You may isolate Achromobacter , Clostridium, Bacillus, Pseudomonas and many more bacteria, so, it is very important to get pure culture. Direct 16S rRNA sequencing will show you genus (maybe species as well) and prove that you can no other bacteria in your strains. Aflter your can chose suitable MLST scheme for species identification - from 4 to 8 different gene fragments with primers designed for particuar gene set.

At the same time you can test biochemical properties by BIOLOG or by conventional way.

You may isolate Achromobacter , Clostridium, Bacillus, Pseudomonas and many more bacteria, so, it is very important to get pure culture. Direct 16S rRNA sequencing will show you genus (maybe species as well) and prove that you can no other bacteria in your strains. Aflter your can chose suitable MLST scheme for species identification - from 4 to 8 different gene fragments with primers designed for particuar gene set.

At the same time you can test biochemical properties by BIOLOG or by conventional way.

It depends on the bacterial characteristics (Gram positive, gram negative, growth on different culture media ...). Though the most available methods ae those based on biochemical/metabolic tests, the easiest method for identifying microorganisms of different origins and characteristics, with a high reliability, is MALDI-TOF mass spectrometry.

The simplest (and cheapest) way might be to 1) get a pure culture in a solid non-selective medium; 2) perform the following tests: Gram, oxidase, and fermentative/oxidative metabolism; and use a multi-test galery of API system. Afterwards, you can progress in the strain identification by using 16S ARNr sequencing or whatever, depending of accuracy level requested.

why not use biolog or PLFA determination,16S rRNA sequencing also can be OK,they are all easy to take ,and PLFA is a new way

I our lab was used identification of endophytes by total DNA isolation and further cloning and sequencing of ITS fragments (we try to avoid culturing).

Thanks to all for their Kind sugestions