Although, I assume the quality of isolated DNA would be good, as you are getting amplificatino of Fungal ITS.

But you can try:

Add 10-30 ng of pure bacterial DNA in 50 microlite wood isolated DNA and try to amplify the 16S rDNA from it. If not succeed means contamination of PCR inhibitory sub in that case follow next step:

In my view, the bacteria will be more easy to come out than others by PCR analysis. I recommend the most common primer pair  27F and 1492R. But if you need to know what kinds of bacteria in the sample? Maybe you need to do DGGE, clone library or using NGS to analyze the sample.

Paula, there are a few  possible reasons for failed PCR for 16S rRNA - 1) wrong primers; 2) bad DNA (inhibitors or cross-linked DNA); 3) wrong PCR conditions

Use several pairs of conservative primers for fragments of different lenght (from 400 to 1200 bp)

Test your DNA for PCR-ability with random primers (for PCR inhibitors)

Heat DNA just before adding into PCR mix at 94oC for 30 sec. (for cross-linked DNA)

Use at least 2 different PCR kits

Use gradient PCR

Dear Paula,

First you design 16S rDNA primers and keep the PCR at optimized conditions you will get the 16S rRNA amplicons. Confirm by running the gel electrophoresis

Hi Paula

I have had the problem with genomic DNA isolated from bean's root getting good results. I recommend you to read the paper I attach here. I hope it helps you.

The best way is to isolate these bacteria and then do the amplification. You will never succeed when the bacteria are present in a large population of different fungi like in a rotting wood.