Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction

Cowart, Dominique A.; Murphy, Katherine R.; Cheng, C-H Christina

doi:10.1007/978-1-0716-2313-8_11

Cited by 5 publications

(2 citation statements)

References 78 publications

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“…Among the different techniques for biodiversity assessment, environmental deoxyribonucleic acid (eDNA), the complex mixture of genomic DNA obtained from an environmental sample, is becoming a key component of the ecologists’ and environmental managers’ toolbox, alluring worldwide attention [ 5 , 6 ]. The science of eDNA provides the opportunity to scrutinize the dynamics of species, populations and communities and map their geographical distribution over large scales as well as over long periods.…”

Section: Introductionmentioning

confidence: 99%

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

Hassan

Sabreena

Poczai

et al. 2022

Biology

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The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.

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Section: Introductionmentioning

confidence: 99%

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

Hassan

Sabreena

Poczai

et al. 2022

Biology

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“…All temperate fish species were conspicuously absent in the negative control samples, thus unlikely to be a result from internal lab contamination. The power and sensitivity of present-day molecular approaches require high standards to minimise the risk of DNA contamination in the field and throughout curation and laboratory handling (Goldberg et al 2016; Llamas et al 2017) Processing ancient and historical specimens, most of which were not collected nor handled for molecular analysis purposes throughout the time stored in scientific collections, increases the risk of DNA contaminants being incorporated into the specimens through, for example, (i) cross-contamination from handling multiple specimens without bench-space and equipment sterilisation, or (ii) transferring specimens and fixatives between collection lots (Knapp et al 2012; Cowart et al 2022). For ancient DNA shotgun sequencing approaches, DNA damage profiles can be assessed to identify modern DNA contaminants (Seersholm et al 2016).…”

Section: Discussionmentioning

confidence: 99%

Unlocking Antarctic molecular time-capsules – recovering historical environmental DNA from museum-preserved sponges

Jeunen,

Mills,

Lamare

et al. 2024

Preprint

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Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA (heDNA), trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.

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Express Estimation of Plankton Size Fractions in the Water Area of Sevastopol in Winter 2021-2022: Model Studies

Ufimceva

Кузнецов

2022

Russian Journal of Biological Physics and Chemisrty

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For the purpose of monitoring the water area of Sevastopol a line of devices for plankton macrofiltration in the size range from 2 mm to 2 microns has been developed. Twelve stations have been chosen from Inkerman to Fiolent with total length of 30 km. From piers far out at sea, 50-500 liters of seawater were sampled from the surface and filtered through a system of successive sieves 2 mm, 300, 150, 84 microns and a 2 μm fiber filter. In the winter of 2021-2022, when the seawater temperature was 8 °C, the diversity of plankton morphotypes was low. For all stations, the number of morphotypes increased as the size fraction decreased in the form of ecological pyramids. It was found that the richness of morphotypes in Inkerman is significantly lower than at other stations. Samples from neighboring stations may differ in the composition of morphotypes up to 50% (spatial section). Also, sea water samples taken at the same station with an interval of 1.5 months differed by 50% in the composition of morphotypes (time slice). The obtained results indicate that the developed technique of sequential filtration gives a visual representation of the state of meso-, micro- and nano-plankton in seawater samples.

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Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction

Cited by 5 publications

References 78 publications

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

Unlocking Antarctic molecular time-capsules – recovering historical environmental DNA from museum-preserved sponges

Express Estimation of Plankton Size Fractions in the Water Area of Sevastopol in Winter 2021-2022: Model Studies

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