I am working on microbial diversity and planing to send samples for Next Generation Sequencing (NGS); Which hypervariable region of 16S rRNA gene will appropriate to target most of bacterial taxa present in seawater.
Hi Rajeev,
This depends a bit on what you need from the study. The V4 region has (probably) the closest to universal primer set and it has the advantage that you can completely sequence through in both directions (on a MiSeq) the amplified region of 254 base and perform sequencing error correction (I do this in the Mother pipeline). I haven't used it, but there seems to be a lot of positive talk about the use of DADA4 in the Qiime package for helping go deal with the issue of sequence error. You might want to check out the recommended protocol from the earth microbiome project, http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/16s/
I use this for a variety of sample types. Again I have to stess that there is no perfect primer set/target region, but V4 has worked well for many, including me.
Good luck,
Frank
Also consider this http://msystems.asm.org/content/1/1/e00009-15 which improves detection of SAR11 clade , which will important for seawater .
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