Techniques for the practical collection of environmental DNA: filter selection, preservation, and extraction

Minamoto, Toshifumi; Naka, Takafumi; Moji, Kazuhiko; Maruyama, Atsushi

doi:10.1007/s10201-015-0457-4

Cited by 113 publications

(112 citation statements)

References 35 publications

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“…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). Other research suggests the fixation of filtered DNA with ethanol may allow sample material to be preserved at room temperature for many days (Minamoto et al 2012;Thomsen et al 2012a;Minamoto et al 2016). However, since this approach is yet to gain widespread acceptance, its use for the preservation of rare target DNA is not recommended.…”

Section: Extraction Of Dna From Water and Icementioning

confidence: 99%

“…For this reason, it may be preferable to filter multiple small volumes of water through separate filters and later combine the DNA collected from each filter via ethanol precipitation (Santas et al 2013). The optimal filter pore size is generally suggested to lie between 0.6 µm and 1.5 µm (Eichmiller et al 2016;Minamoto et al 2016). We suggest using 1.5 µm glass fibre filters (Type 934-AH) to filter water for assessments of vertebrate DNA but smaller filter sizes (e.g.…”

Section: Extraction Of Dna From Water and Icementioning

confidence: 99%

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

Lear¹,

Dickie²,

Banks³

et al. 2018

110

112

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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.

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Section: Extraction Of Dna From Water and Icementioning

confidence: 99%

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

110

112

View full text Add to dashboard Cite

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“…In previous studies, various eDNA sample preservation techniques, such as cooling the water samples in a cool box (Takahara et al 2012;Eichmiller et al 2014;Lacoursière-Roussel et al 2016), freezing the water samples (Takahara et al 2015) and on-ice preservation/ethanol fixation/immersion in lysis buffers of obtained filter samples (Goldberg et al 2011;Takahara et al 2012;Renshaw et al 2015;Minamoto et al 2016), have been followed to decelerate the degradation rate of eDNA. However, on-site filtration requires a sophisticated system setup, and cooling or freezing of water and filter samples requires a cool box or portable freezer, resulting in increased equipment requirements for field sampling and an increased contamination risk.…”

Section: Introductionmentioning

confidence: 99%

A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant

Yamanaka

Minamoto

Matsuura³

et al. 2016

Limnology

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150

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Environmental DNA (eDNA) analysis is a powerful tool within ecology for the study of the distribution or abundance of aquatic species, although the simplification of water sampling is required for enabling light and fast field sampling to expand further application of eDNA analysis. Here, certain candidate chemicals belonging to the group of cationic surfactants were examined for their effectiveness as preservatives for eDNA water samples by simply adding the chemicals to water samples to suppress the degradation of eDNA. The quaternary ammonium compound benzalkonium chloride (BAC) at a final concentration of 0.01% was effective to retain 92% of eDNA derived from the bluegill sunfish Lepomis macrochirus in an 8-h incubation test at ambient temperature, which assumed a transportation of water samples in 1-day field sampling during the daytime. Meanwhile, eDNA in water samples without BAC retained only 14% of the initial eDNA. Moreover, an additional long-term incubation test (up to 10 days) revealed BACtreated samples retained *70 and 50% of bluegill DNA compared to the initial amount after 1-and 10-day incubation at ambient temperature, respectively. Meanwhile, eDNA in naïve samples reduced to 20% after 1-day incubation and reached undetectable levels after 10 days. Up to now, many eDNA studies have adopted on-site filtration followed by filter fixation, which requires many pieces of equipment. Addition of BAC can protect eDNA in water samples with less effort and equipment resulting in an increase of measurement accuracy of the eDNA quantity and detection probability of rare species by preventing the disappearance of rare sequences in water samples.

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“…Minamoto, Naka, Moji, and Maruyama (2016) for selection of filter type for eDNA sampling). Minamoto, Naka, Moji, and Maruyama (2016) for selection of filter type for eDNA sampling).…”

Section: Offshore Samplingmentioning

confidence: 99%

Habitat selection and migration of the common shrimp, Palaemon paucidens in Lake Biwa, Japan—An eDNA‐based study

Kawano

Ishikawa

et al. 2019

Environmental DNA

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Palaemon paucidens has a large population and is an important food source for fish in Lake Biwa, Japan. They are abundant in shallow waters from spring to summer, after which most individuals migrate to offshore deep areas where they remain during autumn and winter. However, some individuals are nonmigratory, remaining in shallow waters over winter. It has been reported that P. paucidens individuals have declined in recent years; a better understanding of its seasonal distribution is needed to manage this species, and basic information on its seasonal distribution is indispensable. We tracked the environmental DNA (eDNA) distribution of P. paucidens in Lake Biwa over a year using a quantitative real-time polymerase chain reaction method.We collected water samples from offshore (both from the surface and from the benthic) and from shallow shore sites adjacent to the shorelines of the main lake and connecting freshwater lagoons. Offshore sampling took place in summer and winter, and shallow shore and lagoon sampling in all four seasons. During summer, eDNA concentrations were significantly higher in shallow and lagoon areas than offshore bottom sites. Conversely, during winter, eDNA concentrations were higher in offshore bottom sites, and relatively high and low eDNA concentrations in lagoons and shallow shore, respectively. These results most likely reflect the spatial and temporal distribution of this species in Lake Biwa. The eDNA concentrations peaked in early August at shallow shore sites in the main lake, with a significant decline in mid-October, while low eDNA concentrations were recorded at offshore bottom sites in late August. These results suggest that P. paucidens migrates from shallow waters to offshore bottom sites between early August and mid-October. These results provide important information for the management of this species. K E Y W O R D Senvironmental DNA (eDNA), Lake Biwa, migration, Palaemon paucidens, quantitative real-time PCR, spatial and temporal distribution | 55 WU et al.

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Techniques for the practical collection of environmental DNA: filter selection, preservation, and extraction

Cited by 113 publications

References 35 publications

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

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

A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant

Habitat selection and migration of the common shrimp, Palaemon paucidens in Lake Biwa, Japan—An eDNA‐based study

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