We have made good experience with the "QIAGEN DNEasy Kit for Plants". This yields good results even for ectomycorrhizal samples as small as you described them.. It works best if you do the lysis step directly within an Eppendorf cup. We have added some large ceramic beads to the buffer and did the lysis for some minutes on a vortex mixer at maximum speed. Freeze-thawing is also an option. The final elution from the column was done in small volumes of elution buffer (30-50 µl). This method yielded enough DNA for PCR-based species identification.

The small sample size is actually beneficial for PCR because you do not have to dilute the DNA solution. Inhibitory substances from plant or fungal tissue will be coextracted in very small amounts, but there will still be enough DNA for PCR. Take a hot-start polymerase, this is important.

With the method outlined above and using rDNA-targeted primers, I was able to identify fungal species in single ectomycorrhizal roots.

We are also using QIAGEN Plant DNEasy kit for extracting DNA from AM fungi colonized roots using 10 to 50 mg of fresh roots. However, we carefully grind them using liquid nitrogen, and recover the material with the lysis solution.

Maximize the mycorrhizal quantity using monosporal culture or  extract from the small amount using QIAGEN DNEasy Kit for Plants. 

Hi....Based on my experience, I should recommend you for wet sieving method. Once you get mycorrhizae spores in good amount you may get a good amount of DNA for your further experiments.

Thank you all for your help; we are planning to try the DNEasy kit.

We often use MoBio microbe DNA extraction kits and add to the garnet beads some larger zirconia beads from biospec (http://www.biospec.com/category/beads_guide_lines/).  We shake the dry root tip with the garnet and zirconia beads for a few minutes before adding any liquid.  Then we shake again with the buffer, etc. as instructed in the kit.  This always works well for us.

wet sieving and decanting technique of Mosse should give you enough spores.

You can also extract your Micorrhyza DNA using the MagMax Express Magnetic Particle Processor (Applied Biosystems). We used this to extract DNA from fungi using a kit for plant, and it was successful. The magnetic particles ensures the correct DNA extraction. The yield and purity quality are excellent for PCR or qPCR.

Regards!

Dra. Didiana Gálvez López

Investigador del Campo Experimental Río Bravo

INIFAP-CIRNE-C. E. Río Bravo, México

Tel. 899-934-1046

Tel. IP 83221

It is an interesting question, I have never extracted DNA from small samples, but I remember an article from Mathias Rillig team. They extracted DNA from small samples of roots and I guess that those fragments weighed like your samples. Please, read this article: Vályi, K., et al. (2014). "Land‐use intensity and host plant identity interactively shape communities of arbuscular mycorrhizal fungi in roots of grassland plants." New Phytologist.doi: 10.1111/nph.13236. I hope it helps you!! They use a common kit that I use regularly without any problem. I think that your extraction will be successful without complicated methods, but you must consider to improve your pcr in order to obtain the amplification from very low quantity of DNA. I extracted DNA from roots but I obtained a very low yield (less than 3 ng per ul), I improved the pcr and I didn't have problems!!! I wish you all the best!

I´m agree with the others' comments. The kit QIAGEN DNEasy Kit works very well, but if you later have problems with the PCR amplifications, you can applied a Nested PCR.

the kit qiagen dneasy kit is a good recommendation for small mycorrhizal samples.

I am working on a project that requires extracting AMF DNA from roots, what is everyone's opinion of using a Zymobiomics DNA kit as opposed to the QIAGEN kit I'm seeing in a lot of these other answers?

https://www.zymoresearch.com/collections/zymobiomics-dna-kits