Exoflagellata

From Palaeos

Cavalier-Smith (2002) introduced the name 'Exoflagellata' for a suggested taxon of bacteria that possessed flagella with their shafts outside the outer membrane, in contrast to Spirochaetes which have the shaft within periplasmic space. This taxon was to include the Planctobacteria and Proteobacteria (including Deferribacteres, Geobacter, Nitrospira and allies). I here co-opt 'Exoflagellata' for the entire clade containing these taxa in the phylogeny shown here. It has to be pointed out that doing so probably contravenes the spirit of Cavalier-Smith's original concept, seeing as Spirochaetes is now within Exoflagellata. However, the exoflagellate state is possibly ancestral for this clade as a whole if the presented phylogeny is correct (and that's a pretty big 'if' - see Eubacteria Phylogeny for an explanation why).

Phylogeny

<==Exoflagellata [Geobacteria, Nitrobacteraceae]
   |  i. s.: Synergistes jonesii
   |         Nitrosospira briensis
   |         Nitrosococcus oceanus
   |         Nitrosolobus multiformis
   |--Geovibriales [Ferrobacteria]
   |    |--Caldithrix Miroshnichenko, Kostrikina et al. 2003
   |    |        `--*C. abyssi Miroshnichenko, Kostrikina et al. 2003
   |    `--+--Deferribacteres
   |       |    |--Geovibrio ferrireducens
   |       |    |--Flexistipes sinusarabici
   |       |    |--Denitrovibrio
   |       |    `--Deferribacter [Deferribacteraceae, Deferrribacterales]
   |       |         `--D. thermophilus
   |       `--+--Nitrospina gracilis
   |          `--Thermodesulfobacterium (see below for synonymy)
   |               |--T. commune
   |               |--T. hveragerdense
   |               `--T. hydrohenophilum
   `--+--+--+--Eobacteria
      |  |  `--+--Planctobacteria
      |  |     `--+--Gemmatimonas Zhang, Sekiguchi et al. 2003 (see below for synonymy)
      |  |        |    `--*G. aurantiaca Zhang, Sekiguchi et al. 2003
      |  |        `--Fibrobacter [Fibrobacteria]
      |  |             |--F. intestinalis
      |  |             `--F. succinogenes
      |  `--+--Acidobacteria [Acidobacteriales]
      |     |    |--Acidobacterium capsulatum
      |     |    `--+--Holophaga foetida
      |     |       `--Geothrix fermentans
      |     `--+--Magnetobacterium bavaricum
      |        |--Leptospirillum ferooxidans
      |        |--Nitrospira [Nitrospirae]
      |        |    `--N. marina
      |        `--Thermodesulfovibrio
      |             |--T. islandicus
      |             `--T. yellowstonii
      `--+--+--Spirochaetes
         |  `--+--Proteobacteria
         |     `--Fusobacteria
         `--Sphingobacteria
              |  i. s.: Beggiatoales
              |           |  i. s.: Leucothrix mucor
              |           `--Beggiatoaceae
              |                |--Beggiatoa
              |                |--Thiothrix nivea
              |                |--Thioploca
              |                `--Thiospirillopsis
              |--Flavobacteria
              `--Chlorobium [Chlorobea, Chlorobi, Chlorobiales, Chlorobibacteria]
                   |--C. vibrioforme
                   `--+--C. limicola
                      `--C. tepidum

Gemmatimonas Zhang, Sekiguchi et al. 2003 [Gemmatimonadaceae, Gemmatimonadales, Gemmatimonadetes]

Thermodesulfobacterium [Thermodesulfobacteria, Thermodesulfobacteriaceae, Thermodesulfobacteriales]

* Type species of generic name indicated

Sphingobacteria

Cytoplasmic membrane with sphingolipids; outer membrane with lipopolysaccharide; flagella absent.

References

Amann, R. I., W. Ludwig & K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59 (1): 143-169.

Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionary Microbiology 52: 7-76.

Hugenholtz, P., C. Pitulle, K. L. Hershberger & N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology 180 (2): 366-376.

Maher, M., R. Palmer, F. Gannon & T. Smith. 1995. Relationship of a novel bacterial fish pathogen to Streptobacillus moniliformis and the fusobacteria group, based on 16S ribosomal RNA analysis. Systematic and Applied Microbiology 18: 79-84.

Miroshnichenko, M. L., N. A. Kostrikina, N. A. Chernyh, N. V. Pimenov, T. P. Tourova, A. N. Antipov, S. Spring, E. Stackebrandt & E. A. Bonch-Osmolovskaya. 2003. Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage. International Journal of Systematic and Evolutionary Microbiology 53: 323-329.

Mori, K., H. Kim, T. Kakegawa & S. Hanada. 2003. A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring. Extremophiles 7: 283-290.

Prescott, L. M., J. P. Harley & D. A. Klein. 1996. Microbiology (3rd ed.) Wm. C. Brown Publishers: Dubuque (Iowa).

Zhang, H., Y. Sekiguchi, S. Hanada, P. Hugenholtz, H. Kim, Y. Kamagata & K. Nakamura. 2003. Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. International Journal of Systematic and Evolutionary Microbiology 53: 1155-1163.

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