A higher DNA damage rate in aqueous eDNA particles suggests intra‐cellular eDNA degradation in cellular environments

Jo, Toshiaki

doi:10.1002/edn3.383

Cited by 2 publications

(3 citation statements)

References 42 publications

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“…Moreover, the DNA damage rate ( λ ) of zebrafish eDNA was higher in PMA treatments (representing viable zebrafish cells) than in non-PMA treatments (representing total zebrafish eDNA). This result supported that, in addition to microbes and their extracellular enzymes in the outer environments, eDNA may be actively degraded by intracellular enzymes such as DNases [35,51,59], implying that DNA in larger eDNA particles may not be stable and may thus provide a fresher signal. Furthermore, λ increased with passage of time only for PMA treatment but not for non-PMA treatment, implying that assessment of eDNA age based on DNA damage rate may be more appropriate to target intact cells.…”

Section: Selective Detection Of Viable Cell-derived Ednamentioning

confidence: 64%

“…As a proof of concept, Jo [59] applied the approach to an eDNA sample and estimated the frequency of mitochondrial DNA damage in zebrafish ( Danio rerio ) eDNA particles in rearing water [59]. According to the study, DNA damage rates could vary depending on filter pore sizes and likely eDNA size fractions, implying the importance of intracellular enzymatic DNA degradation and the state-dependent eDNA persistence against environmental parameter and microbial activity [27,51].…”

Section: Estimation Of Dna Damage Ratementioning

confidence: 99%

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Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

2023

Proc. R. Soc. B.

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Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to the detection of aged eDNA that has long since been released from the individual and is more likely to be detected at a site further away from its source. In order to address the issue, this manuscript focuses on the state of eDNA, proposing new methodologies to estimate the age of eDNA: (1) DNA damage rate, (2) eDNA particle size distribution, and (3) viable cell-derived eDNA. In addition, the manuscript also focuses on the shorter persistence of environmental RNA (eRNA) compared with eDNA, highlighting the application of eRNA and environmental nucleic acid ratio for assessing the age of the genetic materials in water. Although substantial further research is essential to support the feasibility of these methodologies, incorporating time-scale information into eDNA analysis would update current eDNA analysis, improve the accuracy and reliability of eDNA-based monitoring, and further refine eDNA analysis as a useful monitoring tool in ecology, fisheries and various environmental sciences.

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Section: Selective Detection Of Viable Cell-derived Ednamentioning

confidence: 64%

Section: Estimation Of Dna Damage Ratementioning

confidence: 99%

Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

2023

Proc. R. Soc. B.

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“…In addition, it is important to investigate how these factors affect eDNA detection and dynamics within different environments. Despite some progress in understanding the role of bacteria in eDNA detection and persistence, there is still much to be explored in this area (Jo, 2023; Salter, 2018; Zulkefli et al., 2019).…”

Section: Discussionmentioning

confidence: 99%

Environmental DNA–RNA dynamics provide insights for effective monitoring of marine invasive species

Scriver,

von Ammon,

Pochon

et al. 2024

Environmental DNA

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Environmental DNA and RNA (eDNA/eRNA) can serve as molecular tools for biodiversity monitoring and biosecurity surveillance. However, uncertainties still exist regarding the persistence and dynamics of marine nucleic acids in the environment and the effects of post‐sampling storage on species detectability. To bridge these gaps, an experiment was conducted in an Auckland marina, a known New Zealand entry point for marine non‐indigenous species (NIS). We targeted a prominent invader, the Mediterranean fanworm Sabella spallanzanii, for eDNA/eRNA‐based detection. Permeable dialysis bags filled with seawater collected near an S. spallanzanii colony were deployed in the marina to simulate environmental conditions, with a subset of bags stored on ice to mimic field storage conditions. Sabella spallanzanii eDNA/eRNA signal was quantified using droplet digital PCR on samples collected over 24 h of dialysis bag deployment. Results challenged traditional first‐order decay models, showing inconsistent eDNA/eRNA signal patterns and no significant concentration changes between 0 and 24 h. Consequently, total eDNA fragmentation was assessed using the Agilent 2100 Bioanalyzer® electrophoresis system, which revealed a rise in the number of total eDNA fragments and an unexpected increase in the median fragment size of total eDNA under field conditions over time, likely originating from the ambient microbiome. Additional analysis using long‐read sequencing (Oxford Nanopore Technologies, UK) revealed an increase in microbial eDNA reads within the in‐field samples, suggesting potential microbial growth within the dialysis bags. In contrast, the ice‐stored samples exhibited no significant changes in the number of reads assigned to microbial taxa, implying limited microbial growth in cold storage. These findings provide insights into total eDNA dynamics and its potential impact on targeted eDNA concentration and detection. Further comprehensive research on eDNA/eRNA dynamics, particularly focused on eRNA, is essential, as this understanding is crucial for refining survey interpretation and sampling design for effective environmental management.

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A higher DNA damage rate in aqueous eDNA particles suggests intra‐cellular eDNA degradation in cellular environments

Cited by 2 publications

References 42 publications

Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

Environmental DNA–RNA dynamics provide insights for effective monitoring of marine invasive species

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