In this blog, I use the term ‘bacteria’ (with a lower case), as a generic term equivalent to prokaryotes (that is, Bacteria and Archaea). In this I follow the example of the Brock Biology of Microorganisms, a reference textbook in microbiology (and a wonderful read, by the way).
If you are not familiar with these denominations, here is a brief recap:
Since the work of Carl Woese and his landmark paper from 1977, we know that the tree of life has three main branches: the Bacteria, the Archaea, and the Eukarya. Eukarya, or eukaryotes, encompasses every organism with nucleated cells, from protists to fungi, plants and animals. Bacteria and Archaea (formerly known as eubacteria and archaeabacteria) are often grouped together as the prokaryotes, or cells devoid of a nucleus. It is true that most Bacteria and Archaea look at first sight very much alike, but this morphological similarity does not reflect the fundamental separation between the two kingdoms. For this reason, some microbiologists such as Norman Pace, from the University of Colorado, advocate to simply drop the term ‘prokaryotes’.