With PowerMax you can extract DNA from 5 to 10g of soil while PowerSoil it is only from 0.25g. So even if you pool 3 DNA extractions from PowerSoil, you would have DNA from 0.75g, so quite far from the 5-10g of soil used with PowerMax. If your samples are extremely patchy in their distribution of fungi, bigger the sample better it is as you increase the probability to include hotspot. Unless there is a pattern in the “patchiness” of your samples that you could specifically target for DNA extraction (e.g. specific size of aggregates), PowerMax would be better. Overall, bigger amount of soil might (is) better for DNA extraction as it include more of the heterogeneity of the soil (i.e. structure; e.g. different size of aggregates).

“In general” soil is sieved at 2 mm to homogenised and reduce the variability or patchiness in the distribution of microorganisms etc. It may not be enough or relevant when you use only 0.25g of soil for DNA extraction, especially for a really sandy soil.

From my experience using and comparing PowerSoil and PowerMax on bacteria, archaea, fungi and other genes on 2mm sieved soil, PowerMax reduce the variability in abundance data (Q-PCR) and sometimes get higher abundance than PowerSoil (I can’t yet answer for diversity).

The limiting steps with PowerMax: it is much more expensive (3 times more expensive) and takes a bit more time to do than PowerSoil. However, you get much more DNA and could perform more analysis. I would advise PowerWax or any protocol that use more soil or that you could upscale if you think the distribution of fungi is highly variable in your samples.

Hey Balazs,

for sure the MoBio PowerSoil kit worked pretty well. i've not tested the PowerMax kit.

I would recommend to isolate DNA form three small soil samples and pool their amplicons for improving sequencing yield.

good luck.

I performed RFLP analysis on my fungal small subunit RNA gene region PCR results and found multiple banding patterns and had them sequenced and I found that RFLP was not very reliable in this instance. It may be prone to bias in my case due to the fragment length and/or the database I was using for the identification not containing enough complete genomes etc. I just thought I would share my experience with RFLP. Both DNA isolation kits sound good but I am unsure as to whether the alternate sampling techniques would make a difference and ultimately it is determined by quality of product. If you see one technique being better than the other then use the better one.

You could also try salt extraction, which allows any starting amount. If you wish to stick with the kits, there's no way to know until you try both. I'd do one big extraction. Moreover, what do exactly mean with pyrosequecing: possibly Roche 454 platform?

With PowerMax you can extract DNA from 5 to 10g of soil while PowerSoil it is only from 0.25g. So even if you pool 3 DNA extractions from PowerSoil, you would have DNA from 0.75g, so quite far from the 5-10g of soil used with PowerMax. If your samples are extremely patchy in their distribution of fungi, bigger the sample better it is as you increase the probability to include hotspot. Unless there is a pattern in the “patchiness” of your samples that you could specifically target for DNA extraction (e.g. specific size of aggregates), PowerMax would be better. Overall, bigger amount of soil might (is) better for DNA extraction as it include more of the heterogeneity of the soil (i.e. structure; e.g. different size of aggregates).

“In general” soil is sieved at 2 mm to homogenised and reduce the variability or patchiness in the distribution of microorganisms etc. It may not be enough or relevant when you use only 0.25g of soil for DNA extraction, especially for a really sandy soil.

From my experience using and comparing PowerSoil and PowerMax on bacteria, archaea, fungi and other genes on 2mm sieved soil, PowerMax reduce the variability in abundance data (Q-PCR) and sometimes get higher abundance than PowerSoil (I can’t yet answer for diversity).

The limiting steps with PowerMax: it is much more expensive (3 times more expensive) and takes a bit more time to do than PowerSoil. However, you get much more DNA and could perform more analysis. I would advise PowerWax or any protocol that use more soil or that you could upscale if you think the distribution of fungi is highly variable in your samples.

Thanks for your answers.  I've asked meanwhile also MoBio, and this is their answer. I find it also useful:

"In terms of kit chemistry both kits are identical and the only difference will be the bead beating. They both should have similar lysis efficiency and should give you similar profiles assuming that both samples have identical fungal communities in them.

I would recommend mixing the original sample somehow (perhaps a stir rod). Once it is homogenized, I would sample the soil in 1-4 tubes of PowerSoil to assess the fungal community. If the total DNA is less than 20 ug for the 1-4 tubes (combined), you can pool the lysate onto one spin filter to get a final elution of 50 - 100 ul. Although this method can be a bit tedious without a vacuum manifold since you will have to centrifuge the spin filter 3 times per tube. If the DNA for the samples exceeds 20 ug or you do not mind having a large elution volume, you can combine the final elutions resulting in a final volume between 200 - 400 ul. This should give you a good representation of the fungal community.

On the other hand, you could certainly process more soil using the PowerMax kit. The only down side to using the PowerMax is the amount of samples you are going to process. The PowerMax kit is great, but when you have to process many samples, the protocol can be a bit tedious. Since the PowerMax kit can process a much larger sample amount, there is always a chance that a rare fungus gets sampled in the PowerMax kit and not in the PowerSoil kit. I hope that helps! If you have any other questions or concerns, please feel free contacting MO BIO technical support."