A colleague has a question they would love some feedback on regarding PCR primer selection for 16S rRNA gene amplicon surveys. I am posting it below:
I am working on a project aimed to determine the influence of long-term fertilization on soil microbial communities. I am sampling both the rhizosphere and the bulk soil and hope to use the current best choice of primers for targeting bacterial and archaeal 16S rRNA genes. Initially I planned to use the primer pair 341F/785R, which targets the V3-V4 region of 16S and is reported to have good domain coverage for both bacteria and archaea. However, I now also have the option to use separate, archaea (956F/1401R)- or bacteria (969F/1406R) -specific primers, which target the V6-V8 region of 16S. The benefits of the separate primers are better coverage for archaea, and less eukaryotic sequence contamination, but the V3-V4 primers are the standard tool typically used in similar research. Please let me know which primers you would recommend and why. Thank you!