Archaea Eocyte Tree

According to the Tree of Life Web Project, two alternative views on the relationship of the major lineages (omitting viruses) are currently regarded as viable (right - click to enlarge image).

Bacteria

Taxonomy of the bacteria was historically based on phenotypical physical and chemical characteristics – phenetic taxonomy. According to "Bergey's Manual of Systematic Bacteriology", all bacteria can be classified into four divisions, or phyla according to the constituents of their cell walls.

Each division was further subdivided into sections according to :
1. Reaction of the cell wall to the Gram stain due to thick layer of peptidoglycan (Gram +ve) or thin layer of peptidoglycan (Gram -ve). The cell walls of Archaeobacteria contain no peptidoglycan.
2. Shape (left) – cocci (1), pleomorphic (2), bacillus (3), helical (4)
3. Arrangement of cells
4. Oxygen requirement – aerobic, anaerobic, or facultative anaerobe
5. Motility – flagellated, non-motile
6. Specific nutritional requirements
7. Metabolic properties – autotrophic (chemical or photosynthetic), heterotrophic


The advent of genomics and examination of 16s ribosomal RNA has led to modifications in the classification of the prokaryotes, with the older nomenclatures revised into new classifications of Phyla. (diagram at bottom) Woese and Fox proposed the Three Domain system: Eubacteria, Archaea, and Eukaryotes. When Woese and Fox proposed the 3 Domain system, the term 'Urkaryotes' was proposed for ancestors of eukaryotes prior to their endosymbiotic acquisition of mitochondria and chloroplasts from prokaryotes.

"Misunderstanding the Bacteriological Code"

The Three Domain system is increasingly accepted. Free Full Text Article : Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Woese CR, Fox GE. Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088-90.


Left - click to enlarge image: Horizontal gene transfer - gene swapping - has blurred the evolutionary relationships (image) of prokaryotes, and continues to provide a mechanism for the sharing of antibiotic resistance between bacteria. See: Trees, vines and nets: Microbial evolution changes its face.

Phylogenetic separation into evolutionary relationships (clades), based on comparison of genomes is likely to supplant phenotypical (phenetic) taxonomies of the prokaryotes.(nomenclature)


Right - click to enlarge image: Based on Woese's proposed scheme based on the 16s subunit of ribosomal RNA, which appears to better illustrate evolutionary relationships within the 3 domains.

Endosymbiotic transfer events

Right - click to enlarge image: Proposed endosymbiotic transfer events between the three Domains and the six Kingdoms of Life.

Both the Eubacteria and Archaea are prokaryotes, while animals, fungi, plants, and protists are eukaryotes.

The yellow asterisk * indicates the last universal common ancestor (LUCA), or universal cenancestor, which is hypothesized as being at the ancestral root of all living organisms. Not the earliest or simplest living organism, and not necessarily the sole example of its type, this organism possessed the genetic material that diverged (about 3.5 Ga) into all current living organisms. A number of terms are employed to refer to the universal cenancestor – last universal ancestor (LUA), last common ancestor (LCA), or last universal common ancestor (LUCA).