The Release Rate of Environmental DNA from Juvenile and Adult Fish

Maruyama, Atsushi; Nakamura, Keisuke; Yamanaka, Hiroki; Kondo, Michio; Minamoto, Toshifumi

doi:10.1371/journal.pone.0114639

Cited by 290 publications

(380 citation statements)

References 21 publications

Supporting

Mentioning

339

Contrasting

Order By: Relevance

“…For example, in an aquarium study of Idaho giant salamanders (Dicamptodon aterrimus), rate of eDNA production related positively to salamander biomass (Pilliod et al 2014). A similar trend of eDNA production positively related to biomass was observed in Bluegill Sunfish (Maruyama et al 2014). However, when corrected Conserv Genet (2016) 17:1-17 3 for biomass, juvenile Bluegill Sunfish released eDNA at a higher rate than adults (target amplicon copies per hour per gram fish body weight), leading the authors to conclude that ontogenetic factors such as changes in behavior and metabolism influence eDNA production.…”

Section: Introductionmentioning

confidence: 62%

The ecology of environmental DNA and implications for conservation genetics

2015

View full text Add to dashboard Cite

Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA-myriad interactions between extraorganismal genetic material and its environment-and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

show abstract

Section: Introductionmentioning

confidence: 62%

The ecology of environmental DNA and implications for conservation genetics

2015

View full text Add to dashboard Cite

show abstract

“…Understanding variability in DNA shedding rates across species will also strengthen quantitative estimates (Maruyama et al . 2014; Klymus et al . 2015).…”

Section: Discussionmentioning

confidence: 99%

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

et al. 2015

View full text Add to dashboard Cite

Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource‐intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5 km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species’ eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as ~60 m. eDNA reliably detected vertebrates with low false‐negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.

show abstract

“…Once the water is collected, it should be filtered and stored as soon as possible since the quality and quantity of DNA present in water decreases rapidly (Thomsen et al 2012a;Maruyama et al 2014). For example, Maruyama et al (2014) observed detectable concentrations of bluegill fish (Lepomis macrochirus) to decline by half in under 7 h at 20 o C. Even when unfiltered water is frozen at -20 o C, reductions of amplifiable DNA as great as ten-fold are reported in the literature (Cornelisen et al 2012).…”

Section: Extraction Of Dna From Water and Icementioning

confidence: 99%

“…For example, Maruyama et al (2014) observed detectable concentrations of bluegill fish (Lepomis macrochirus) to decline by half in under 7 h at 20 o C. Even when unfiltered water is frozen at -20 o C, reductions of amplifiable DNA as great as ten-fold are reported in the literature (Cornelisen et al 2012). Therefore, it is preferable to filter samples as soon as possible after sampling, and to preserve the filtered material at low temperature; studies have shown filters (and associated DNA) can be stored at -20 o C for later DNA extraction without significant loss of amplifiable DNA (Gilpin et al 2013).…”

Section: Extraction Of Dna From Water and Icementioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

112

View full text Add to dashboard Cite

Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

show abstract

The Release Rate of Environmental DNA from Juvenile and Adult Fish

Cited by 290 publications

References 21 publications

The ecology of environmental DNA and implications for conservation genetics

The ecology of environmental DNA and implications for conservation genetics

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Contact Info

Product

Resources

About