That's a very interesting question. Unfortunately my experience on this issue is not different. Microbes identified through colony characteristics and biochemical tests were observed quite different when subjected DNS sequencing 7sing Blast NCBI databank. It's difficult to make , which test is correct...but eventually we stuck to NCBI results....

Bruna de Carvalho Faria Lima Lopes

Since your background look a bit different from the environmental microbiology, I could list some basic points you might need to think about

Hi,

PCR using universal 16S primers is fairly quick, but not quantitative. For Gram-negative organisms, you can get away with doing PCR on the bacteria themselves without isolating DNA first. Many of them lyse when heated to 95C. For qPCR, you'd have to isolate DNA.

First, you identifiy the colony morphology of the bacteria, later biochemical test were observed, again it confuses, best way using 16S rRNA gene sequencing for identification of soil bacterial.

The 16S ribosomal RNA gene sequencing.

By molecular characterization of the selected strain by sequencing the 16S

rRNA gene.

Thank you all for taking the time to answer this question. I appreciate it.

Article Isolation and Analysis of Microbial Communities in Soil, Rhi...

This article is very complete to answer to your request.

The best way to get a very good representative of bacterial groups is by metagenomics! U can directly target for DNA of the bacterial groups. For further analysis,use pcr-dgge... denaturing gradient gel electrophoresis, which will give you a clear picture of bacterial types based on band products. Final purification and sequence analysis will provide names band on alignment. Good luck