Hi Martin,

We also try to extract DNA from clays containing a lot of humic and fulvic acids. I think we tried almost every commercial kit available on the market, attempted evry protocol variations, without much succes. The producers are not keen to explain in detail the content of the kits. I consider the kits as expensive black boxes. Clay in combination of humic acids is a double challenge as clay minerals interact like hell with charged macromolecules and humic acids have a identical behaviour as DNA/RNA so they pose a competion problem. I designed a complete new protocol based on the benificial properties of Potasium ethyl xanthogenate and SDS. I am trying to get the protocol publishe in the very near future. If you wish I keep you posted as soon as the paper is accepted and published.

Kind regards.

try to use beat beating protocol as described by Yu and morisson 2004. or can try Mo Bio power lyzer soil kit.

Try to use fecal extraction kit - MoBio - can help - is working great as I know

could also try to use skim milk (Takada-Hosino and Matsumoto, 2004) which works as an adsorption competitor. It seemed skim milk works well on Andisols which are orgnaic-rich soils.

Well My team is working on Isolation of DNA from Crude oil/ hydrocarbon contaminated soil, so is always full of organics, humic acids and all sort of oil debris. We are using UltraClean Soil DNA Isolation Kits from Mo Bio and it works like wonders for us! You may also give it a try. Hopefully it'll work for you too.

Hi there,

I strongly recommend the article that I attached, surely should be interesing for you. I hope this helps.

I use the Qiagen Stool sample kit (and slightly adapted the protocol for optimisation) it contains InhibitEx tablets that mop up any PCR inhibiting substances within the soil such as humic acids which is good.

Nath

Thanks a lot to all of you!

Charles, you didn't attach any article;-)

I'm sorry for that, Martin. I hope this time works well. I attach again.

Thanks, Carles - it did work!

Hi,

I use the PowerSoil DNA ISolation Kit (MO-Bio) and works very well with andisoil and ultisoil with very high organic matter content (13-24%). Is important to storage the samples freeze (-80°C). Good luck

Hi Martin,

We also try to extract DNA from clays containing a lot of humic and fulvic acids. I think we tried almost every commercial kit available on the market, attempted evry protocol variations, without much succes. The producers are not keen to explain in detail the content of the kits. I consider the kits as expensive black boxes. Clay in combination of humic acids is a double challenge as clay minerals interact like hell with charged macromolecules and humic acids have a identical behaviour as DNA/RNA so they pose a competion problem. I designed a complete new protocol based on the benificial properties of Potasium ethyl xanthogenate and SDS. I am trying to get the protocol publishe in the very near future. If you wish I keep you posted as soon as the paper is accepted and published.

Kind regards.

Thanks, Hugo! To some extent, I agree with you: kits are easy to use when they work, but expensive. However, if they don't work, there is hardly any way of optimizing (since you don't get any information...)....

Yes, please keep me updated re. your paper!

Cheers!

We use the Macherey-Nagel Nucleospin Soil Kit with good results on high organic matter soils and composts. Expensive but works fine.

If the downstream application involves PCR, the attached paper may be useful.

It does, Philipp - Thanks!

Is the polymerase commercially available?

Doreen - Hugo Moors' posting makes a lot of sense, Jock.

I'd be happy to provide you with the expression plasmid for the polymerase subject to a standard MTA.

Please contact our contracts manager Tanya Izzard ([email protected]), who will sort out the details.

Hogo Moors - did you get the method published? :-)

It would be interesting to read.

Dear Tobias,

Until now the method as such is not yet published. It is (partially) described into the Supporting information of the paper you can find on the following link:

http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12171/abstract

I presented the method as poster presenation at IGD-TP conference in Manchester, I will present it at the "CLAYS IN NATURAL AND ENGINEERED BARRIERS FOR RADIOACTIVE WASTE CONFINEMENT" conference in Brussels, 23-26 March 2015. And I will also describe and mention the method during the FEMS-2015 conference in Maastrich, 7-11June 2015, if this abstract of mine is selected as oral presentation.

In case I decide to publish my method earlier, I will let know on this forum.

Kind regards, Hugo Moors

Thanks, Hugo!

I would love to be updated once the method will be published!

Hi, we work with ashes volcanic soils with high organic matter content and use a commercial kit from MO-BIO with very well results.

Try the new PureLink Microbiome DNA Purification Kit – it has robust protocols for stool and soil http://www.thermofisher.com/order/catalog/product/A29790?ICID=search-product

@Hugo, can you explain the role of the lysis buffer and why the overnight 70C incubation? Thanks!

Dear André,

The lysis buffer contains four components which principally makes divalent anions unusable for nucleases, blocks frayed edges of minerals, dissolves parts of the membranes of microbes (=lyse the cells), destroys unwanted proteins and maintains the pH of the lysis solution. The overnight incubation at 70°C is needed to obtain sufficient lysis action so that you extract detectable nucleic acids.