C Phylogenetic Tree Atlas of Bacterial and Archaeal Cell Structure Home

CPhylogenetic Tree

A species is a unique group of organisms and is the first rung on the ladder of taxonomic classifications that stretches all the way up to the three domains of life: Bacteria, Archaea and Eukarya. How exactly a species is defined, though, is a surprisingly complicated question, especially for single-celled organisms. For most animals, species boundaries are defined by the infertility of offspring from matings across that boundary. This does not always work, though, and many species are defined by geographical, rather than reproductive, separation. For organisms that reproduce asexually, the boundaries are even more nebulous and often simply reflect a fairly arbitrary degree of difference, either morphological or genetic. Also, remember that bacteria and archaea frequently exchange genes, or larger stretches of DNA, through horizontal gene transfer (for a familiar example, think of the transfer of antibiotic resistance). This further blurs the lines between species. In an extreme view, perhaps we should think of environments less as collections of species than as pools of genes temporarily stored in a variety of containers. Still, despite its inexactness, taxonomic classification provides a useful way to trace biological traits so we can begin to answer questions like how the machines you see in this book may have evolved.

This phylogenetic tree shows the relatedness of the species in this book. The length of the branches separating two species from their last common ancestor is proportional to the amount of time that they have been evolving separately. Remember that individual species of Bacteria and Archaea can be as evolutionarily divergent from one another as they are from us. The deeper we go into the past, toward the center of the tree, the less accurate the predictions of relatedness become. The branch point between Bacteria/Archaea and Eukaryotes is particularly hazy, and a topic of lively debate. We’re still discovering new species, and even higher-order clades, and the computational tools we have to detect genetic relationships are improving, so this tree, too, will continue to evolve.

Staphylococcus aureus

Mycoplasma genitalium


  1. 2.1 Membrane

Listeria monocytogenes


  1. 2.2 Cell Wall

Methanobacterium formicicum

Prosthecobacter debontii

Halomicrobium mukohataei

Mycobacterium marinum

Delftia acidovorans

Methylomicrobium alcaliphilum

Clostridium thermocellum

Nitrosopumilus maritimus

Methanospirillum hungatei

Haloarcula argentinensis


  1. 2.9 DNA

Simkania negevensis


  1. 3.1 Coccoid

Brucella abortus


  1. 3.2 Rod: Variety

Hylemonella gracilis

Verrucomicrobium spinosum


  1. 3.6 Prosthecate

Prosthecobacter vanneervenii

Haloquadratum walsbyi


  1. 3.7 Square

Rhodopseudomonas palustris

Methyloprofundus sedimenti

Thiomonas intermedia

Lysobacter antibioticus

Halorubrum litoreum

Haloferax gibbonsii

Halohasta litchfieldiae

Hyphomonas neptunium

Tetrasphaera remsis

Idiomarina loihiensis

Sphingopyxis alaskensis

Sulfolobus acidocaldarius

Pseudomonas flexibilis

Proteus mirabilis

Helicobacter hepaticus

Treponema primitia

Flavobacterium johnsoniae

Mycoplasma pneumoniae

Azospirillum brasilense

Magnetospirillum magneticum


  1. 7.6 Magnetotaxis

Sporomusa acidovorans

Gluconacetobacter hansenii


  1. 9.2 Biofilm Matrix

Legionella pneumophila

Amoebophilus asiaticus

Pseudoalteromonas luteoviolacea

Porphyromonas gingivalis

Bdellovibrio bacteriovorus / Vibrio cholerae

Bdellovibrio bacteriovorus / Escherichia coli

Bdellovibrio bacteriovorus + Escherichia coli minicell

Bacteroidetes JT5

Haloferax gibbonsii Brucella abortus Helicobacter pylori Methanoregula formicica Pseudoalteromonas luteoviolacea Asgard group Magnetospirillum magneticum Campylobacter jejuni Chrysiogenetes Deferribacteres Hydrogenovibrio crunogenus Porphyromonas gingivalis Sulfolobus solfataricus Myxococcus xanthus Lysobacter antibioticus Cupriavidus necator Archaea incertae sedis Pseudomonas flexibilis Methylomicrobium alcaliphilum Halohasta litchfieldiae Delftia acidovorans Caulobacter crescentus Candidatus Krumholzibacteriota Agrobacterium tumefaciens Listeria monocytogenes Mycoplasma genitalium Staphylococcus aureus Nitrospinae/Tectomicrobia group Tetrasphaera remsis Idiomarina loihiensis Borrelia burgdorferi Halothiobacillus neapolitanus Halobacterium salinarum Caldiserica/Cryosericota group unclassified Bacteria Prosthecobacter vanneervenii Salmonella typhimurium Candidatus Hydrothermarchaeota Shewanella oneidensis Dictyoglomi Bacillus subtilis Chloroflexi Thermotogae Haloquadratum walsbyi Verrucomicrobium spinosum Hyphomonas neptunium Sphingopyxis alaskensis Nitrospirae EUKARYOTES Fusobacteria Methyloprofundus sedimenti Azospirillum brasilense DPANN group Bdellovibrio bacteriovorus Proteus mirabilis Halomicrobium mukohataei Acetonema longum Thermodesulfobacteria Clostridium thermocellum Pseudomonas aeruginosa Coleospermum Acidobacteria Elusimicrobia Thiomonas intermedia Mycoplasma pneumoniae Methanospirillum hungatei Aquificae Rhodopseudomonas palustris Synergistetes Methanobacterium formicicum Escherichia coli Halorubrum litoreum Amoebophilus asiaticus Sporomusa acidovorans Coprothermobacterota Thermococcus kodakaraensis Haloarcula argentinensis Bacteroidetes JT5 Hylemonella gracilis Mycobacterium marinum Calditrichaeota Nitrosopumilus maritimus Gluconacetobacter hansenii Treponema primitia Legionella pneumophila unclassified Archaea environmental samples Prosthecobacter debontii Flavobacterium johnsoniae Sulfolobus acidocaldarius Simkania negevensis Helicobacter hepaticus Vibrio cholerae Bacteria incertae sedis BACTERIA ARCHAEA