We are trying to extract DNA from soil samples, these samples are collected from the Namib Desert, the site is about 20 Kilometers from the Atlantic Ocean. The soil has a high salt concentration and there is a limited amount of organic matter. We've use the kits, which gave use a low DNA yield. We've tried a standardized method for metagenomic DNA extraction published in "An improved method suitable for isolation of high-quality metagenomic DNA from diverse soils" by Kumar Verma1 • Himanshi Singh1 • Prakash C. Sharma - 2017. But we've used PEG 6000 not 8000, as we only have PEG 6000 at the moment.
I'd appreciate anyone sharing a protocol that can work for these tricky samples. We've tried even the water kit. Kindly assist.
Thanks.
Dear Elise Ndatulumukwa Nghalipo . Try to use the DNeasy Powerlyzer PowerSoil DNA Isolation kit (Qiagen),former Powerlyzer PowerSoil (MoBio).
https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/dna-purification/microbial-dna/dneasy-powerlyzer-powersoil-kit/#orderinginformation
We Have used this kit very often, with high yield and quality, for several contrasting soils in Brazil. One tip for high salt concetratrions is to double the steps 2 and 3 from the protocol.
I hope it helps.
Best regards,
Dear Dennis Goss-Souza , thank you so much for your recommendation. I highly appreciate it. We've tried with that same kit before and have done quite a number of modifications to it, but it didn't help..we still got low DNA yield.
We'll try and modify the manual protocol and see what we'll get.
Many thanks,
E
Finding the best method for soil DNA extraction can be quite tricky. My first suggestion is to add a known amount of microbial cells (best would be a soil isolate) or pure standard DNA to your soil samples and narrow down the problem: do you have low biomass or is the soil matrix preventing the recovery of DNA from your samples?
Here is also a literature recommendation: DOI: 10.1128/AEM.00019-16
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