Primer Comparison for Cave Bacteria and Archaea

Amplified 16S rRNA gene libraries have long been utilized for environmental profiling of prokaryotic communities. To improve comparability of such studies, a loose consensus has developed around the use of Earth Microbiome Project (EMP) primers targeting the V4 region of the gene (515F/806R). To verify how well these primers work with lava cave bacterial and archaeal communities that possess a high proportion of unclassified lineages, we investigated the coverage of EMP vs. alternative archaea-specific (519F/1017R) and bacteria-specific (27F/515R) primers. We validated V4 EMP primers for Bacteria, but showed that Archaea diversity is better captured with the archaea-specific primer set.