I could not imagine why it shouldn't work. In my experience (prokaryotes) humic acid, clay, charcoal and high concentrations of Mg and Ca ions were the most disturbing parts in soil samples. I prefered PowerSoil from MoBio. Please let me know, if it works with vertebrate DNA as well.

Hi Megan,

I think it will depend on the kit you are using. I'm not used to microbial DNA extraction from soil, but it is likely that each kit will use different procedures and steps to achieve that isolation.

Hence, in order to assess if one specific kit is suitable to your project, you should consider each step of these kits and evaluate if in the whole protocol is any specific step to be capable of discriminate between prokaryotic and eukaryotic DNA or something similar.

I know there are kits pretending isolate only bacterial DNA even from complex samples where eDNA is present using some differences like methylation. (Anyway they seem not to be too much efficient so their capability to discriminate between these types of DNA is quite poor). If you want to isolate eDNA, probably these are not the best kits for your purposes.

Thanks for your responses. Here is what mo Bio Tech support said--Add a proteinase K digest to the protocol. Add 20 ul of Proteinase K (20 mg/ml) to the bead tube, along with the Bead Solution, Solution C1 and the soil sample at the beginning. You may not need to do much bead beating. It's only necessary to break down the tissue into smaller bits, not to lyse the cells. If the vertebrate tissue is already small then you can go right to the Pro K digest. Otherwise bead beat on a vortex for between 1-10 minutes and then incubate the bead tube at 65 C for 30 minutes. Centrifuge and proceed to the C2 step. 

Dear Megan,

I have no experience of DNA isolation from the soil. But the device (the link below) seems to me is capable to work wonders in this plan.

http://www.borealgenomics.com/aurora/applications/

All the best,

Vladimir