The multiple states of environmental DNA and what is known about their persistence in aquatic environments

Mauvisseau, Quentin; Harper, Lynsey R.; Sander, Michael; Hanner, Robert; Deiner, Kristy

doi:10.22541/au.163638394.41572509/v1

Cited by 17 publications

(27 citation statements)

References 60 publications

(90 reference statements)

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“…Microorganismal eDNA (from bacteria, archaea, algae, protozoa, and microscopic animals) can be present in either extracellular form or as intact, living organisms. For macroorganisms, such as fish, eDNA is generally extraorganismal (i.e., released from the organism into the environment), either as free‐floating or particle‐bound, extracellular molecules or contained in organelles (mitochondria or nuclei) or tissue and cellular debris (Mauvisseau et al, 2022; Pawlowski et al, 2018). The eDNA technique was developed over 20 years ago to analyse microbial communities found in environmental samples (Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012).…”

Section: Introductionmentioning

confidence: 99%

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

et al. 2022

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Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods.Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and costeffective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.

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Section: Introductionmentioning

confidence: 99%

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

et al. 2022

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“…Our observations on eDNA persistence in the littoral zone of Geneva Lake are however to be extrapolated to other lakes with certain precautions since the persistence, degradation and transport of eDNA signals in water are influenced by many factors, such as eDNA characteristics, abiotic environmental factors and biotic factors (Harrison, Sunday and Rogers, 2019; Wang et al ., 2021). These complex mechanisms vary according to the species and environments studied, and divergent results have been obtained regarding eDNA degradation in freshwaters (Mauvisseau et al ., 2021), improving our understanding of eDNA persistence in the aquatic environment is clearly needed to help interpret future eDNA surveillance results.…”

Section: Discussionmentioning

confidence: 99%

“…Also, to maximize detection, DNA isolated from all states (e.g. intracellular, dissolved, particle absorbed) could be utilized, by performing water filtration using different pore sizes as recommended by (Mauvisseau et al ., 2021). The persistence, degradation and transport of eDNA signals in lakes are complex mechanisms involving multiple biotic and abiotic factors, our understanding of these mechanisms is still limited and further study of how environmental parameters affect eDNA decay in aquatic environments is needed.…”

Section: Discussionmentioning

confidence: 99%

A quantitative eDNA-based method to monitor fish spawning in lakes: application to European perch and whitefish

Vautier

Chardon

Goulon

et al. 2022

Preprint

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There is an urgent need to evaluate the effects of anthropogenic pressures and climatic change on fish populations dynamics. When monitored in lakes, the spawning of fish is generally assessed using traditional, mostly destructive or damaging, methods as gillnetting and collection of fertilized eggs. Over the last decade, environmental DNA (eDNA) based methods have been widely developed for the detection of aquatic species, offering a non-invasive alternative method to conventional biomonitoring tools. In particular, the emergence of new methods as the droplet digital PCR (ddPCR) offer the possibility to quantify an absolute eDNA signal in a very sensitive way and at a low cost. Here, we developed and implemented a quantitative eDNA method to monitor the spawning activity of two fish species, European perch and whitefish. ddPCR protocols were formalized based on existing and newly designed COI primers, and were applied during four spawning periods in lake Geneva. The results demonstrate the efficiency of eDNA coupled with ddPCR to identify the timing and duration of the spawning periods, as well as the peak of the spawning activity for the targeted species. In addition, the use of a control species (i.e., quantification of the eDNA signal of a fish that does not reproduce during the monitoring period) was shown to be relevant to clearly discriminate fluctuations of the eDNA signal associated to the spawning activity from the baseline eDNA signal. For future implementation, we recommend using an integrative sampling strategy (e.g., pooled samples for a give station) to smooth the local variability of the eDNA signal. These results show that we reached an operational level to use these non-invasive eDNA methods to monitor the spawning periods of these two fish species in large lakes.

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“…Isolation of mitochondria can be done for example by differential centrifugation, which has been successfully applied as an enrichment step to avoid the biases arising from PCR on bulk samples of invertebrates, yet this has not yet been tested on eDNA samples (Zhou et al 2013). That said, current knowledge of the state of eDNA in different environmental conditions is sparse (Mauvisseau et al 2021), and isolation of full mitochondrial organelles may end up discarding a lot of dissolved or particle bound target DNA from an environmental sample. Bait capture methods on eDNA samples were tested to enrich target DNA, however it is likely the omission of amplification combined with the high dilution factor of target DNA in environmental samples led to reduced species detection rates when the bait capture approach was compared to more conventional PCR based metabarcoding (Wilcox et al 2018).…”

Section: Discussionmentioning

confidence: 99%

The bacterial hitchhiker’s guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind

Hintikka

Carlsson

2021

Preprint

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Environmental DNA (eDNA) metabarcoding from water samples has, in recent years, shown great promise for biodiversity monitoring. However, universal primers targeting the cytochrome oxidase I (COI) marker gene popular in metazoan studies have displayed high levels of nontarget amplification. To date, enrichment methods bypassing amplification have not been able to match the detection levels of conventional metabarcoding. This study evaluated the use of universal metabarcoding primers as capture probes to either isolate target DNA, or to remove nontarget DNA, prior to amplification by using biotinylated versions of universal metazoan and bacterial barcoding primers, namely metazoan COI and bacterial 16S. Additionally, each step of the protocol was assessed by amplifying both COI and bacterial 16S to investigate the effect on the metazoan and bacterial communities. Bacterial abundance increased in response to the captures (COI library), while the quality of the captured DNA was improved. The metazoan-based probe captured bacterial DNA in a range that was also amplifiable with the 16S primers, demonstrating the ability of universal capture probes to isolate larger fragments of DNA from eDNA. This concept could be applied to metazoan metabarcoding, by using a truly conserved site without a high-level taxonomic resolution as a target of capture, to isolate DNA spanning over a nearby barcoding region, which can then be processed through conventional metabarcoding by amplification protocol.

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The multiple states of environmental DNA and what is known about their persistence in aquatic environments

Cited by 17 publications

References 60 publications

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

A quantitative eDNA-based method to monitor fish spawning in lakes: application to European perch and whitefish

The bacterial hitchhiker’s guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind

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