I am looking for suggestions for improving amplification of soil DNA using ITS primers. The soil samples range in concentration from 9-40 ng DNA/ul). Attached are photos of gel confirmation using 5 ul DNA in the PCR (wells 1-24: samples diluted to 10 ng/ul, wells 25-48: samples undiluted). 1:100 dilutions of a subset of samples yielded even weaker bands on the gel.
I am using ITS4-Fun and 5.8S-Fun primers as described in Taylor et al 2016 (https://aem.asm.org/content/aem/early/2016/10/03/AEM.02576-16.full.pdf) to target fungal genes for amplicon sequencing. Thermocycler conditions are 96C for 2 min, 27 cycles of denaturation at 94C for 30sec, 58C for 40sec, 72C for 2 min, with final extension at 72C for 10 min. I am using the following PCR reagents per sample: 21.5 ul Platinum SuperMix High Fidelity (Invitrogen 12532016), 0.5 ul bovine serum albumin (BSA 20 mg/ml; Fisher BP675-1), 1.25 ul of each ITS primer, 5 ul template DNA. I prepare the PCR cocktails in a stripwell plate inside a cold plate.
The only thing I can think of to try is to increase the number of cycles in the thermocycler. Any suggestions would be greatly appreciated.