|Escherichia coli cells magnified 25,000 times|
Gibbons and Murray 1978
Traditionally gram staining results were most commonly used as a classification tool, consequently until the advent of molecular phylogeny, the Kingdom Monera (as the domains Bacteria and Archaea were known then) was divided into four phyla,
- Gracilicutes (gram-negative, it is split in many groups, but some authors still use it in a narrower sense)
- Firmacutes [sic] (gram-positive, subsequently corrected to Firmicutes, today it excludes the Actinobacteria)
- Mollicutes (gram variable, posteriorly renamed as Tenericutes, e.g. Mycoplasma)
- Mendosicutes (uneven gram stain, "methanogenic bacteria" now known as methanogens and classed as Archaea)
This taxon was revived in 2006 by Cavalier-Smith as an infrakindgom containing the phyla Spirochaetae, Sphingobacteria (FCB), Planctobacteria (PVC), and Proteobacteria. It is a gram-negative clade that branched off from other bacteria just before the evolutionary loss of the outer membrane or capsule, and just after the evolution of flagella. This taxon is not generally accepted and the three-domain system is followed.
An almost identical taxon called Hydrobacteria was defined in 2009 using bioinfomatic methods. It is in contrast to the other major group of eubacteria called Terrabacteria. The analysis also altered the internal phylogeny of this group, with PVC-FCB-Spirochaetae placed forming a clade next to Proteobacteria. What was PVC is described as polyphyletic. However, in the other subsequent phylogenetic analyzes, the PVC group was recovered as monophyletic.
Recent phylogenetic analyzes have found that proteobacteria are a paraphyletic phylum that could encompass several recently discovered candidate phyla and other phyla such as Spirochaetes, Acidobacteria, Chrysiogenetes, Deferribacteres and possibly Aquificae. This suggests that Gracilicutes or Hydrobacteria as a clade may comprise several candidates more closely related to Proteobacteria, Spirochaetes, PVC group, and FCB group than to bacteria from the clade Terrabacteria. Some of these phyla were classified as part of the proteobacteria. For example, Cavalier-Smith in his proposal of the 6 kingdoms included Acidobacteria, Aquificae, Chrysiogenetes and Deferribacteres as part of the proteobacteria.
According to the phylogenetic analysis of Hug (2016), the relationships could be the following.
According to the phylogenetic analysis of Zhu (2019), the relationships could be the following:
The following graph shows Cavalier-Smith's version of the tree of life, indicating the status of Gracilicutes. However, this tree is not supported by any molecular analysis so it should not be considered phylogenetic.
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Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria
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- Karthik Anantharaman et al. 2016, Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Nature Communications DOI: 10.1038/ncomms13219
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