What is a good Microbiology atlas for Bacteriology as online version?
Not sure what you are exactly looking for? If you change the question or comment I can update my answer...

NCBI's taxonomy site has a listing of bacteria.  Encyclopedia of life is also great. 

Then there's UCSC's microbial genome browser. 

Biocyc is  great reference for bacterial genes.  to get into E coli, which is the model bacterium there's Port Eco featuring 130 E coli genomes.  

Am Soc Micro has an excellent E coli/ Salmonella site based on their classic reference - you have to pay for access though.