License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: In development
We are still developing and optimizing this protocol
Created: September 10, 2022
Last Modified: September 13, 2023
Protocol Integer ID: 69796
Abstract
For the isolation of microbial genomic DNA from all soil types, including difficult samples such as compost, sediment, and manure.
Guidelines
Materials
PowerBead Pro Tubes
MB Spin Columns
Solution CD1
Solution CD2
Solution CD3
Solution EA
Solution C5
Solution C6
Microcentrifuge Tubes (2 ml)
Elution Tubes (1.5 ml)
Collection Tubes (2 ml)
Microcentrifuge
Pipettor
Safety warnings
Solution EA and Solution C5 are flammable
DO NOT add bleach or acidic solutions directly to the sample preparation waste.
Before start
Ensure that the PowerBead Pro Tubes rotate freely in the centrifuge without rubbing.
If Solution CD3 has precipitated, heat at 60°C until precipitate dissolves.
Perform all centrifugation steps at room temperature (15–25°C).
Prepare sample & Cell lysis
Prepare sample & Cell lysis
Spin the PowerBead Pro Tube briefly to ensure that the beads have settled at the bottom.
Add up to 250 mg of soil and 800 µL of Solution CD1. Vortex briefly to mix.
Homogenize samples thoroughly using one of the following methods:
Secure the PowerBead Pro Tube horizontally on a Vortex Adapter for 1.5–2 ml tubes (cat. no. 13000-V1-24). Vortex at maximum speed for 00:10:00 .
10m
Use a PowerLyzer 24 Homogenizer. PowerBead Pro Tubes must be properly balanced in the tube holder of the PowerLyzer 24 Homogenizer. We recommend homogenizing the soil at 2000 rpm, 00:00:30 , pausing for 00:00:30 , then homogenizing again at 2000 rpm, 00:00:30 .
1m 30s
Use a TissueLyser II. Place the PowerBead Pro Tube into the TissueLyser Adapter Set 2 x 24 (cat. no. 69982) or 2 ml Tube Holder (cat. no. 11993) and Plate Adapter Set (cat. no. 11990). Fasten the adapter into the instrument and shake for00:05:00 at speed 25 Hz. Reorient the adapter so that the side that was closest to the machine body is now furthest from it. Shake again for 5 min at a speed of 25 Hz.
5m
Centrifuge the PowerBead Pro Tube at 15000 rpm, 00:01:00 .
1m
Transfer the supernatant to a clean 2 ml Microcentrifuge Tube (provided).
Inhibitor removal
Inhibitor removal
1m 5s
1m 5s
Add 200 µL of Solution CD2 and vortex for 00:00:05 .
5s
Centrifuge at 15000 x g, 00:01:00 . Avoiding the pellet, transfer up to 700 µL of supernatant to a clean 2 ml Microcentrifuge Tube (provided).
1m
Bind DNA
Bind DNA
1m 5s
1m 5s
Add 600 µL of Solution CD3 and vortex for 00:00:05 .
5s
Load 650 µL of the lysate onto an MB Spin Column and centrifuge at 15000 x g, 00:01:00 .
1m
Discard the flow-through and repeat step 8 to ensure that all of the lysate has passed through the MB Spin Column.
Carefully place the MB Spin Column into a clean 2 ml Collection Tube (provided). Avoid splashing any flow-through onto the MB Spin Column.
Wash
Wash
4m
4m
.Add 500 µl of Solution EA to the MB Spin Column. Centrifuge at 15000 x g, 00:01:00 .
1m
Discard the flow-through and place the MB Spin Column back into the same 2 ml Collection Tube.
Add 500 µL of Solution C5 to the MB Spin Column. Centrifuge at 15000 x g, 00:01:00 .
1m
Discard the flow-through and place the MB Spin Column into a new 2 ml Collection Tube (provided).
Centrifuge at up to 16000 x g, 00:02:00 . Carefully place the MB Spin Column into a new 1.5 ml Elution Tube (provided).
2m
Elute
Elute
1m
1m
Add 50 µL ~100 µL of Solution C6 to the center of the white filter membrane.
Centrifuge at 15000 x g, 00:01:00 . Discard the MB Spin Column. The DNA is now ready for downstream applications.