I'm trying to identify and isolate Pseudomonas and Bradyrhizobium strains from rhizosphere and endophytic compartments of a tree. I plated the strains on selective media (King's B. for Pseudomonas and YEM for Bradyrhizobium) and purified the colonies grown by picking them and let them grow on separate plates. There is a lot of variety in morphologies.
When I had grown colonies of bacteria and was able to pick up single colonies I did a 16s rDNA pcr reaction on the colonies. After sequencing the 16s rDNA sequence I did a quick BLAST search to annotate the sequences and thus the bacteria to a species. But from all colonies till now (already 25 reactions sequenced) I only found that they allign best to Bacillus. I think this is strange because there should be a lot of variety according to their morphology.
Does anyone has a solution for this? Is it, for example possible to exclude the Bacillus group from the BLAST search? Or does this mean my colonies are still contaminated?
This is probably not enough information to answer my question but maybe you have experience with doing this and have some ideas.