I am trying to extract community DNA from deep-sea sediments using MP BIOMEDICALS FastDNA™ SPIN Kit for Soil. I have used starting material from 50 mg (recommended amount for marine sediments) to 500 mg (maximum amount the column can maintain). I have also used the bead-beater homeginzer as recommneded in this protocol.

Quantitating my sample using Nanodrop I find concentrations of 6 ng/uL or less. Using a Qubit fluorometer DNA yields are non existent, and the same is seen when running the samples on an agarose gel.

I am thinking of switching kits as I am running out of samples, and I have repeated this extraction thrice.

Any advice, suggestions, or recommendations would be appreciated.