Powersoil dna isolation kit

Manufactured by Qiagen

Sourced in United States, Germany, United Kingdom, Netherlands, China, Canada

The PowerSoil DNA Isolation Kit is a laboratory equipment product designed for the isolation and purification of DNA from a variety of soil and environmental samples. It is a standardized and streamlined process that enables the extraction of high-quality genomic DNA from complex soil matrices.

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DNA isolation kit (207 citations) PowerSoil kit (109 citations) DNA kits (7 citations)

1 171 protocols using powersoil dna isolation kit

Culture-independent DNA extraction from grapes and yeast

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The initial step for our culture independent approach was the extraction of DNA directly from grapevines. The pellets obtained after grape juice centrifugation were re-hydrated with 480 μL Phosphate-buffered saline (PBS), with vigorous agitation. A 20 μL aliquot of 20 mg/mL lyticase (Sigma) was added to the samples, which were subsequently incubated at 37°C for 20 min. Then, the samples were treated with 2.5 μL volume of 20 mg/mL Proteinase K (Merck) incubated at 37°C for 45 min. The Power Soil DNA Isolation Kit (Mo-Bio Laboratories, Inc.) was used for DNA extraction according to the manufacturer’s instructions.
In the case of yeast isolates, each of the colonies selected was suspended in 200 μL PBS, with vigorous agitation, followed by centrifugation at 5.000 × g for 5 min. The pellets formed were washed with TE-NaCl (Tris 10mM pH7, EDTA 1 mM, NaCl 0.15 M) and centrifuged at 5.000 × g for 5 min. Subsequently, a 20 μL volume of 20 mg/mL lyticase (Sigma) was added to the samples, which were subsequently incubated at 37°C for 20 min. Finally, the samples were treated with 2.5 μL volume of 20 mg/mL Proteinase K (Merck) incubated at 37°C for 45 min. The Power Soil DNA Isolation Kit (Mo-Bio Laboratories, Inc.) was used for DNA extraction according to the manufacturer’s instructions. All the DNA obtained was froze at -20°C until processed.

Jara C., Laurie V.F., Mas A, & Romero J. (2016). Microbial Terroir in Chilean Valleys: Diversity of Non-conventional Yeast. Frontiers in Microbiology, 7, 663.

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Soil and Root Microbiome DNA Extraction

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All samples were processed few hours after collection. Rhizospheric soil of five adjacent plants was combined as an individual sample. Roots were shaken to remove loose soil. Remaining attached soil (i.e. rhizospheric soil) was collected using sterile brushes. A total of 0.25 g of rhizospheric soil was used for DNA extraction with PowerSoil DNA Isolation Kit following the manufacturer’s instructions (MO BIO Laboratories, Inc.).
For Root-associated samples, roots from five plants were washed twice with sterilized water. Approximately 1 g of root tissue was pooled and washed in 15 ml 70% ethanol for 30 seconds. After washing with sterilized water, the roots were washed with 5% NaClO for 30 minutes and then washed with sterilized water. Roots were homogenized in liquid nitrogen with mortar and pestle and used for DNA extraction with PowerSoil DNA Isolation Kit (MO BIO Laboratories, Inc).

Rascovan N., Carbonetto B., Perrig D., Díaz M., Canciani W., Abalo M., Alloati J., González-Anta G, & Vazquez M.P. (2016). Integrated analysis of root microbiomes of soybean and wheat from agricultural fields. Scientific Reports, 6, 28084.

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Environmental Microbiome Sampling and DNA Extraction

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Samples included in the study were collected from a variety of environmental sources (for N values see Table 1). Built environment samples were collected using sponges and swabs from healthcare facilities, offices, and gyms throughout the United States. Following collection, DNA samples were extracted with the PowerSoil DNA Isolation kit (Qiagen, Hilden, Germany). Wastewater treatment plant (WWTP) influent and effluent were collected by grab sampling, and DNA was extracted using previously described methods (Teachey et al., 2019) . Poultry samples were collected from poultry litter, DNA was extracted and purified using previously described methods (Oladeinde et al., 2019) . Mock community isolates were extracted using the PowerSoil DNA Isolation kit (Qiagen, Hilden, Germany).

Beaudry M.S., Thomas J.C., Baptista R.P., Sullivan A., Norfolk W.A., Devault A., Enk J., Kieran T.J., Rhodes O.E., Perry A.K., Halpin A.L., Bayona‐Vásquez N.J., Oladeinde A., Lipp E.K., Sánchez S., & Glenn T.C. (2021). Escaping the Fate of Sisyphus: Assessing Resistome Hybridization Baits for Antimicrobial Resistance Gene Capture.

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Metagenomic sequencing of environmental samples

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Metagenomic DNA of snow, ice, and seawater samples was extracted from 0.22-μm filters with a PowerSoil DNA Isolation Kit (Qiagen, Germantown, USA) following its protocol. The concentration of DNA was quantified by Qubit DNA Assay Kit with a Qubit 2.0 fluorometer (Invitrogen, Carlsbad, CA, USA), and the quality was checked by gel electrophoresis. The sequencing library was prepared using the KAPA hyper Prep Kit (Roche, Shanghai, China). The shotgun sequencing was performed on Illumina NovaSeq 6000 Platform PE150 (Illumina, San Diego, CA, USA) with 150 bp paired-end reads. Genomic DNA of sediment samples from TY038 and TY042 stations was extracted from ~ 5 g by modified SDS method as descript in a previous study [33 (link)]. DNA of sediment samples from GT04 station was extracted from ~ 0.3 g of sediment per sample using PowerSoil® DNA Isolation Kit (QIAGEN, Germany). The sequence library was built in Beijing Genome Institution (BGI, Shenzhen, China) and sequenced on the BGI MGISEQ-2000 platform, which has been reported can obtain comparable results as Illumina platform [34 (link)].

Liu Y., Zhang Z., Ji M., Hu A., Wang J., Jing H., Liu K., Xiao X, & Zhao W. (2022). Comparison of prokaryotes between Mount Everest and the Mariana Trench. Microbiome, 10, 215.

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DNA Extraction from Sediments and Water

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DNA was extracted from sediments using the PowerSoil DNA isolation kit (Qiagen, Germany). A prewashing step was performed using solution S0 (0.1 M EDTA, 0.1 M Tris (pH 8.0), 1.5 M NaCl, 0.1 M NaH₂PO₄, and Na₂HPO₄) [39 (link)], due to the acidity of some samples and the presence of heavy metals. Briefly, 300 mg of sediments were washed with 1.5 mL of solution S0 overnight in a horizontal shaker at 180 rpm at 4 °C, and the sediment was recovered by centrifugation at 12,000× g for 5 min and repeatedly washed with S0 until the supernatant appeared clear. After washing, the sediments were transferred to PowerBead Tubes (Qiagen, Germany), and the extraction proceeded as described by the manufacturer’s instructions.
Additionally, a quarter of the filtered water samples was used for DNA extraction using the PowerSoil DNA isolation kit (Qiagen, Germany). The filter was transferred into the PowerBead Tubes (Qiagen, Germany) to proceed with the DNA extraction according to the manufacturer’s protocol. DNA concentration was measured using Qubit^® dsDNA HS (Invitrogen, OR, USA).

Agramont J., Gutiérrez-Cortez S., Joffré E., Sjöling Å, & Calderon Toledo C. (2020). Fecal Pollution Drives Antibiotic Resistance and Class 1 Integron Abundance in Aquatic Environments of the Bolivian Andes Impacted by Mining and Wastewater. Microorganisms, 8(8), 1122.

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Microbial Community Analysis of Sludge Samples

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The sludge samples were collected from GAC0 and GAC5 reactors at the end of experiment. The total DNAs of all samples were extracted using the Power Soil^TM DNA isolation kit (Mo-Bio Laboratories Inc., CA). Labels of “HAc0”, “HPr0”, “HBu0” stand for the sludge samples taken from GAC0 with respective substrate, and “HAc1”, “HPr1”, “HBu1” stand for the samples taken from GAC5. The microbial community of samples was analyzed by using high-throughput pyrosequencing on an Illumina platform (Illumina Miseq PE300). Amplicon libraries were constructed for pyrosequencing using bacterial primers 515F (50-GTG CCA GCM GCC GCG GTA A-30) and 806R (50-GGA CTA CHVGGG TWT CTA AT-30) for the V4–V5 region of the microbial 16SrRNA gene (Xu et al., 2015 (link)). Sequencing data has been deposited into public database NCBI, and the accession number is SRP134710 (https://www.ncbi.nlm.nih.gov/sra/SRP134710).

Xu S., Han R., Zhang Y., He C, & Liu H. (2018). Differentiated stimulating effects of activated carbon on methanogenic degradation of acetate, propionate and butyrate. Waste Management (New York, N.y.), 76, 394-403.

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Extraction and Analysis of Rhizosphere Microbiome

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The rice roots were washed with distilled water more than three times to remove the soil particles adhering to the root surface and were then rinsed with sterile water. The iron plaque was then extracted from the root materials using a dithionite-citrate-bicarbonate (DCB) solution as described previously13 (link), and the DCB-extract solution was centrifuged at 16,000 × g for 10 min to pellet any microorganisms present on the plaque. The genomic DNA was extracted from the precipitated products of the DCB extract (iron plaque), bulk soil and rhizosphere soil using the PowerSoil^TM DNA Isolation Kit (MO BIO Laboratories, Inc., Carlsbad, CA) according to the manufacturer’s instructions. The details of the 16S rRNA gene PCR, 454 pyrotag sequencing and bioinformatic analysis are presented in the Supporting Information.

Hu M., Li F., Liu C, & Wu W. (2015). The diversity and abundance of As(III) oxidizers on root iron plaque is critical for arsenic bioavailability to rice. Scientific Reports, 5, 13611.

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Extraction of Microbial DNA from Fermentation

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DNA was extracted from samples of fermentation broth using the PowerSoil^TM DNA Isolation Kit (MO BIO Laboratories, CA, United States). Samples were thawed and centrifuged for 10 min at 12,000 g and the pellets were washed twice in Tris-EDTA buffer (10 mM Tris-HCl, 1 mM EDTA). Subsequent steps were performed following the PowerSoil kit instructions.

Naimi S., Zirah S., Taher M.B., Theolier J., Fernandez B., Rebuffat S.F, & Fliss I. (2020). Microcin J25 Exhibits Inhibitory Activity Against Salmonella Newport in Continuous Fermentation Model Mimicking Swine Colonic Conditions. Frontiers in Microbiology, 11, 988.

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Genomic DNA Extraction and Quantification

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Total genomic DNA was extracted from the samples using the PowerSoil^TM DNA Isolation Kit (MO BIO Laboratories, Carlsbad, CA, US) according to the manufacturer’s protocol. After extraction, the DNA concentration was measured with the Qubit dsDNA BR assay kit (Invitrogen, Carlsbad, CA, USA) using the Qubit® 2.0 Fluorometer. The integrity of the gDNA was assessed by 1% agarose gel electrophoresis at 50 V for 2 hours. The extracted DNA was stored at -80°C before further PCR analysis.

Van Leuvenhaege C., Vandelannoote K., Affolabi D., Portaels F., Sopoh G., de Jong B.C., Eddyani M, & Meehan C.J. (2017). Bacterial diversity in Buruli ulcer skin lesions: Challenges in the clinical microbiome analysis of a skin disease. PLoS ONE, 12(7), e0181994.

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Metagenomic Analysis of Wastewater Samples

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The samples were collected from PETL (N17° 32.396 E78° 14.590) at the same time as for a previous culture-based study of ours [8 (link)] where we also described sampling and DNA extraction procedures in more detail. Briefly, grab samples of water from the equilibrator (EQR), aeration tank no.1 (AER1), aeration tank no. 2 (AER2), settling tank (STL) and sludge samples from the secondary sludge (SS) and old dried sludge (OS) were collected in sterile containers. These samples were stored on ice and transported overnight to the National Center for Cell Science, in Pune, Maharashtra, India. The sampling was authorized by the Pollution Control Board of Andhra Pradesh and supervised by the manager of PETL.
The total genomic DNA was extracted from concentrated water samples and sludge samples using PowerSoil^TM DNA Isolation Kit (MoBio Laboratories Inc., Carlsbad, USA) according to manufacturer´s instructions. The extracted DNA was quantified using a Nanodrop spectrophotometer (J H Bio innovations, Secunderabad, India) and stored at -20°C until further use.

Marathe N.P., Shetty S.A., Shouche Y.S, & Larsson D.G. (2016). Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production. PLoS ONE, 11(11), e0165914.

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