Recommendations for the processing and storage of water samples before polymerase chain reaction (PCR) analysis

Gilpin, Brent; Devane, Megan L.; Nourozi, F.; Robson, Beth; Scholes, Paula; Lin, Shen

doi:10.1080/00288330.2013.797915

Cited by 9 publications

(4 citation statements)

References 9 publications

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“…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). 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).…”

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

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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%

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

show abstract

“…The filters were stored at -20°C in sterilised 50 mL plastic tubes until use. Extreme care was taken to avoid long storage periods and all groundwater filtrations and DNA extractions were carried out immediately as delays may alter the apparent microbial community composition in such samples (Gilpin et al 2013). Bacterial genomic DNA extractions were performed using ZR Fungal/ Bacterial DNA kits (Zymo Research, USA) as described in Sirisena et al (2013).…”

Section: Dna Extractionmentioning

confidence: 99%

Relationships between molecular bacterial diversity and chemistry of groundwater in the Wairarapa Valley, New Zealand

Sirisena

Daughney

Moreau

et al. 2014

New Zealand Journal of Marine and Freshwater Research

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Groundwater plays an important role in New Zealand water supplies and hence monitoring activities are conducted regularly. Most monitoring programmes aim to evaluate groundwater chemistry and almost completely overlook the microbial component in this ecosystem. In our present study, the bacterial community structure of groundwater in the Wairarapa Valley was examined using the terminal restriction fragment length polymorphism (T-RFLP), and relationships between bacterial community structure and groundwater chemistry, aquifer confinement and groundwater usage were explored. In addition, the results from this study were compared with a previous T-RFLP survey of the same area in an attempt to detect changes in bacterial community structure over time. The data obtained suggested that bacterial community structure was related to groundwater chemistry, especially to redox conditions. Species composition showed minimal variation over time if groundwater chemistry remained unchanged. These findings reflect the potential of using bacterial communities as biological indicators to evaluate the health of groundwater ecosystems. We suggest that it is important to include this type of broad bacterial diversity assessment criteria into regular groundwater monitoring activities.

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“…The filters were stored at -20 °C in sterilized 50-ml plastic tubes until use. Extreme care was taken to avoid long storage periods and all groundwater filtrations and DNA extractions were carried out immediately as delays may alter the apparent microbial community composition in such samples (Gilpin et al 2013). Bacterial genomic DNA extractions were performed using ZR Fungal/Bacterial DNA kits (Zymo Research, United States) as described in .…”

Section: Dna Extractionmentioning

confidence: 99%

“…Briefly, 2 L of groundwater from each site was filtered through a sterile 0.22 µm nitrocellulose membrane filter (Millipore, Australia). The filtrations were carried out immediately as delays could alter the natural microbial community composition in these samples (Gilpin et al 2013). The PCR amplicon library preparation and 454 pyrosequencing.…”

Section: Dna Extraction and 454 Pyrosequencingmentioning

confidence: 99%

Molecular characterization of bacterial diversity in New Zealand groundwater

Sirisena¹

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<p>Groundwater is a globally important natural resource and an integral part of the water supply in New Zealand. Due to high demand, the quality and availability of groundwater are both extensively monitored in New Zealand and globally, under State-of-the-Environment (SOE) monitoring programmes. SOE groundwater monitoring in New Zealand mainly evaluates hydrochemistry and until this thesis has largely overlooked the biotic component. Microbes including bacteria play a crucial role in ecosystem functioning by mediating biogeochemical processes in subsurface environments. Therefore, analysis of microbiological content will enable better evaluation of the health of groundwater ecosystems that is not fully reflected by chemical data alone. This project characterizes the bacterial diversity in New Zealand groundwater at national and regional scales using molecular methods and explores the underlying factors that shape the bacterial community structure. A simple molecular profiling tool, Terminal Restriction Fragment Length Polymorphism (T-RFLP) was used to determine community structure at local and national scales. The results revealed considerable diversity that was driven by groundwater chemistry. Roche 454-pyrosequencing was then used to obtain a deeper insight into New Zealand groundwater ecosystems, and showed that bacterial communities have many low abundance taxa and relatively few highly abundant species. In addition, microbial diversity is mainly related to the redox potential of the groundwater. But, despite this relationship, Pseudomonas spp. were the dominant genus at many sites even those with diverse chemistries and environmental factors. The final phase of the project set the platform to test whether these Pseudomonas spp. have acquired genetic material from other species via horizontal gene transfer (HGT) enabling them to adapt into a diverse range of habitats. A whole-genome sequencing approach (Illumina MiSeq platform) was used to develop six metagenomic databases as a resource to test this hypothesis. Initial results show some evidence for HGT and further investigations are underway. Overall, the knowledge generated across all phases of this project provides novel insights into New Zealand groundwater ecosystems and creates a scientific basis for the future inclusion of microbial status assessment criteria into regional and national groundwater monitoring programmes and related policies in New Zealand.</p>

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Recommendations for the processing and storage of water samples before polymerase chain reaction (PCR) analysis

Cited by 9 publications

References 9 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

Relationships between molecular bacterial diversity and chemistry of groundwater in the Wairarapa Valley, New Zealand

Molecular characterization of bacterial diversity in New Zealand groundwater

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