Soil sample DNA extraction (SuperSoil)

Yin-Tse Huang, Hsin-Mao Wu, Jie Hao Ou, Yu-Hsuan Fan

Published: 2023-06-07 DOI: 10.17504/protocols.io.rm7vzbzj2vx1/v1

Abstract

A method for fungal and bacterial DNA extraction.

Steps

Sample preparation & Cell lysis

1.

Add 0.2mL ⌀=1.0 mm zirconia beads, 0.2mL ⌀=0.5 mm zirconia beads, 800µL SD1 solution, 0.5g Sample into a 1.5 ml microcentrifuge tube. Vortex briefly to mix.

Note
If the SD1 solution is precipitated, leave it at room temperature for 30 minutes, it will become transparent again.

Note
If the soil is too loose and fills up the whole microcentrifuge tube, you can separate them into 2 microcentrifuge tubes for the downstream workflow. And centrifuge 2 microcentrifuge tubes at the final step to merge them.

Note
If your sample is hard to lyse, you can try the following methods:After adding solution SD1, incubate at 65 ℃ for 10 minutesAdd 3 additional stainless steel beads and use 2.0 ml screw vials for your samples

2.

Homogenize samples using Vortex-Genie® 2 with SI-H524 Horizontal microtube holder. Vortex at maximum speed for 0h 4m 0s

Note
Be careful when removing the microcentrifuge tube from the holder. Press the lid and slowly loosen the tube with another hand.

3.

Centrifuge the 1.5 ml microcentrifuge tube at14000rpm,25°C

Inhibitor precipitation

4.

Add 200µL SD2 solution to a clean 1.5 ml microcentrifuge tube.

5.

Transfer 500µL supernatant to the tube in the previous step. Vortex 0h 0m 5s for mixing.

Note
White precipitate forms.If too much AlCl3 (CD2) is added, it will cause all the DNA to be precipitated along with the inhibitory substances.

Note
If there is any suspended substance, you can use P200 and turn it to 150 μl and suck the supernatant up 3 times.

6.

Centrifuge at14000rpm,25°C

DNA binding

7.

Add 600µL SD3 solution to a clean 1.5 ml microcentrifuge tube. Avoiding the pellet, transfer up to 700µL of supernatant from the previous step to that tube. Vortex 0h 0m 5s for mixing.

Note
If Solution CD3 has precipitated, heat at 60°C until the precipitate dissolves.

8.

Take 650µL to spin column (with collection tube) and centrifuge at14000rpm,25°C

9.

Discard the flow-through and repeat step 8 to ensure all the lysates have passed through the spin column.

10.

Carefully place the spin column into a clean 2 ml collection tube. Avoid splashing any flow-through onto the spin column.

Wash

11.

Add 500µL of Solution SEA to the spin column. Centrifuge at 14000rpm,25°C

Note
Solution SEA may leaks or suck back causing contamination.

12.

Discard the flow-through and return the spin column to the same 2 ml collection tube.

13.

Add 500µL 80% ethanol to the spin column. Centrifuge at 14000rpm,25°C

Note
Ethanol may leaks or suck back causing contamination.

14.

Discard the flow-through and place the spin column into a new 2 ml collection tube.

15.

Centrifuge at 14000rpm,25°C Carefully place the spin column into the new 1.5 ml microcentrifuge tube

Note
Ethanol can interfere with downstream DNA applications, such as PCR, restriction digests, and gel electrophoresis. Make sure to centrifuge for 3 minutes.

Elute

16.

Add 50µL RNase-free water (DEPC-treated water) to the center of the white filter membrane.

Note
Alternative for RNase-free water: TE(Tris-EDTA) buffer

17.

Centrifuge at 14000rpm,25°C Discard the spin column. The DNA will be in the microcentrifuge tube.

Quality and quantity assessment

18.

Use BioTek Take3 & Take3 Trio Microvolume Plates to measure the quality and quantity of your specimens. And then upload them to Google Drive (1 MolecularWork (Direct edit) 分生實驗號碼 (直接編輯) w_ Primer list)

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