Concering bacterial annotation see this post, it has many useful links:

A Quick Way To Annotate Entire Bacterial Genomes To Go?

See also these three papers about bacterial ontology and metagenomivs:

Methodology and Ontology in Microbiome Research, 2014

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4250566/

Applying the Gene Ontology in microbial annotation

http://sci-hub.cc/10.1016/j.tim.2009.04.003#

Metagenomics and biological ontology

http://sci-hub.cc/10.1016/j.shpsc.2007.09.001#

There are many tools out there for annotating bacterial/archaeal genomes. My suggestion is to try multiple tools and do a comparison, especially if your analysis is hypothesis-driven.

For quick annotation (in the matter of minutes) - my suggestion would be prokka https://github.com/tseemann/prokka

For fairly quick and ease in visualization in terms of metabolic pathways (in the matter of hours) - I feel like blastkoala http://www.kegg.jp/blastkoala/ is pretty good.

For detailed annotation but may not be as rigorous - RAST is quite neat. http://rast.nmpdr.org/

For rigorous and publication quality - IMG/ER would be my recommendation but the caveat is the time. IMG/ER only does one annotation a month and if you missed the queue, you may have to wait up to a month. https://img.jgi.doe.gov/cgi-bin/mer/main.cgi