the three domains of life
Ask how many fundamentally different kinds of living thing there are, and biology's modern answer is three. At the deepest level, all cellular life falls into three domains: Bacteria, Archaea, and Eukarya. This is the broadest grouping there is, sitting above kingdoms, and it is built not on appearance but on molecular ancestry read from genes.
The surprise is where the line falls. To the naked eye Bacteria and Archaea look alike: both are small single cells with no nucleus, which is why they were long lumped together as 'prokaryotes'. But Carl Woese, comparing the sequences of ribosomal RNA in the 1970s, found that Archaea are molecularly as different from Bacteria as either is from us. The third domain, Eukarya, contains everything with nucleated cells: protists, fungi, plants, and animals, ourselves included. Reading the family tree from gene sequences shows that eukaryotes are in some respects closer cousins of the Archaea than of the Bacteria.
This three-domain view, founded on molecular evidence, is a landmark of molecular biology because it showed that sequence data could rewrite the deepest branches of the tree of life, branches that no microscope could resolve. It also reframes the prokaryote-eukaryote divide: 'prokaryote' usefully describes a cell without a nucleus, but it is not one natural group, since it spans two of the three domains. The three domains are the modern map of who is related to whom at the root of life.
The microbes thriving in boiling hot springs and acidic mine drainage are mostly Archaea, not Bacteria. They look bacterial under a microscope, but their ribosomal RNA sequences place them on a separate deep branch of life.
Molecules, not microscopes, revealed Archaea as a third domain of life.
The three-domain tree is well supported but not the last word: there is active debate about whether eukaryotes arose from within the Archaea, which would make 'three domains' really two with eukaryotes nested inside one branch.