Soil Nucleic Acid Isolation

DNA and RNA isolation from soil samples is limited in many ways becuase of co-extraction of organic contaminants other than nucleic acids.  Humic acid and humic-like substances are the main group of contaminants that limit the downstream applications of nucleic acids.  Nucleic and humic acids have similar characteristics, and are therefor difficult to separate.  The other issue is isolation efficiency and because of the heterogenous nature of soil samples and the various organic contaminants, a portion of nucleic acid is invariably lost in the process of isolation.  DNA and RNA extraction from soils is often more difficult than from many other ecological samples.  It has been estimated that one gram of soil contains approximately 109 prokaryotes and more than 2000 genome types, with an average genome type representing less than 0.5% of the soil community.  There is sufficient DNA in 1 g of soil to extend 993 miles.    


Our Kits

Mini Prep

To process up to 500 mg of soil samples

Midi Prep

To process between 2 and 4 gm of soil samples

Three Options for Purification

Direct Precipitation without the aid of solid phase extraction.  

A simple and easy protocol using silica membranes.

Our magnetic beads-based protocol is readily amenable for automation.


Homogenization

 The homogenization efficiency is significantly improved by using high density beads.  Our specialized beads have a density of 6.2 g/cc while steel has a density of 7.9 g/cc, zirconia has a density of 5.5 g/cc and garnet has a density of 2.24 g/cc.  We have five different sizes of beads in defined proportions to deal with differences in cell sizes.  Compatible with a variety of homogenization tools.  


Lysis Buffer

 Our lysis buffer does it all!  It preserves your samples after collection for up to 7 days at room temperature, resuspends and lyse the cells in combination with mechanical bead beating, denatures proteins and neutralizes humic acids and related compounds, preventing them from forming covalent bonds with nucleic acids.   


Wash Buffer I

Wash Buffer i is a unique formulation that precipitates humic acid and other related compounds on the silica matrices, thus preventing it from co-eluting with nucleic acids.  This avoids the need for extra precipitation steps that could potentially result in loss of nucleic acids. 


Mini Prep - Lyse’N‘Trap Soil DNA Isolation

To process up to 500 mg of soil samples

Spin Column based protocol

Bead tubes with 3 different bead types in 5 different sizes

Use Lysis Buffer to store and transport samples; up to 7 days

Directly bind nucleic acids to silica membranes

No need to precipitate proteins and humic acids


Catalog Number        Quantity          Price       
SLDMN-02-10                10                   $ 45.00

SLDMN-02-50               50                   $ 150.00

SLDMN-02-100             100                 $ 250.00

_______________________________________ 

Brief Protocol

1. Add up to 500 mg of soil samples in to Bead Tubes and add 1200 µl of Lysis Buffer. Vortex for about 10 seconds to resuspend the soil mass. 

2. Homogenize soil samples either by vortexing for 5 minutes or using a bead beater as per manufacturers’ instructions.

3. Centrifuge Bead Tubes at 7,000 x g for 1 minute and transfer supernatant to a 1.7 ml collection tube.

4. Centrifuge at 10,000 x g for 5 minutes and transfer supernatant to a 2 ml collection tube.

5. Add 1000 µl of Bind Buffer and mix by inverting at least 10 times.

6. Load the lysate directly on to spin columns and process the entire volume by centrifuging at 10,000 x g for 1 minute.

7. Wash the columns with 500µl of Wash Buffer I and discard flow through. Repeat this step with Wash Buffer II.

8. Centrifuge the empty spin baskets at 10,000 x g for 1 minute to remove salts.

9. Transfer the empty spin baskets to a new 1.7 ml collection tube and add 50 to 100 µl of Elution Buffer and centrifuge at 10,000 x g for 1 minute.  Discard the spin basket and store DNA as per your requirements.

Mini Prep - Lyse’N‘Pellet Soil DNA Isolation

To process up to 500 mg of soil samples

Direct precipitate nucleic acids from lysate

Bead tubes with 3 different bead types in 5 different sizes

Use Lysis Buffer to store and transport samples; up to 7 days

No solid phase purification

No need to precipitate proteins and humic acids


Catalog Number        Quantity          Price       
SLDMN-01-10                10                   $ 45.00

SLDMN-02-50               50                  $ 100.00

SLDMN-01-100             100                 $ 190.00

_______________________________________ 

Brief Protocol

1. Add up to 500 mg of soil samples in to Bead Tubes and add 1.2 ml of Lysis Buffer. Vortex for about

10 seconds to resuspend the soil mass.
2. Homogenize soil samples either by vortexing for 5 minutes or using a bead beater as per manufacturers’ instructions.
3. Centrifuge Bead Tubes at 7,000 x g for 1 minute and transfer supernatant to a 1.5 ml collection tube.
4. Centrifuge at 10,000 x g for 5 minutes and transfer supernatant to a 2 ml collection tube.
5. Add 1 ml of Bind Buffer and invert at least 10 times.
6. Centrifuge at 10,000 x g for 5 minutes and discard supernatant, making sure to retain the pellet.
7. Wash the pellet in 1 ml of Wash Buffer II. Add 1 ml of Wash Buffer II and invert the tubes gently without disturbing the pellet. Decant the wash buffer gently.
8. Add 500 µl of Wash Buffer I and resuspend the pellet by pipetting up and down. Centrifuge at 
10,000 xg for 3 minutes and discard supernatant.

9. Wash pellets with Wash Buffer II. Add 500 µl of Wash Buffer II and invert the tubes gently, at least 5 times. Centrifuge at 10,000 x g for 5 minute. Discard supernatant and centrifuge one more time at 10,000 x g for 1 minute to collect the residual Wash Buffer II. Remove the collected Wash Buffer II carefully and air dry pellets for 10 to 15 minutes at room temperature.

10. Resuspend the pellets in 200 µl of Elution Buffer and centrifuge one more time at 10,000 x g for 1 minute. Depending on your sample type, you may see a pellet, without disturbing the pellet remove the supernatant to a 1.5 ml collection tube.

Mini Prep - Lyse’N‘Trap Soil DNA Isolation

To process up to 500 mg of soil samples

Spin Column based protocol

Bead tubes with 3 different bead types in 5 different sizes

Use Lysis Buffer to store and transport samples; up to 7 days

Directly bind nucleic acids to silica membranes

No need to precipitate proteins and humic acids


Catalog Number        Quantity          Price       
SLDMN-02-10                10                   $ 45.00

SLDMN-02-50               50                   $ 150.00

SLDMN-02-100             100                 $ 250.00

_______________________________________ 

Brief Protocol

1. Add up to 500 mg of soil samples in to Bead Tubes and add 1200 µl of Lysis Buffer. Vortex for about 10 seconds to resuspend the soil mass. 

2. Homogenize soil samples either by vortexing for 5 minutes or using a bead beater as per manufacturers’ instructions.

3. Centrifuge Bead Tubes at 7,000 x g for 1 minute and transfer supernatant to a 1.7 ml collection tube.

4. Centrifuge at 10,000 x g for 5 minutes and transfer supernatant to a 2 ml collection tube.

5. Add 1000 µl of Bind Buffer and mix by inverting at least 10 times.

6. Load the lysate directly on to spin columns and process the entire volume by centrifuging at

10,000 x g for 1 minute.

7. Wash the columns with 500µl of Wash Buffer I and discard flow through. Repeat this step with Wash Buffer II.

8. Centrifuge the empty spin baskets at 10,000 x g for 1 minute to remove salts.

9. Transfer the empty spin baskets to a new 1.7 ml collection tube and add 50 to 100 µl of Elution Buffer and centrifuge at 10,000 x g for 1 minute.

Discard the spin basket and store DNA as per your requirements.