Hi Samaddar,

If you are looking for total diversity of that particular sampling site then you can go with these primers 27F, 1492R, 926F and 1100R for bacterial 16S and for Archeal 16S amplification up1F up2R, M13F, M13R, and Arf25F, Arf1517R.

Best wishes,

Pooja

You can use universal primers for bacterial 16S rRNA

Bakt_341F: CCTACGGGNGGCWGCAG

Bakt_805R: GACTACHVGGGTATCTAATCC)

and for archaeal 16S rRNA

ARC1-F '5-TCYGKTTGATCCYGSCRGAG-3'

ARC1-R '5-TGGGTCTCGCTCGTTG-3'

Hi Sandipan. It depends on your research question. If you are specifically interested in archaea, you should then use the primers you mentioned separately for archaea and bacteria. If not, I would suggest to use the EMP primers 515F–806R (http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/16s/), which target both archaea and bacteria. It is really enough to target the major archaea groups. More importantly, it is the mostly used primer set for microbiome study. It can make your study comparable to the other published studies.

Thanks all for your comments. Haitao Wang I agree with your suggestion but I guess the 515F/806R are shown to be biased against both the Crenarchaeota/Thaumarchaeota (https://msystems.asm.org/content/1/1/e00009-15) so after going through some articles I found that the V4-V5 primers 515F/926R performs well and can reduce bias and can detect more environmentally important taxa including archaea. I just posted here as I thought it might be helpful.

Best,

Sandipan