What may be the efficient method for high throughput DNA extraction from soil. Kindly provide me some protocol.
Dear Maliha,
It is important what kind of soil you want to extract DNA from. No general protocol is available. I have been having problems mainly with soils containing high ratio of organic matter and acidic ones. You should be able to extract DNA with phenol/chlororm extraction, but every type of soil might require some adaptation of a protocol. Have a look at this paper: Innovative methods for soil DNA purification tested in soils with widely differing characteristics (2008) by Sagova-Mareckova et al. Available in the list of my publications. Perhaps it helps. LC
I use Mobio laboratories inc. kits to do this; they are standardized and include protocols. They also include some suggestions on how to modify their protocol based on your soils, and if you call them directly they are often able to give further advice on the phone. I have used their kits on a variety of soils from all over the world and had no problems. The one drawback is that all their solutions are proprietary, so it's a bit harder to customize the extraction, but since it's standardized it makes it easier to compare against other publications. I suggest perusing their product information to see if any of their kits would work for your application. Link is attached.
I tested out 15 different methods (both kits and normal protocols), and for each method I tested several modifications. Afterwards, DNA concentration was measured with Nanodrop and Qubit, to show us the bias that is introduced with the Nanodrop (and it is immense!). Then we did DGGE for both 16S regions and functional genes. In the end, for our samples, the PowerLyzer PowerSoil kit by MoBio was the best one, as it gave us a good amount of DNA (concentration) and the DNA was the most diverse, based on the DGGE.
But in the end, the kit you choose depends on what you want or what you're working with. I'd advise you to test some things. But I know most people are against that, since it takes time and money. But for me, the two months I spent on this part were totally worth it.
If you want the protocol for the PowerLyzer kit, you can easily find it online. However, I talked with MoBio a lot and we changed the protocol together to obtain even better results.
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