I typically use kits for DNA extraction, with some additions, and have
done well with difficult sediment samples. The two kits I tend to use
are the Bio101 FastDNA SPIN kit for soil and the MoBio PowerSoil kit. In
addition to these kits, I have on occasion added a heating step at 70C
for 1 hour at the beginning while the cells are in the detergent buffer.
Plant kits can also be good for removing other interfering substances.
I have also had the problem where I got DNA, but not so much that it was
easy to tell, however, the subsequent PCR was blocked by an interferent
of some kind, making me think my extraction was bad. If you think this
might be your problem, the Promega Wizard DNA clean-up kit is great for
making bad DNA usable.
University of Massachusetts