Chromatibacteria

Electron micrographs of Thermomonas haemolytica, from Busse et al. (2002). Scale bars = 200 nm.

Belongs within: Proteobacteria.
Contains: Neisseriaceae, Nitrosomonadales, Hyphomicrobiaceae, Burkholderiales, Xanthomonas, Ectothiorhodospiraceae, Chromatiaceae, Legionella, Methylococcaceae, Oceanospirillales, Thiotrichales, Alteromonadaceae, Aeromonas, Pasteurellaceae, Enterobacterales, Vibrio.

The Chromatibacteria are a diverse clade of bacteria united by molecular data, including the ‘beta’ and ‘gamma’ branches of the Proteobacteria (Cavalier-Smith 2002).

<==Chromatibacteria
    |  i. s.: Curacaobacter balticaSC03
    |         PseudomasNL03
    |         Fulvimonas soliMCS03
    |         Massilia timonaeCV03
    |         Paucimonas lemoigneiCV03
    |         Sarcobium lyticumALS95
    |         Aquicella Santos et al. 2004VP IJSEM04
    |           |--*A. lusitana Santos, Pinhal et al. 2004VP IJSEM04
    |           `--A. siphonis Santos, Pinhal et al. 2004VP IJSEM04
    |--BetaproteobacteriaGH01
    |    |  i. s.: Rhodocyclaceae [Rhodocyclales]GH01
    |    |           |--Azoarcus indigensBG-M11, IT03
    |    |           |--PropionibacterGH01
    |    |           |--Propionivibrio pelophilus (Meijer et al. 1999) Brune et al. 2002GH01, JC08
    |    |           |--Thauera selenatisBG-M11, PHK96
    |    |           |--Zoogloea ramigeraGH01, CV03
    |    |           |--Sterolibacterium denitrificansBG-M11
    |    |           `--RhodocyclusI01
    |    |                |--R. purpureusI01
    |    |                `--R. tenuis [=Rhodospirillum tenue]I01
    |    |         Methylophilaceae [Methylophilales]GH01
    |    |           |--Methylobacillus Yordy & Weaver 1977GH01, DDT03
    |    |           |    `--M. flagellatumL92
    |    |           |--Methylovorus Govorukhina & Trotsenko 1991GH01, DDT03
    |    |           |    `--M. mays Doronina et al. 2001JC08
    |    |           `--Methylophilus Jenkins, Byrom & Jones 1987GH01, DDT03
    |    |                |--M. leisingeriJC08
    |    |                `--M. methylotrophusDH92
    |    |         Tremblaya princepsVLM14
    |    |         Kingella denitrificansZ92
    |    |         Thiosphaera pantotrophaZ92
    |    |--HydrogenophilusLK01
    |    |    |--H. hirschiiIT03
    |    |    `--H. thermoluteolusIT03
    |    `--+--NeisseriaceaeWK13
    |       `--+--+--Methylotenera mobilisWK13
    |          |  `--NitrosomonadalesGH01
    |          `--+--HyphomicrobiaceaeWK13
    |             `--+--BurkholderialesWK13
    |                `--+--Candidatus Accumulibacter phosphatisWK13
    |                   `--Aromatoleum aromaticumWK13
    `--Gammaproteobacteria [Aeromonadales, Chromatiales]GH01
         |  i. s.: SuccinivibrionaceaeGH01
         |           |--SuccinivibrioGH01
         |           |--AnaerobiospirillumGH01
         |           |--RuminobacterGH01
         |           `--Succinimonas amylolyticaGH01, SJ92
         |         Moranella endobiaVLM14
         |         Kangiella koreensisWK13
         |--+--ThermomonasMCS03
         |  |    |--T. fusca Mergaert, Cnockaert & Swings 2003MCS03
         |  |    `--+--T. brevis Mergaert, Cnockaert & Swings 2003MCS03
         |  |       `--+--*T. haemolyticaMCS03
         |  |          `--T. hydrothermalisMCS03
         |  `--Xanthomonadaceae [Xanthomonadales]GH01
         |       |--XanthomonasMCS03
         |       |--Frateuria aurantiaGH01, LK02
         |       |--NevskiaGH01
         |       |--Pseudoxanthomonas taiwanensisGH01, SJ04
         |       |--RhodanobacterGH01
         |       |--Xylella fastidiosaGH01, CF04
         |       |--Lysobacter [Lysobacteraceae, Lysobacterales]GH01
         |       |    |--L. antibioticusZ92
         |       |    `--L. enzymogenesWGJ98
         |       `--StenotrophomonasGH01
         |            |--S. acidaminiphilaMCS03
         |            `--S. maltophiliaMCS03
         `--+--EctothiorhodospiraceaeGC02
            `--+--ChromatiaceaeGC02
               `--+--Cardiobacteriaceae [Cardiobacteriales]GH01
                  |    |--Cardiobacterium hominisGC02
                  |    |--Dichelobacter nodosusGH01, WK13
                  |    `--SuttonellaGH01
                  |--LegionellalesGH01
                  |    |--Coxiella [Coxiellaceae]GH01
                  |    |    `--C. burnetiiPK03
                  |    `--LegionellaceaeS92
                  |         |--LegionellaGC02
                  |         |--FluoribacterS92
                  |         `--TatlockiaS92
                  `--+--MethylococcaceaeGC02
                     `--+--+--OceanospirillalesGC02
                        |  `--+--ThiotrichalesDDT03
                        |     `--MethylobacterDDT03
                        |          |--M. capsulatusE92
                        |          `--M. whittenburyiDDT03
                        `--+--+--Alishewanella fetalisRU03
                           |  `--RheinheimeraRU03
                           |       |--R. balticaRU03
                           |       `--R. pacifica Romanenko, Uchino et al. 2003RU03
                           `--+--AlteromonadaceaeRU03
                              `--+--+--AeromonasRU03
                                 |  `--+--PasteurellaceaeGC02
                                 |     `--EnterobacteralesRU03
                                 `--+--Tolumonas auensisRS03
                                    `--+--+--Oceanisphaera Romanenko, Schumann et al. 2003RS03
                                       |  |    `--*O. litoralis Romanenko, Schumann et al. 2003RS03
                                       |  `--OceanimonasRS03
                                       |       |--O. baumaniiRS03
                                       |       `--O. doudoroffiiRS03
                                       `--+--Ferrimonas balearicaRS03
                                          `--Vibrionaceae [Vibrionales]RS03
                                               |--VibrioRU03
                                               |--EnhydrobacterGH01
                                               `--AllomonasGH01
Nomina invalida: Azoarcus buckelii Mechichi et al. 2002JC08
                 Thauera aminoaromatica Mechichi et al. 2002JC08
                 Thauera chlorobenzoica Song et al. 2001JC08
                 Thauera phenylacetica Mechichi et al. 2002JC08

*Type species of generic name indicated

References

[ALS95] 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.

[BG-M11] Borgonie, G., A. García-Moyano, D. Litthauer, W. Bert, A. Bester, E. van Heerden, C. Möller, M. Erasmus & T. C. Onstott. 2011. Nematoda from the terrestrial deep subsurface of South Africa. Nature 474: 79–82.

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.

[CV03] Coenye, T., M. Vancanneyt, M. C. Cnockaert, E. Falsen, J. Swings & P. Vandamme. 2003. Kerstersia gyiorum gen. nov., sp. nov., a novel Alcaligenes faecalis-like organism isolated from human clinical samples, and reclassification of Alcaligenes denitrificans Rüger and Tan 1983 as Achromobacter denitrificans comb. nov. International Journal of Systematic and Evolutionary Microbiology 53: 1825–1831.

[CF04] Creevey, C. J., D. A. Fitzpatrick, G. K. Philip, R. J. Kinsella, M. J. O’Connell, M. M. Pentony, S. A. Travers, M. Wilkinson & J. O. McInerney. 2004. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proceedings of the Royal Society of London Series BBiological Sciences 271: 2551–2558.

[DH92] Dijkhuizen, L., & W. Harder. 1992. Applications of prokaryotes. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 197–206. Springer-Verlag: New York.

[DDT03] Doronina, N. V., T. D. Darmaeva & Y. A. Trotsenko. 2003. Methylophaga alcalica sp. nov., a novel alkaliphilic and moderately halophilic, obligately methylotrophic bacterium from an east Mongolian saline soda lake. International Journal of Systematic and Evolutionary Microbiology 53: 223–229.

[E92] Eady, R. R. 1992. The dinitrogen-fixing bacteria. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 534–553. Springer-Verlag: New York.

[GH01] Garrity, G. M., & J. G. Holt. 2001. The road map to the Manual. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 119–166. Springer.

[GC02] Golyshin, P. N., T. N. Chernikova, W.-R. Abraham, H. Lünsdorf, K. N. Timmis & M. M. Yakimov. 2002. Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. International Journal of Systematic and Evolutionary Microbiology 52: 901–911.

[IJSEM04] IJSEM. 2004. Validation list no. 95: Validation of publication of new names and new combinations previously effectively published outside the IJSEM. International Journal of Systematic and Evolutionary Microbiology 54: 1–2.

[I01] Imhoff, J. F. 2001. The anoxygenic phototrophic purple bacteria. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 631–637. Springer.

[IT03] Inagaki, F., K. Takai, H. Hirayama, Y. Yamato, K. H. Nealson & K. Horikoshi. 2003. Distribution and phylogenetic diversity of the subsurface microbial community in a Japanese epithermal gold mine. Extremophiles 7: 307–317.

[JC08] Judicial Commission of the International Committee on Systematics of Prokaryotes. 2008. Status of strains that contravene Rules 27 (3) and 30 of the International Code of Nomenclature of Bacteria. Opinion 81. International Journal of Systematic and Evolutionary Microbiology 58: 1755–1763.

[L92] Lidstrom, M. E. 1992. The aerobic methylotrophic bacteria. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 431–445. Springer-Verlag: New York.

[LK02] Lisdiyanti, P., H. Kawasaki, Y. Widyastuti, S. Saono, T. Seki, Y. Yamada, T. Uchimura & K. Komagata. 2002. Kozakia baliensis gen. nov., sp. nov., a novel acetic acid bacterium in the α-proteobacteria. International Journal of Systematic and Evolutionary Microbiology 52: 813–818.

[LK01] Ludwig, W., & H.-P. Klenk. 2001. Overview: A phylogenetic backbone and taxonomic framework for procaryotic systematics. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 49–65. Springer.

[MCS03] Mergaert, J., M. C. Cnockaert & J. Swings. 2003. Thermomonas fusca sp. nov. and Thermomonas brevis sp. nov., two mesophilic species isolated from a denitrification reactor with poly(ε-caprolactone) plastic granules as fixed bed, and emended description of the genus Thermomonas. International Journal of Systematic and Evolutionary Microbiology 53: 1961–1966.

[NL03] Notomista, E. A. Lahm, A. Di Donato & A. Tramontano. 2003. Evolution of bacterial and archaeal multicomponent monooxygenases. Journal of Molecular Evolution 56: 435–445.

[PK03] Park, M.-Y., K. S. Ko, H. K. Lee, M.-S. Park & Y.-H. Kook. 2003. Legionella busanensis sp. nov., isolated from cooling tower water in Korea. International Journal of Systematic and Evolutionary Microbiology 53: 77–80.

[PHK96] Prescott, L. M., J. P. Harley & D. A. Klein. 1996. Microbiology 3rd ed. Wm. C. Brown Publishers: Dubuque (Iowa).

[RS03] Romanenko, L. A., P. Schumann, N. V. Zhukova, M. Rohde, V. V. Mikhailov & E. Stackebrandt. 2003. Oceanisphaera litoralis gen. nov., sp. nov., a novel halophilic bacterium from marine bottom sediments. International Journal of Systematic and Evolutionary Microbiology 53: 1885–1888.

[RU03] Romanenko, L. A., M. Uchino, E. Falsen, N. V. Zhukova, V. V. Mikhailov & T. Uchimura. 2003. Rheinheimera pacifica sp. nov., a novel halotolerant bacterium isolated from deep sea water of the Pacific. International Journal of Systematic and Evolutionary Microbiology 53: 1973–1977.

[SJ92] Schlegel, H. G., & H. W. Jannasch. 1992. Prokaryotes and their habitats. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 75–125. Springer-Verlag: New York.

[SC03] Sjöling, S., & D. A. Cowan. 2003. High 16S rDNA bacterial diversity in glacial meltwater lake sediment, Bratina Island, Antarctica. Extremophiles 7: 275–282.

[SJ04] Spring, S., U. Jäckel, M. Wagner & P. Kämpfer. 2004. Ottowia thiooxydans gen. nov., sp. nov., a novel facultatively anaerobic, N2O-producing bacterium isolated from activated sludge, and transfer of Aquaspirillum gracile to Hylemonella gracilis gen. nov., comb. nov. International Journal of Systematic and Evolutionary Microbiology 54: 99–106.

[S92] Stackebrandt, E. 1992. Unifying phylogeny and phenotypic diversity. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 19–47. Springer-Verlag: New York.

[VLM14] Van Leuven, J. T., R. C. Meister, C. Simon & J. P. McCutcheon. 2014. Sympatric speciation in a bacterial endosymbiont results in two genomes with the functionality of one. Cell 158: 1270–1280.

[WK13] Williams, K. P., & D. P. Kelly. 2013. Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. International Journal of Systematic and Evolutionary Microbiology 63 (8): 2901–2906.

[WGJ98] Wright, D. S., L. D. Graham & P. A. Jennings. 1998. Cloning of a Lysobacter enzymogenes gene that encodes an arginyl endopeptidase (endoproteinase Arg-C). Biochimica et Biophysica Acta 1443: 369–374.

[Z92] Zumpft, W. G. 1992. The denitrifying prokaryotes. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 554–582. Springer-Verlag: New York.

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