Dneasy Powersoil Kit Handbook: For The Isolation of Microbial Genomic Dna From All Soil Types
Dneasy Powersoil Kit Handbook: For The Isolation of Microbial Genomic Dna From All Soil Types
Dneasy Powersoil Kit Handbook: For The Isolation of Microbial Genomic Dna From All Soil Types
Sample to Insight__
Contents
Kit Contents ............................................................................................................... 3
Storage ..................................................................................................................... 4
Quality Control........................................................................................................... 5
Introduction ................................................................................................................ 6
MB Spin Columns 50 2 x 50
Solution C2 15 ml 2 x 15 ml
Solution C3 15 ml 2 x 15 ml
Solution C4 72 ml 2 x 72 ml
Solution C5 30 ml 2 x 30 ml
Solution C6 9 ml 2 x 9 ml
Intended Use
All DNeasy products are intended for molecular biology applications. These products are not
intended for the diagnosis, prevention or treatment of a disease.
All due care and attention should be exercised in the handling of the products. We
recommend all users of QIAGEN products to adhere to the NIH guidelines that have been
developed for recombinant DNA experiments, or to other applicable guidelines.
WARNING: Do not use bleach to clean the inside of the QIAvac® 24 Plus manifold.
CAUTION
DO NOT add bleach or acidic solutions to directly to the sample
preparation waste
PowerBead Tubes and Solution C4 contain guanidine salts, which can form highly reactive
compounds when combined with bleach. If liquid containing these buffers is spilt, clean with
a suitable laboratory detergent and water. If the spilt liquid contains potentially infectious
agents, clean the affected area first with laboratory detergent and water, and then with 1%
(v/v) sodium hypochlorite.
Quality Control
In accordance with QIAGEN’s ISO-certified Quality Management System, each lot of
DNeasy PowerSoil Kits is tested against predetermined specifications to ensure consistent
product quality.
The DNeasy PowerSoil Kit uses a humic substance/brown color removal procedure. This
procedure is effective at removing PCR inhibitors from even the most difficult soil types.
Environmental samples are added to a bead beating tube for rapid and thorough
homogenization. Cell lysis occurs by mechanical and chemical methods. Total genomic
DNA is captured on a silica membrane in a spin column format. DNA is then washed and
eluted from the membrane. The isolated DNA is ready for PCR analysis and other
downstream applications.
The DNeasy PowerSoil Kit does not require homogenization using a high velocity bead
beater. However, if the microorganism of interest requires stronger homogenization than
provided by a vortex, or if using a bead beater is desired, the DNeasy PowerSoil Kit may be
used in conjunction with the PowerLyzer® 24 Homogenizer (110/220V) (cat. no. 13155).
We now offer DNeasy PowerLyzer PowerSoil Kits (cat. no. 12855-50 and 12855-100) with
bead tubes suitable for high-powered bead beating of soil. For more information about these
High-throughput options
We offer a vacuum-based protocol for faster processing without centrifugation for the
DNA-binding and column-washing steps for MB Spin Columns. The QIAvac 24 Plus
Manifold allows for processing of up to 24 MB Spin Column preps at a time. For additional
high-throughput options, we offer the DNeasy PowerSoil HTP 96 Kit for processing up to
2 x 96 samples using a centrifuge capable of spinning two 96 well blocks stacked
(13 cm x 8 cm x 5.5 cm) at 2500 x g. For 96-well homogenization of soil, we offer the
TissueLyser II and Plate Adapter Set (cat. no. 85300 and 11990, respectively.)
Purification of DNA using the DNeasy PowerSoil Kit can be automated on the QIAcube®.
The innovative QIAcube uses advanced technology to process QIAGEN spin columns,
enabling seamless integration of automated, low-throughput sample prep into your
laboratory workflow. Sample preparation using the QIAcube follows the same steps as the
If automating the DNeasy PowerSoil Kit on the QIAcube, the instrument may process fewer
than 50 samples due to dead volumes, evaporation and additional reagent consumption by
automated pipetting. QIAGEN only guarantees 50 sample preps with manual use of the
DNeasy PowerSoil Kit.
For more information about the automated procedure, see the relevant protocol sheet
available at www.qiagen.com/MyQIAcube. Up-to-date protocol sheets can be downloaded
free of charge, or may be obtained by contacting QIAGEN Technical Services at
support.qiagen.com.
Microcentrifuge (10,000 x g)
Pipettors (50 μl–500 μl)
Vortex-Genie 2 Vortex
Vortex Adapter for 24 (1.5-2.0 ml) tubes (cat. no. 13000-V1-24)
100% ethanol (for the QIAvac 24 Plus Manifold protocol only)
QIAvac 24 Plus Manifold
Important Notes
Make sure the 2 ml PowerBead Tubes rotate freely in your centrifuge without rubbing.
Shake to mix Solution C4 before use.
Procedure
1. Add 0.25 g of soil sample to the PowerBead Tube provided. Gently vortex to mix.
2. Add 60 μl of Solution C1 and invert several times or vortex briefly.
Note: Solution C1 may be added to the PowerBead tube before adding soil sample
3. Secure PowerBead Tubes horizontally using a Vortex Adapter for 24 (1.5–2.0 ml) tubes
(cat. no. 13000-V1-24).
4. Vortex at maximum speed for 10 min.
Note: If using the 24-place Vortex Adapter for more than 12 preps, increase the vortex
time by 5–10 min.
5. Centrifuge tubes at 10,000 x g for 30 s.
6. Transfer the supernatant to a clean 2 ml Collection Tube.
Note: Expect between 400–500 μl of supernatant. Supernatant may still contain some
soil particles.
7. Add 250 μl of Solution C2 and vortex for 5 s. Incubate at 2–8°C for 5 min.
Note: You can skip the 5 min incubation. However, if you have already validated the
DNeasy PowerSoil extractions with this incubation we recommend you retain the step.
8. Centrifuge the tubes for 1 min at 10,000 x g.
9. Avoiding the pellet, transfer up to 600 μl of supernatant to a clean 2 ml Collection Tube.
10. Add 200 μl of Solution C3 and vortex briefly. Incubate at 2–8°C for 5 min.
Procedure
1. Add 0.25 g of soil sample to the PowerBead Tube provided. Gently vortex to mix.
Note: After your sample has been loaded into the PowerBead Tube, the next step is a
homogenization and lysis procedure. The PowerBead Tube contains a buffer that will (a)
help disperse the soil particles, (b) begin to dissolve humic acids and (c) protect nucleic
acids from degradation. Gentle vortexing mixes the components in the PowerBead Tube
and begins to disperse the sample in the buffer.
2. If Solution C1 has precipitated, heat at 60°C until precipitate dissolves. Add 60 μl of
Solution C1 to sample and invert several times or vortex briefly.
Note: Solution C1 may be added to the PowerBead tube before adding soil sample.
Solution C1 contains SDS and other disruption agents required for complete cell lysis. In
addition to aiding cell lysis, SDS is an anionic detergent that breaks down fatty acids
and lipids associated with the cell membrane of several organisms. If it gets cold, it will
form a white precipitate in the bottle. Heating to 60°C will dissolve the SDS but will not
harm it or the other disruption agents. Solution C1 can be used while it is still warm.
3. Secure PowerBead Tubes horizontally using a Vortex Adapter for 24 (1.5–2.0 ml) tubes
(cat. no. 13000-V1-24).
4. Vortex at maximum speed for 10 min.
Note: If using the 24-place Vortex Adapter for more than 12 preps, increase the vortex
time by 5–10 min. Vortexing is critical for complete homogenization and cell lysis. Cells
are lysed by a combination of chemical agents from steps 1–4 and mechanical shaking
7. Add 250 μl of Solution C2 and vortex for 5 s. Incubate at 2–8°C for 5 min.
Note: You can skip the 5 min incubation. However, if you have already validated the
DNeasy PowerSoil extractions with this incubation we recommend you retain the step.
Solution C2 is patented Inhibitor Removal Technology (IRT). It contains a reagent that can
precipitate non-DNA organic and inorganic material including humic substances, cell
debris and proteins. It is important to remove contaminating organic and inorganic
matter that may reduce DNA purity and inhibit downstream DNA applications.
For each sample lysate, use one MB Spin Column. Keep the MB Spin Column in the
attached 2 ml Collection Tube and continue using the Collection Tube as an MB Spin
Column holder until needed for the vacuum manifold protocol.
Label each Collection Tube top and MB Spin Column to maintain sample identity. If the
MB Spin Column becomes clogged during the vacuum procedure, switch to the
centrifugation protocol.
100% ethanol will be needed for step 8 of this protocol.
Procedure
1. Connect the QIAvac 24 Plus to the vacuum source using the QIAvac Connecting System
(for more details, refer to the QIAvac 24 Plus Handbook, Appendix A, page 16).
2. Insert a VacValve into each Luer slot of the QIAvac 24 Plus that is to be used. Close
unused Luer slots with Luer plugs or close the inserted VacValve.
3. Insert a VacConnector into each VacValve. Perform this step directly before starting the
purification to avoid exposure of VacConnectors to potential contaminants in the air.
4. Place an MB Spin Column into each VacConnector on the manifold.
5. Transfer 650 µl of prepared sample lysate (from step 13 of the centrifugation protocol) to
an MB Spin Column.
6. Turn on the vacuum source and open the VacValve of the port. Hold the tube in place
when opening the VacValve to keep the MB Spin Column steady. Allow the lysate to
pass through the MB Spin Column completely.
7. After the lysate has passed through the column completely, load again with 650 µl of
lysate. Continue until all the lysate has been loaded onto the MB Spin Column. Close the
VacValve of that port.
Soil processing
a) Amount of soil to process The QIAGEN DNeasy PowerSoil Kit is designed to process 0.25 grams of
soil. For inquiries regarding the use of larger sample amounts, please contact
Technical Support for suggestions.
b) Soil sample is high in Remove contents from PowerBead Tube (beads and solution) and transfer into
water content another sterile microcentrifuge tube (not provided). Add soil sample to
PowerBead Tube and centrifuge at room temperature for 30 seconds at
10,000 x g. Remove as much liquid as possible with a pipet tip. Add beads
and bead solution back to PowerBead Tube, gently vortex to mix and resume
protocol from Step 2.
DNA
a) DNA does not amplify Make sure to check DNA yields by gel electrophoresis or spectrophotometer
reading. An excess amount of DNA will inhibit a PCR reaction.
Diluting the template DNA should not be necessary with DNA isolated using
the QIAGEN PowerSoil DNA Kit; however, it should still be attempted.
If DNA will still not amplify after trying the steps above, then PCR optimization
(changing reaction conditions and primer choice) may be needed.
b) Eluted DNA is brown If you observe coloration in your samples, please contact Technical Support
for suggestions.
c) Concentrating eluted The final volume of eluted DNA will be 100 μl. The DNA may be
DNA concentrated by adding 4 μl of 5 M NaCl and inverting 3–5 times to mix.
Next, add 200 μl of 100% cold ethanol and invert 3–5 times to mix.
Centrifuge at 10,000 x g for 5 minutes at room temperature. Decant all
liquid. Remove residual ethanol in a speed vac, a dessicator or air dry.
Resuspend precipitated DNA in sterile water or sterile 10 mM Tris.
d) DNA floats out of a well This usually occurs because residual Solution C5 remains in the final sample.
when loading a gel Prevent this by being careful in step 19 and not transferring liquid onto the
bottom of the spin filter basket. Ethanol precipitation (described in
“Concentrating eluted DNA”) is the best way to remove residual Solution C5.
e) Storing DNA DNA is eluted in Solution C6 (10 mM Tris) and must be stored at –20°C to
–80°C to prevent degradation. DNA can be eluted in TE without loss, but the
EDTA may inhibit downstream reactions such as PCR and automated
sequencing. DNA may also be eluted with sterile DNA-free PCR grade water
(cat. no. 17000-10).
a) Cells are difficult to lyse After adding Solution C1, incubate at 70°C for10 minutes. Resume protocol
from step 3.
b) Reduction of shearing of After adding Solution C1, vortex 3–4 seconds, then heat to 70°C for 5
DNA minutes. Vortex 3–4 seconds. Heat another 5 minutes. Vortex 3–4 seconds.
This alternative procedure will reduce shearing but may also reduce yield.
DNeasy PowerMax Soil Kit (10) For 10 preps: Isolate microbial DNA
from large quantities of soil; great for 12988-10
samples with low microbial load
RNeasy PowerSoil Total RNA Kit For 25 preps: Isolate high-quality total
12866-25
(25) RNA from all soil types
Glass Bead Tubes, 0.5 mm (50) Ready-to-use bead tubes for rapid
and reliable biological sample lysis
13116-50
from a wide variety of starting
materials
Glass Bead Tubes, 0.1 mm (50) Ready-to-use bead tubes for rapid
and reliable biological sample lysis
13118-50
from a wide variety of starting
materials
For up-to-date licensing information and product-specific disclaimers, see the respective
QIAGEN kit handbook or user manual. QIAGEN kit handbooks and user manuals are
available at www.qiagen.com or can be requested from QIAGEN Technical Services or your
local distributor.
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1104560 HB-2257-001 05/2017 DNeasy PowerSoil Kit Handbook 05/2017