There are two kinds of microorganisms that are divided into prokaryotes and those include bacteria and archaea. But not all bacteria and archaea belong to prokaryotes. Complicated subject, isn’t it? Here is more information on the differences between these two microorganisms.

Both bacteria and archaea have different Ribosomal RNAs (rRNA). Archea have three RNA polymerases like eukaryotes, but bacteria have only one. Archaea have cell walls that lack peptidoglycan and have membranes that enclose lipids with hydrocarbons rather than fatty acids (not a bilayer). These lipids in the membranes of archaea are unique and contain ether linkages between the glycerol backbones rather than ester linkages. Archaea resembles eukaryotes more than bacteria. Their ribosomes work more like eukaryotic ribosomes than bacterial ribosomes.

These two microorganisms also differ in genetic and biochemical ways. Only within the last couple of decades, archaea were recognized as a distinct domain of life. They are extremophiles, meaning they thrive in physically or geochemically extreme conditions. They have similar ecological roles as bacteria. Both of these organisms react to various antibiotics in a different way.

Summary:

Archaea: cell membrane contains ether linkages; cell wall lacks peptidoglycan; genes and enzymes behave more like Eukaryotes; have three RNA polymerases like eukaryotes; and extremophiles

Bacteria: cell membrane contains ester bonds; cell wall made of peptidoglycan; have only one RNA polymerase; react to antibiotics in a different way than archea do.