I have just started using qPCR to quantify my16S rRna bacterial community in lake water. I use Molecular biology grade water as NTC (no tempelate control), I was just wondering if there are any recent publications on such water's bacterial community concentration? to kind of compare my results with other people (to get an idea of how much contamination I should consider)? I need to know this to further consider my lake water bacterial concentration compared to MG water as I have really low quantities (mainly considering brGDGT work).
Thanks!
Hello Fatemeh
Interesting question! MG water might not be your primary concern, although I did not have came across a paper.
There might be another concern regarding the Taq polymerase you are using. Most Taq enzymes are recombinant enzymes produced in E. coli. I expect to have some DNA contaminations in all recombinant Taq polymerase enzymes. Therefore I recommend to use a native Taq polymerase, it may also have some DNA but not belonged to an abundant species.
Ali Javadmanesh
hi Ali; thanks for the answer! I actually don’t use Taq as a probe and rather use a dye called SYBR green; but you Point out an interesting factor, I should probably look into SYBR green concentrations as well.
Hello again
I did not mean TaqMan! I ment Taq polymerase which exists in any master mix either SYBR green-based or Probe-based.
Good luck
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