Fish environmental DNA is more concentrated in aquatic sediments than surface water

Turner, Catherine; Uy, Karen L.; Everhart, Robert Christopher

doi:10.1016/j.biocon.2014.11.017

Cited by 425 publications

(491 citation statements)

References 99 publications

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“…Vertical transport (i.e. settling) of fish eDNA and accumulation in pond and river sediments was recently described by Turner et al (2015). The high concentrations of sedimentary fish eDNA they observed also suggest that resuspension of settled eDNA represents an important element of eDNA ecology.…”

Section: Introductionmentioning

confidence: 62%

“…Much of this work has focused on aquatic habitats in laboratory (Dejean et al 2011;Thomsen et al 2012b;Goldberg et al 2013;Barnes et al 2014;Strickler et al 2015), while several studies have occurred in aquatic field settings (Thomsen et al 2012a;Merkes et al 2014). Turner et al 2015 presented one of the first comparisons of accumulation of eDNA in open-water versus aquatic sediment samples. Fewer studies have examined eDNA persistence in terrestrial environments (Andersen et al 2012).…”

Section: Fate: What Factors Influence Edna Persistence?mentioning

confidence: 99%

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The ecology of environmental DNA and implications for conservation genetics

2015

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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.

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Section: Introductionmentioning

confidence: 62%

Section: Fate: What Factors Influence Edna Persistence?mentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

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“…The number of chloroplast DNA copies results mainly from the number of chloroplasts per cell and the number of chloroplast genomes per chloroplast, which vary across diatom taxa (Bedoshvili et al 2009). Other aspects regarding taphonomy are the preservation potential of DNA Pedersen et al 2015) versus diatom valves (Ryves et al 2006) and the different representations of DNA versus valves in the various lake habitats, for example caused by different transport characteristics and adsorption of DNA to sediments (Torti et al 2015;Turner et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

et al. 2016

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The Arctic treeline ecotone is characterised by a steep vegetation gradient from arctic tundra to northern taiga forests, which is thought to influence the water chemistry of thermokarst lakes in this region. Environmentally sensitive diatoms respond to such ecological changes in terms of variation in diatom diversity and richness, which so far has only been documented by microscopic surveys. We applied next-generation sequencing to analyse the diatom composition of lake sediment DNA extracted from 32 lakes across the treeline in the Khatanga region, Siberia, using a short fragment of the rbcL chloroplast gene as a genetic barcode. We compared diatom richness and diversity obtained from the genetic approach with diatom counts from traditional microscopic analysis. Both datasets were employed to investigate diversity and relationships with environmental variables, using ordination methods. After effective filtering of the raw data, the two methods gave similar results for diatom richness and composition at the genus level (DNA 12 taxa; morphology 19 taxa), even though there was a much higher absolute number of sequences obtained per genetic sample (median 50,278), compared with microscopic counts (median 426). Dissolved organic carbon explained the highest percentage of variance in both datasets (14.2 % DNA; 18.7 % morphology), reflecting the compositional turnover of diatom assemblages along the tundra-taiga transition. Differences between the two approaches are mostly a consequence of the filtering process of genetic data and limitations of genetic references in the database, which restricted the determination of genetically identified sequence types to the genus level. The morphological approach, however, allowed identifications mostly to species level, which permits better ecological interpretation of the diatom data. Nevertheless, because of a rapidly increasing reference database, the genetic approach with sediment DNA will, in the future, enable reliable Electronic supplementary material The online version of this article (doi:10.1007/s10933-016-9926-y) contains supplementary material, which is available to authorized users. 123J Paleolimnol DOI 10.1007/s10933-016-9926-y investigations of diatom composition from lake sediments that will have potential applications in both paleoecology and environmental monitoring.

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“…25 Strickler et al 26 investigated the effects of temperature, pH and UVB radiation on eDNA in water and found that it degraded faster in warmer water, with a neutral pH and a moderate UVB level. Because these conditions are also amenable to microbial growth, the authors speculated that eDNA breakdown was at least partially facilitated by microbial action.…”

Section: Edna In Aquatic Ecosystemsmentioning

confidence: 99%

“…27 However, the fact that DNA may be concentrated and survive much longer in sediments may be a complicating factor. 25 DNA dispersal in flowing streams and rivers is also a concern, as it may give false positive results downstream where the organism in question is not found. DNA dispersal was investigated by Laramie et al 28 who traced eDNA of Chinook salmon (Oncorhynchus tshawytscha), and Deiner et al 29 who studied eDNA of a daphnid (Daphnia longispina) and swollen river mussel (Unio tumidus).…”

Section: Edna In Aquatic Ecosystemsmentioning

confidence: 99%

DNA-based identification of aquatic invertebrates useful in the South African context?

Venter¹,

Bezuidenhout²

2016

S. Afr. J. Sci.

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The concept of using specific regions of DNA to identify organisms – processes such as DNA barcoding – is not new to South African biologists. The African Centre for DNA Barcoding reports that 12 548 plant species and 1493 animal species had been barcoded in South Africa by July 2013, while the Barcode of Life Database (BOLD) contains 62 926 records for South Africa, 11 392 of which had species names (representing 4541 species). In light of this, it is surprising that aquatic macroinvertebrates of South Africa have not received much attention as potential barcoding projects thus far – barcoding of aquatic species has tended to focus on invasive species and fishes. Perusal of the BOLD records for South Africa indicates a noticeable absence of aquatic macroinvertebrates, including families used for biomonitoring strategies such as the South African Scoring System. Meanwhile, the approach of collecting specimens and isolating their DNA individually in order to identify them (as in the case of DNA barcoding), has been shifting towards making use of the DNA which organisms naturally shed into their environments (eDNA). Coupling environmental and bulk sample DNA with high-throughput sequencing technology has given rise to metabarcoding, which has the potential to characterise the whole community of organisms present in an environment. Harnessing barcoding and metabarcoding approaches with environmental DNA (eDNA) potentially offers a non-invasive means of measuring the biodiversity in an environment and has great potential for biomonitoring. Aquatic ecosystems are well suited to these approaches – but could they be useful in a South African context?

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Fish environmental DNA is more concentrated in aquatic sediments than surface water

Cited by 425 publications

References 99 publications

The ecology of environmental DNA and implications for conservation genetics

The ecology of environmental DNA and implications for conservation genetics

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

DNA-based identification of aquatic invertebrates useful in the South African context?

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