoring, and conservation of biodiversity holds great promise. While many studies apply eDNA techniques in aquatic systems to determine the presence or absence of a given species, using eDNA for the purpose of species density or biomass predictions remains a challenge, especially for freshwater invertebrates that shed exoskeletons. Here, we aimed to determine whether and how eDNA concentrations relate to exoskeleton‐shedding invertebrate densities. We used microcosms holding different densities of a common invertebrate freshwater species, Daphnia magna. During 2 weeks, we monitored temporal dynamics of eDNA and the eDNA/density relationship by taking water samples and quantifying eDNA concentrations with the droplet digital PCR. The setup included one treatment without and one with homogenization before sampling, to test the effects of admixture on the relation between eDNA concentration and density. Daphnia magna individuals were removed after 1.5 weeks to track DNA degradation rates. In the stagnant water setup, hardly any DNA was detected before D. magna removal. Within days after removal, eDNA concentrations became undetectable. No significant correlation between D. magna density and eDNA concentrations was observed. In the homogenization treatment, a significant positive correlation between eDNA concentration and densities was demonstrated for the days around D. magna removal, albeit with some within‐treatment variability. Our results show that, given adequate time for eDNA production and degradation to stabilize, positive correlations between eDNA and organism densities in water with sufficient homogenization are detectable for exoskeleton‐shedding invertebrates. Therefore, our study indicates that—although difficult—using eDNA to quantify freshwater exoskeleton‐shedding invertebrate densities may be possible under field conditions if circumstances result in frequent homogenization of the water column.

Authors 7

1. Krijn Baptist Trimbos corresponding Aachen Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands Institute of Environmental Sciences (CML)

   Leiden University

   Affiliation as printed

   Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands

   Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands

2. Ellen Cieraad Aachen Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands Institute of Environmental Sciences (CML)

   Leiden University

   Affiliation as printed

   Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands

   Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands

3. Maarten J. J. Schrama Aachen Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands Institute of Environmental Sciences (CML)

   Leiden University

   Affiliation as printed

   Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands

   Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands

4. Aagje I. Saarloos Aachen Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands Institute of Environmental Sciences (CML)

   Leiden University

   Affiliation as printed

   Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands

   Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands

5. C.J.M. Musters Aachen Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands Institute of Environmental Sciences (CML)

   Leiden University

   Affiliation as printed

   Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands

   Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands

6. Laura D. Bertola

   City College of New York · City University of New York

   Affiliation as printed

   Department of Biology City College of New York City University of New York New York NY USA

   Department of Earth and Atmospheric Sciences City College of New York City University of New York New York NY USA

   Department of Biology, City College of New York, City University of New York, New York, NY, USA

   Department of Earth and Atmospheric Sciences, City College of New York, City University of New York, New York, NY, USA

7. Peter M. van Bodegom Aachen Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands Institute of Environmental Sciences (CML)

   Leiden University

   Affiliation as printed

   Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands

   Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands