Bacillus

Gram-stained culture of Bacillus subtilis, copyright Y tambe.

Belongs within: Bacilli.

Bacillus is a diverse genus of rod-shaped, aerobic or facultatively anaerobic Gram-positive bacteria that produce dormant endospores when exposed to unfavorable conditions.

<==Bacillus
    |--+--B. pumilus VK03
    |  `--B. subtilis VK03 [incl. B. subtilis var. niger CV66]
    `--+--B. firmus VK03
       |--B. lentus VK03
       |--+--B. benzoevorans VK03
       |  `--+--B. circulans VK03
       |     `--B. nealsonii Venkateswaran, Kempf et al. 2003 VK03
       |--+--B. megaterium VK03
       |  `--+--B. flexus VK03
       |     `--B. simplex VK03
       `--+--+--‘B. macroides’ VK03
          |  `--B. psychrosaccharolyticus VK03
          `--+--B. niacini VK03
             `--+--B. fumarioli VK03
                `--‘B. pseudomegaterium’ VK03

Bacillus incertae sedis:
  B. aeolius Gugliandolo, Maugeri et al. 2003^VP IJSEM03
  B. alcalophilus PHK96
  B. amyloliquefaciens PHK96
  B. anthracis KE03
  B. azotofixans E92
  B. brevis CM92
  ‘B. caldolyticus’ DC03
  B. caldotenax C-S02
  B. cereus VK03
  B. coagulans PHK96
  B. fastidiosus PHK96
  B. haloalkaliphilus MO03
  B. halodenitrificans SJ04
  B. halodurans Z03
  B. infernus KGP02
  B. larvae White 1906 BB37
  B. laterosporus Z92
  B. licheniformis VK03
  B. methanolicus DC03
  B. mycoides VK03
  B. nitritollens Z92
  B. pantothenticus Z92
  B. pasteurii PHK96
  B. pluton White 1906 BB37
  B. popilliae PHK96
  B. psychrophilus PHK96
  B. pulvefaciens Z92
  B. pycnoticus AS92
  B. schlegelii AS92
  B. selenitireducens Switzer Blum et al. 2001 JC08
  B. sphaericus VK03
  B. stearothermophilus MN03
  B. subterraneus Kanso, Greene & Patel 2002 KGP02
  B. thermantarcticus Nicolaus et al. 2002 JC08
  B. thermocatenulatus DC03
  B. thermocloacae DC03
  B. thermoruber DC03
  B. thuringiensis L91
    |--B. t. var. thuringiensis L91
    `--B. t. var. israelensis L91

*Type species of generic name indicated

REFERENCES

[AS92] Aragno, M., & H. G. Schlegel. 1992. The mesophilic hydrogen-oxidizing (knallgas) 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 2^nd ed. vol. 1 pp. 344–384. Springer-Verlag: New York.

[BB37] Bishopp, F. C., & C. E. Burnside. 1937. In memorian: Gershom Franklin White. Proceedings of the Entomological Society of Washington 39 (7): 184–188.

[C-S02] 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.

[CM92] Coughlan, M. P., & F. Mayer. 1992. The cellulose-decomposing bacteria and their enzyme systems. 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 2^nd ed. vol. 1 pp. 460–516. Springer-Verlag: New York.

[CV66] Curds, C. R., & J. M. Vandyke. 1966. The feeding habits and growth rates of some freshwater ciliates found in activated-sludge plants. Journal of Applied Ecology 3: 127–137.

[DC03] Duan, Y. P., H. F. Castro, T. E. Hewlett, J. H. White & A. V. Ogram. 2003. Detection and characterization of Pasteuria 16S rRNA gene sequences from nematodes and soils. International Journal of Systematic and Evolutionary Microbiology 53: 105–112.

[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 2^nd ed. vol. 1 pp. 534–553. Springer-Verlag: New York.

[IJSEM03] IJSEM. 2003. Validation list no. 94. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. International Journal of Systematic and Evolutionary Microbiology 53: 1701–1702.

[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.

[KGP02] Kanso, S., A. C. Greene & B. K. C. Patel. 2002. Bacillus subterraneus sp. nov., an iron- and manganese-reducing bacterium from a deep subsurface Australian thermal aquifer. International Journal of Systematic and Evolutionary Microbiology 52: 869–874.

[KE03] Kobayashi, K., S. D. Ehrlich, A. Albertini, G. Amati, K. K. Andersen, M. Arnaud, K. Asai, S. Ashikaga, S. Aymerich, P. Bessieres, F. Boland, S. C. Brignell, S. Bron, K. Bunai, J. Chapuis, L. C. Christiansen, A. Danchin, M. Débarbouillé, E. Dervyn, E. Deuerling, K. Devine, S. K. Devine, O. Dreesen, J. Errington, S. Fillinger, S. J. Foster, Y. Fujita, A. Galizzi, R. Gardan, C. Eschevins, T. Fukushima, K. Haga, C. R. Harwood, M. Hecker, D. Hosoya, M. F. Hullo, H. Kakeshita, D. Karamata, Y. Kasahara, F. Kawamura, K. Koga, P. Koski, R. Kuwana, D. Imamura, M. Ishimaru, S. Ishikawa, I. Ishio, D. Le Coq, A. Masson, C. Mauël, R. Meima, R. P. Mellado, A. Moir, S. Moriya, E. Nagakawa, H. Nanamiya, S. Nakai, P. Nygaard, M. Ogura, T. Ohanan, M. O’Reilly, M. O’Rourke, Z. Pragai, H. M. Pooley, G. Rapoport, J. P. Rawlins, L. A. Rivas, C. Rivolta, A. Sadaie, Y. Sadaie, M. Sarvas, T. Sato, H. H. Saxild, E. Scanlan, W. Schumann, J. F. M. L. Seegers, J. Sekiguchi, A. Sekowska, S. J. Séror, M. Simon, P. Stragier, R. Studer, H. Takamatsu, T. Tanaka, M. Takeuchi, H. B. Thomaides, V. Vagner, J. M. van Dijl, K. Watabe, A. Wipat, H. Yamamoto, M. Yamamoto, Y. Yamamoto, K. Yamane, K. Yata, K. Yoshida, H. Yoshikawa, U. Zuber & N. Ogasawara. 2003. Essential Bacillus subtilis genes. Proceedings of the National Academy of Sciences of the USA 100 (8): 4678–4683.

[L91] Liehne, P. F. S. 1991. An Atlas of the Mosquitoes of Western Australia. Health Department of Western Australia.

[MN03] Moffitt, M. C., & B. A. Neilan. 2003. Evolutionary affiliations within the superfamily of ketosynthases reflect complex pathway associations. Journal of Molecular Evolution 56: 446–457.

[MO03] Müller, V., & A. Oren. 2003. Metabolism of chloride in halophilic prokaryotes. Extremophiles 7: 261–266.

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

[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.

[VK03] Venkateswaran, K., M. Kempf, F. Chen, M. Satomi, W. Nicholson & R. Kern. 2003. Bacillus nealsonii sp. nov., isolsted from a spacecraft-assembly facility, whose spores are γ-radiation resistant. International Journal of Systematic and Evolutionary Microbiology 53: 165–172.

[Z03] Zeigler, D. R. 2003. Gene sequences useful for predicting relatedness of whole genomes in bacteria. International Journal of Systematic and Evolutionary Microbiology 53: 1893–1900.

[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 2^nd ed. vol. 1 pp. 554–582. Springer-Verlag: New York.

Corynebacterium

Gram-stained Corynebacterium diphtheriae, from the Centers for Disease Control and Prevention.

Belongs within: Actinomycetales.

Corynebacterium is a diverse genus of high G+C, rod-shaped, Gram-positive bacteria found in a wide range of habitats, including soil, aquatic habitats or in association with animal tissues (Vela et al. 2003).

Corynebacterium [Corynebacteriaceae]
    |  i. s.: C. dismutans PHK96
    |         C. insidiosum K-WK92
    |         C. manihot PHK96
    |         C. michisanense MN03
    |         C. mooreparkense Brennan et al. 2001 JC08
    |         C. nephridii Z92
    |         C. nigricans Shukla, Bernard et al. 2004^VP IJSEM04
    |         C. poinsettiae PHK96 [=Co. flaccumfaciens ssp. poinsettiae K92, Curtobacterium poinsettiae K92]
    |         C. simplex PHK96
    |--+--C. amycolatum VM03
    |  `--+--C. freneyi VM03
    |     `--C. xerosis VM03
    `--+--+--+--C. terpenotabidum VM03
       |  |  `--C. variabile VM03
       |  `--+--C. bovis VM03
       |     `--+--+--C. auriscanis VM03
       |        |  `--C. suicordis Vela, Mateos et al. 2003 VM03
       |        `--+--C. urealyticum VM03
       |           `--+--C. falsenii VM03
       |              `--C. jeikeium VM03
       `--+--+--C. efficiens VM03
          |  `--+--C. callunae VM03
          |     `--C. glutamicum VM03
          `--+--+--+--C. ammoniagenes VM03
             |  |  `--C. casei Brennan et al. 2001 VM03, JC08
             |  `--+--C. flavescens VM03
             |     `--C. phocae VM03
             |--+--C. spheniscorum Goyache, Vela et al. 2003 GV03
             |  `--+--+--C. argentoratense VM03
             |     |  `--+--C. felinum VM03
             |     |     `--C. testudinoris VM03
             |     `--+--C. vitaeruminis VM03
             |        `--+--C. kutscheri VM03
             |           `--+--*C. diphtheriae GV03, VM03
             |              `--+--C. pseudotuberculosis VM03
             |                 `--C. ulcerans VM03
             `--+--+--+--C. durum VM03
                |  |  `--C. matruchotii VM03 [=Bacterionema matruchotii S92]
                |  `--+--+--+--C. cystitidis VM03
                |     |  |  `--C. pilosum VM03
                |     |  `--+--C. mastitidis VM03
                |     |     `--C. renale VM03
                |     `--+--+--C. glucuronolyticum VM03
                |        |  `--C. seminale VM03
                |        `--+--C. kroppenstedtii VM03
                |           `--Turicella otitidis VM03
                `--+--+--+--C. striatum VM03
                   |  |  `--+--C. aurimucosum Yassin et al. 2002 VM03, JC08
                   |  |     `--C. minutissimum VM03
                   |  `--+--+--C. accolens VM03
                   |     |  `--C. macginleyi VM03
                   |     `--+--C. propinquum VM03
                   |        `--C. pseudodiphtheriticum VM03
                   `--+--C. camporealensis VM03
                      `--+--+--C. riegelii VM03
                         |  `--+--C. sundsvallense VM03
                         |     `--C. thomssenii VM03
                         `--+--C. appendicis VM03
                            `--+--+--C. auris VM03
                               |  `--C. capitovis VM03
                               `--+--C. mycetoides VM03
                                  `--+--C. coyleae VM03
                                     `--+--C. afermentans VM03
                                        `--C. mucifaciens VM03

*Type species of generic name indicated

REFERENCES

[GV03] Goyache, J., A. I. Vela, M. D. Collins, C. Ballesteros, V. Briones, J. Moreno, P. Yorio, L. Domínguez, R. Hutson & J. F. Fernández-Garayzábal. 2003. Corynebacterium spheniscorum sp. nov., isolated from the cloacae of wild penguins. International Journal of Systematic and Evolutionary Microbiology 53: 43–46.

[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.

[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.

[K92] Kado, C. I. 1992. Plant pathogenic 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 2^nd ed. vol. 1 pp. 659–674. Springer-Verlag: New York.

[K-WK92] Korn-Wendisch, F., & H. J. Kutzner. 1992. The family Streptomycetaceae. 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 2^nd ed. vol. 1 pp. 921–995. Springer-Verlag: New York.

[MN03] Moffitt, M. C., & B. A. Neilan. 2003. Evolutionary affiliations within the superfamily of ketosynthases reflect complex pathway associations. Journal of Molecular Evolution 56: 446-457.

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

[S92] Schaal, K. P. 1992. The genera Actinomyces, Arcanobacterium, and Rothia. 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 2^nd ed. vol. 1 pp. 850–905. Springer-Verlag: New York.

[VM03] Vela, A. I., A. Mateos, M. D. Collins, V. briones, R. A. Hutson, L. Domínguez & J. F. Fernández-Garayzábal. 2003. Corynebacterium suicordis sp. nov., from pigs. International Journal of Systematic and Evolutionary Microbiology 53: 2027–2031.

[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 2^nd ed. vol. 1 pp. 554–582. Springer-Verlag: New York.

Fusobacteria

Stained culture of Fusobacterium nucleatum, copyright J. Michael Miller.

Belongs within: Life.

The Fusobacteria are a group of anaerobic, Gram-negative, rod-shaped bacteria with a chemoorganotrophic heterotrophic metabolism (Garrity & Holt 2001).

<==Fusobacteria [Fusobacteriaceae, Fusobacteriales]
    |  i. s.: Ilyobacter GH01
    |         Cetobacterium GH01
    |--+--Leptotrichia buccalis MP95
    |  `--+--Sebaldella termitidis [=Bacteroides termitidis] MP95
    |     `--Streptobacillus moniliformis MP95
    `--+--Propionigenium modestum MP95
       `--Fusobacterium MP03
            |  i. s.: F. perfoetens PHK96
            |--F. necrogenes MP95
            |--+--F. varium MP95
            |  `--+--F. mortiferum MP95
            |     `--F. ulcerans MP95
            `--+--+--F. gonidiaformans MP95
               |  `--F. necrophorum MP95
               `--+--F. russii MP95
                  `--+--+--F. alocis MP95
                     |  `--F. simiae MP95
                     `--+--F. nucleatum MP95
                        `--F. periodonticum MP95

Nomen invalidum: Leptotrichia trevisanii Tee, Midolo et al. 2002^VP JC08

*Type species of generic name indicated

REFERENCES

[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.

[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.

[MP95] 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.

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

Polyangiaceae

Fruiting body of Nannocystis exedens, copyright Leibniz-Institut DSMZ.

Belongs within: Deltaproteobacteria.

The Polyangiaceae are a group of myxobacteria with stout, rigid rod-shaped cells that tend to sink into the agar in culture, and change little in shape when producing myxospores.

Polyangiaceae [Sorangineae]
    |--+--‘Sorangium cellulosum’ IJ03
    |  `--Chondromyces IJ03
    |       |--C. apiculatus IJ03
    |       `--C. crocatus IJ03
    `--+--+--Polyangium vitellinum IJ03
       |  `--Haliangium IJ03
       |       |--H. ochraceum IJ03
       |       `--H. tepidum IJ03
       `--+--Plesiocystis Iizuka, Jojima et al. 2003 IJ03
          |    `--*P. pacifica Iizuka, Jojima et al. 2003 IJ03
          `--Nannocystis IJ03
               |--‘N. aggregans’ IJ03
               `--N. exedens IJ03

*Type species of generic name indicated

REFERENCES

[IJ03] Iizuka, T., Y. Jojima, R. Fudou, A. Hiraishi, J.-W. Ahn & S. Yamanaka. 2003. Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan. International Journal of Systematic and Evolutionary Microbiology 53: 189–195.

Cystobacterineae

Fruiting bodies of Myxococcus xanthus, copyright Michiel Vos.

Belongs within: Deltaproteobacteria.

The Cystobacterineae are a group of myxobacteria with slender, flexible rod-shaped cells that tend to form thin, filmlike swarms on agar and transform into myxospores via sustantial shortening and fattening.

Cystobacterineae [Cystobacteraceae, Myxococcaceae]
    |--Stigmatella aurantiaca IJ03
    `--+--+--Cystobacter fuscus IJ03
       |  `--+--Angiococcus disciformis IJ03
       |     `--Archangium [Archangiaceae] IJ03
       |          `--A. gephyra IJ03
       `--+--Melittangium lichenicola IJ03
          `--Myxococcus IJ03
               |--M. coralloides IJ03
               |--M. fulvus PHK96
               |--M. stipitatus PHK96
               `--M. xanthus IJ03

*Type species of generic name indicated

REFERENCES

[IJ03] Iizuka, T., Y. Jojima, R. Fudou, A. Hiraishi, J.-W. Ahn & S. Yamanaka. 2003. Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan. International Journal of Systematic and Evolutionary Microbiology 53: 189–195.

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

Rhodobacteraceae

Maricaulis maris, copyright Patrick Viollier.

Belongs within: Alphaproteobacteria.
Contains: Paracoccus.

The Rhodobacteraceae are a diverse group of Gram-negative bacteria including both photo- and chemoheterotrophic taxa, primarily found in aquatic environments.

Rhodobacteraceae [Rhodobacterales]
    |--+--Oceanicaulis Strömpl, Hold et al. 2003 SH03
    |  |    `--*O. alexandrii Strömpl, Hold et al. 2003 SH03
    |  `--Maricaulis SH03
    |       |--M. parjimensis SH03
    |       `--+--M. maris SH03
    |          `--M. washingtonensis SH03
    `--+--+--Hirschia baltica SH03
       |  `--Hyphomonas SH03
       |       |--H. jannaschiana SH03
       |       `--H. polymorpha SH03
       `--Caulobacteraceae [Caulobacterales] GH01
            |--Asticcacaulis GH01
            |--Phenylobacterium GH01
            |--Brevundimonas GH01
            |    |--B. diminuta SH03
            |    `--B. vesicularis IT03
            `--Caulobacter SH03
                 |--C. crescentus IT03
                 `--C. vibrioides SH03

Rhodobacteraceae incertae sedis:
  Rhodobacter MK03
    |--R. azotoformans I01
    |--R. blasticus [=Rhodopseudomonas blastica] I01
    |--R. capsulatus MK03
    |--R. sphaeroides I01
    `--R. veldkampii I01
  Ahrensia GH01
  Amaricoccus GH01
  Antarctobacter GH01
  Gemmobacter GH01
  Octadecabacter GH01
  Paracoccus GH01
  Rhodovulum GH01
    |--R. adriaticum [=Rhodobacter adriaticus, Rhodopseudomonas adriatica] I01
    |--R. euryhalinum [=Rhodobacter euryhalinus] I01
    |--R. strictum I01
    `--R. sulfidophilum [=Rhodobacter sulfidophilus, Rhodopseudomonas sulfidophila] I01
  Roseivivax GH01
    |--R. halodurans I01
    `--R. halotolerans I01
  Roseobacter GH01
    |--R. denitrificans I01
    `--R. litoralis I01
  Roseovarius tolerans GH01, I01
  Rubrimonas cliftonensis GH01, I01
  Ruegeria GH01
  Sagittula GH01
  Staleya GH01
  Stappia GH01
  Sulfitobacter GH01

*Type species of generic name indicated

REFERENCES

[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 2^nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 119–166. Springer.

[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 2^nd 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.

[MK03] 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.

[SH03] Strömpl, C., G. L. Hold, H. Lünsdorf, J. Graham, S. Gallacher, W.-R. Abraham, E. R. B. Moore & K. N. Timmis. 2003. Oceanicaulis alexandrii gen. nov., sp. nov., a novel stalked bacterium isolated from a culture of the dinoflagellate Alexandrium tamarense (Lebour) Balech. International Journal of Systematic and Evolutionary Microbiology 53: 1901–1906.

Paracoccus

Paracoccus denitrificans, copyright Richard Ewans-Gowing.

Belongs within: Rhodobacteraceae.

Paracoccus is a genus of Gram-negative, mostly non-motile bacteria found growing on a wide range of organic substances.

<==Paracoccus
    |--+--P. kondratievae Doronina & Trotsenko 2001 BJ03, JC08
    |  `--+--P. methylutens BJ03
    |     `--+--P. pantotrophus BJ03
    |        `--P. versutus BJ03
    `--+--+--P. kocurii BJ03
       |  `--+--P. alkenifer BJ03
       |     `--P. solventivorans BJ03
       |--+--P. zeaxanthinifaciens Berry, Janssens et al. 2003 BJ03
       |  `--+--P. carotinifaciens BJ03
       |     `--P. marcusii BJ03
       `--+--+--P. alcaliphilus BJ03
          |  `--P. aminovorans BJ03
          `--+--P. thiocyanatus BJ03
             `--+--P. aminophilus BJ03
                `--P. denitrificans BJ03

*Type species of generic name indicated

REFERENCES

[BJ03] Berry, A., D. Janssens, M. Hümbelin, J. P. M. Jore, B. Hoste, I. Cleenwerck, M. Vancanneyt, W. Bretzel, A. F. Mayer, R. Lopez-Ulibarri, B. Shanmugam, J. Swings & L. Pasamontes. 2003. Paracoccus zeaxanthinifaciens sp. nov., a zeaxanthin-producing bacterium. International Journal of Systematic and Evolutionary Microbiology 53: 231–238.

[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.

Burkholderiales

Tomato stem infected with Ralstonia solanacearum, copyright Clemson University.

Belongs within: Chromatibacteria.
Contains: Alcaligenaceae, Comamonadaceae, Burkholderia.

The Burkholderiales are a group of Gram-negative bacteria united by phylogenetic analyses.

Burkholderiales GH01
    |--Burkholderiaceae GH01
    |    |--Burkholderia BL03
    |    |--Cupriavidus GH01
    |    |--Lautropia GH01
    |    `--Thermothrix thiopara GH01, PHK96
    `--+--Pandoraea BL03
       |    |  i. s.: P. apista CV03
       |    |--P. sputorum BL03
       |    `--+--P. norimbergensis BL03
       |       `--P. pulmonicola BL03
       `--+--Candidatus Glomeribacter Bianciotto, Lumini et al. 2003 BL03
          |    `--*G. gigasporarum Bianciotto, Lumini et al. 2003 BL03
          `--Ralstonia [Ralstoniaceae] BL03
               |  i. s.: R. eutropha NL03
               |         R. metallidurans NL03
               |--R. solanacearum BL03
               `--+--R. gilardii BL03
                  `--R. paucula BL03

Burkholderiales incertae sedis:
  Alcaligenaceae GH01
  ‘Pseudomonas’ testosteroni PHK96
  Comamonadaceae GH01
  Oxalobacteraceae GH01
    |--Oxalobacter GH01
    |--Duganella GH01
    |--Janthinobacterium GH01
    |--Telluria GH01
    `--Herbaspirillum VV03
         |--*H. seropedicae VV03
         |--H. frisingense Kirchhof et al. 2001 JC08
         |--H. lusitanum Valverde, Velázquez et al. 2003 VV03
         `--H. rubrisubalbicans [=Pseudomonas rubrisubalbicans] VV03

*Type species of generic name indicated

REFERENCES

[BL03] Bianciotto, V., E. Lumini, P. Bonfante & P. Vandamme. 2003. ‘Candidatus Glomeribacter gigasporarum’ gen. nov., sp. nov., an endosymbiont of arbuscular mycorrhizal fungi. International Journal of Systematic and Evolutionary Microbiology 53: 121–124.

[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.

[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 2^nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 119–166. Springer.

[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.

[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.

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

[VV03] Valverde, A., E. Velázquez, C. Gutiérrez, E. Cervantes, A. Ventosa & J.-M. Igual. 2003. Herbaspirillum lusitanum sp. nov., a novel nitrogen-fixing bacterium associated with root nodules of Phaseolus vulgaris. International Journal of Systematic and Evolutionary Microbiology 53: 1979–1983.

Alcaligenaceae

Sample of Bordetella bronchiseptica, from the Centers for Disease Control and Prevention.

Belongs within: Burkholderiales.

The Alcaligenaceae are a diverse group of Gram-negative bacteria united by molecular phylogenetic analysis. Members have been found in a range of terrestrial and aquatic environments, with some being animal pathogens.

<==Alcaligenaceae
    |  i. s.: Pelistega europaea GH01, CVC03
    |         Sutterella GH01
    |         Taylorella equigenitalis GH01, CVC03
    |--Alcaligenes CVF03
    |    |--*A. faecalis CVC03
    |    |    |--A. f. var. faecalis PHK96
    |    |    `--A. f. var. myxogenes PHK96
    |    |--A. defragans CVF03
    |    `--A. eutrophus NL03
    `--+--Pigmentiphaga kullae CVF03
       `--+--Kerstersia Coenye, Vancanneyt et al. 2003 CVF03, CVC03
          |    `--*K. gyiorum Coenye, Vancanneyt et al. 2003 CVC03
          `--+--Achromobacter Yabuuchi & Yano 1981 CVF03
             |    |  i. s.: A. lyticus WGJ98
             |    |--+--A. piechaudii [=Alcaligenes piechaudii] CVF03
             |    |  `--A. spanius Coenye, Vancanneyt et al. 2003 CVF03
             |    `--+--*A. xylosoxidans CVF03
             |       `--+--A. insolitus Coenye, Vancanneyt et al. 2003 CVF03
             |          `--+--A. denitrificans (Rüger & Tan) Coenye, Vancanneyt et al. 2003 CVF03, CVC03 (see below for synonymy)
             |             `--A. ruhlandii [=Alcaligenes ruhlandii] CVF03
             `--Bordetella CVF03
                  |--B. petrii CVF03
                  `--+--B. avium CVF03
                     `--+--B. trematum CVF03
                        `--+--B. hinzii CVF03
                           `--+--+--*B. pertussis CVC03, CVF03
                              |  `--B. holmesii CVF03
                              `--+--B. bronchiseptica CVF03
                                 `--B. parapertussis CVF03

Achromobacter denitrificans (Rüger & Tan) Coenye, Vancanneyt et al. 2003 CVF03, CVC03 [=Alcaligenes denitrificans Rüger & Tan 1983 CVC03, Achromobacter xylosoxidans ssp. denitrificans CVC03]

*Type species of generic name indicated

REFERENCES

[CVC03] 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 orgtanism 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.

[CVF03] Coenye, T., M. Vancanneyt, E. Falsen, J. Swings & P. Vandamme. 2003. Achromobacter insolitus sp. nov. and Achromobacter spanius sp. nov., from human clinical samples. International Journal of Systematic and Evolutionary Microbiology 53: 1819–1824.

[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.

[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.

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

[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.

Comamonadaceae

Cells of Comamonas testosteroni, from Weiss et al. (2013).

Belongs within: Burkholderiales.

The Comamonadaceae are a diverse group of mostly aerobic and heterotrophic bacteria that are united by molecular phylogenetic analyses.

<==Comamonadaceae
    |--+--Variovorax paradoxus MSF03
    |  `--Xylophilus ampelinus MSF03
    `--+--Rhodoferax fermentans MSF03
       `--+--Acidovorax MSF03
          |    |--A. facilis MSF03
          |    `--+--A. avenae MSF03
          |       `--A. konjaci MSF03
          `--+--Aquaspirillum MSF03
             |    |--A. magnetotacticum PHK96 [=Magnetospirillum magnetotacticum ALS95]
             |    |--A. metamorphum ALS95
             |    |--A. psychrophilum MSF03
             |    |--A. serpens PHK96
             |    `--A. sinuosum PHK96
             `--+--Alicycliphilus Mechichi, Stackebrandt & Fuchs 2003 MSF03
                |    `--*A. denitrificans Mechichi, Stackebrandt & Fuchs 2003 MSF03
                `--+--Xenophilus azovorans MSF03
                   `--+--Hydrogenophaga MSF03
                      |    |--H. intermedia Contzen et al. 2001 MSF03, JC08
                      |    `--+--+--H. flava MSF03
                      |       |  `--H. pseudoflava MSF03
                      |       `--+--H. palleronii MSF03
                      |          `--H. taeniospiralis MSF03
                      `--+--Delftia acidovorans MSF03
                         `--+--Brachymonas denitrificans MSF03
                            `--Comamonas MSF03
                                 |  i. s.: C. koreensis Chang et al. 2002 JC08
                                 |--C. testosteroni MSF03
                                 `--+--C. terrigena MSF03
                                    `--+--C. denitrificans Gumaelius et al. 2001 MSF03, JC08
                                       `--C. nitrativorans MSF03

Comamonadaceae incertae sedis:
  Rubrivivax gelatinosus CV03, I01 [=Rhodocyclus gelatinosus I01, Rhodopseudomonas gelatinosa I01]
  Ideonella CV03
  ‘Alcaligenes’ latus CV03
  Aquabacterium GH01
  Leptothrix GH01
    |--L. cholodnii PHK96
    |--L. discophora PHK96
    `--L. lopholea PHK96
  Polaromonas GH01
  Roseateles GH01
  Sphaerotilus natans GH01, PHK96
  Thiomonas thermosulfata GH01, MK03

Nomen invalidum: Rhodoferax antarcticus Madigan et al. 2001 JC08

*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.

[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.

[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.

[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.

[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.

[MSF03] Mechichi, T., E. Stackbrandt & G. Fuchs. 2003. Alicycliphilus denitrificans gen. nov., sp. nov., a cyclohexanol-degrading, nitrate-reducing β-proteobacterium. International Journal of Systematic and Evolutionary Microbiology 53: 147–152.

[MK03] 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.

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

Burkholderia

Cells of Burkholderia cepacia, from the Centers for Disease Control and Prevention.

Belongs within: Burkholderiales.

Burkholderia is a genus of rod-shaped, usually motile, Gram-negative bacteria, members of which are obligately aerobic and able to utilise poly-beta-hydroxybutyrate for growth. Species of this genus may be facultative pathogens of plants or animals (including humans), or they may be environmentally significant soil bacteria.

<==Burkholderia
    |  i. s.: B. fungorum GP03
    |         B. graminis PR03
    |         B. hospita Goris, Dejonghe et al. 2003^VP IJSEM03
    |         B. kururensis NL03
    |         B. picketii NL03
    |         B. pseudomallei WR03
    |         B. solanacearum [=Pseudomonas solanacearum] PHK96
    |         B. terricola Goris, Dejonghe et al. 2003^VP IJSEM03
    |         B. vietnamiensis SC03
    |--Candidatus B. kirkii BL03
    `--+--B. caryophylli BL03
       `--+--B. cepacia BL03 [=Pseudomonas cepacia PHK96]
          `--B. gladioli BL03

*Type species of generic name indicated

REFERENCES

[BL03] Bianciotto, V., E. Lumini, P. Bonfante & P. Vandamme. 2003. ‘Candidatus Glomeribacter gigasporarum’ gen. nov., sp. nov., an endosymbiont of arbuscular mycorrhizal fungi. International Journal of Systematic and Evolutionary Microbiology 53: 121–124.

[GP03] Gupta, R. S., M. Pereira, C. Chandrasekara & V. Johari. 2003. Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues. International Journal of Systematic and Evolutionary Microbiology 53: 1833–1842.

[IJSEM03] IJSEM. 2003. Validation list no. 89. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. International Journal of Systematic and Evolutionary Microbiology 53: 1–2.

[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.

[PR03] Peix, A., R. Rivas, P. F. Mateos, E. Martínez-Molina, C. Rodríguez-Barrueco & E. Velázquez. 2003. Pseudomonas rhizosphaerae sp. nov., a novel species that actively solubilizes phosphate in vitro. International Journal of Systematic and Evolutionary Microbiology 53: 2067–2072.

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

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

[WR03] Wenzel, M., R. Radek, G. Brugerolle & H. König. 2003. Identification of the ectosymbiotic bacteria of Mixotricha paradoxa involved in movement symbiosis. European Journal of Protistology 39 (1): 11–23.

Xanthomonas

Flag leaves showing symptoms of infection with Xanthomonas translucens, copyright E. A. Milus.

Belongs within: Chromatibacteria.

Xanthomonas is a genus of motile, rod-shaped bacteria found growing in association with plants, often causing diseases such as bacterial spots and blights.

Xanthomonas
    |--X. albilineans RG04
    |--X. arboricola RG04
    |    |--X. a. pv. arboricola RG04
    |    `--X. a. pv. juglandis RG04
    |--X. axonopodis RG04
    |    |--X. a. pv. axonopodis RG04
    |    |--X. a. pv. alfalfae RG04
    |    |--X. a. pv. allii (Kadota, Uehara et al.) Roumagnac, Gagnevin et al. 2004 (see below for synonymy) RG04
    |    |--X. a. pv. aurantifolii RG04
    |    |--X. a. pv. begoniae RG04
    |    |--X. a. pv. citri RG04
    |    |--X. a. pv. citrumelo RG04
    |    |--X. a. pv. coracanae RG04
    |    |--X. a. pv. glycines RG04
    |    |--X. a. pv. malvacearum RG04
    |    |--X. a. pv. manihotis RG04
    |    |--X. a. pv. phaseoli RG04
    |    |    |--X. a. pv. p. var. phaseoli RG04
    |    |    `--X. a. pv. p. var. fuscans RG04
    |    |--X. a. pv. sesbaniae RG04
    |    |--X. a. pv. vesicatoria RG04
    |    `--X. a. pv. vitians RG04
    |--X. bromi RG04
    |--X. campestris RG04
    |--X. cassavae RG04
    |--X. codiaei RG04
    |--X. cucurbitae RG04
    |--X. cynarae RG04
    |--X. fragariae RG04
    |--X. hortorum RG04
    |    |--X. h. pv. hortorum RG04
    |    `--X. h. pv. pelargonii RG04
    |--X. hyacinthi RG04
    |--X. maltophila PHK96
    |--X. melonis RG04
    |--X. oryzae RG04
    |--X. pisi RG04
    |--X. populi RG04
    |--X. sacchari RG04
    |--X. theicola RG04
    |--X. translucens RG04
    |--X. vasicola RG04
    |    |--X. v. pv. vasicola RG04
    |    `--X. v. pv. holcicola RG04
    `--X. vesicatoria RG04

Xanthomonas axonopodis pv. allii (Kadota, Uehara et al.) Roumagnac, Gagnevin et al. 2004 [=X. campestris pv. allii Kadota, Uehara et al. 2000] RG04

*Type species of generic name indicated

REFERENCES

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

Roumagnac, P., L. Gagnevin, L. Gardan, L. Sutra, C. Manceau, E. R. Dickstein, J. B. Jones, P. Rott & O. Pruvost. 2004. Polyphasic characterization of xanthomonads isolated from onion, garlic and Welsh onion (Allium spp.) and their relatedness to different Xanthomonas species. International Journal of Systematic and Evolutionary Microbiology 54: 15–24.

Ectothiorhodospiraceae

Culture of Thialkalivibrio, copyright Dimitri Yu. Sorokin.

Belongs within: Chromatibacteria.

The Ectothiorhodospiraceae are a group of phototrophic and chemotrophic bacteria that live in saline and alkaline growth conditions (Imhoff 2001).

Characters (from Imhoff 2001): Phototrophic or chemotrophic; phototrophic members depositing elemental sulphur outside their cells during oxidation of sulphide. Lamellar intracellular membrane structures present. Photosynthetic pigment (if present) bacteriochlorophyll a or b; cytochrome c type c₅₅₁; major quinones MK-8/Q-8, MK-7/Q-7 or Q-8; major fatty acid C_18:1 (60–75%).

Ectothiorhodospiraceae [Ectothiorhodaceae]
    |--+--+--Thiorhodospira sibirica H-RM03
    |  |  `--Thiorhodovibrio winogradskyi H-RM03
    |  `--+--Thiorhodococcus minor H-RM03 [=T. minus I01]
    |     `--Allochromatium H-RM03
    |          |--A. minutissimum [=Chromatium minutissimum] I01
    |          |--A. vinosum H-RM03 [=Chromatium vinosum I01]
    |          `--A. warmingii [=Chromatium warmingii] I01
    `--+--+--+--Arhodomonas aquaeolei ST03
       |  |  `--Nitrococcus mobilis ST03
       |  `--Halorhodospira ST03
       |       |--+--*H. halophila H-RM03 [=Ectothiorhodospira halophila I01]
       |       |  `--H. neutriphila Hirschler-Réa, Matheron et al. 2003 (nom. inv.) H-RM03, JC08
       |       `--+--H. abdelmalekii ST03 [=Ectothiorhodospira abdelmalekii I01]
       |          `--H. halochloris ST03 [=Ectothiorhodospira halochloris I01]
       `--+--Ectothiorhodospira ST03
          |    |--E. mobilis H-RM03
          |    `--+--+--E. shaposhnikovii H-RM03
          |       |  `--E. vacuolata H-RM03
          |       `--+--E. marismortui H-RM03
          |          `--+--E. haloalkaliphila H-RM03
          |             `--E. marina H-RM03
          `--Thialkalivibrio ST03
               |--T. denitrificans ST03
               `--+--+--T. nitratireducens Sorokin, Tourova et al. 2003 ST03
                  |  `--T. paradoxus ST03
                  `--+--+--T. jannaschii ST03
                     |  `--T. versutus ST03
                     `--+--T. nitratis ST03
                        `--T. thiocyanoxidans ST03

*Type species of generic name indicated

REFERENCES

[H-RM03] Hirschler-Réa, A., R. Matheron, C. Riffaud, S. Mouné, C. Eatock, R. A. Herbert, J. C. Willison & P. Caumette. 2003. Isolation and characterization of spirilloid purple phototrophic bacteria forming red layers in microbial mats of Mediterranean salterns: description of Halorhodospira neutriphila sp. nov. and emendation of the genus Halorhodospira. International Journal of Systematic and Evolutionary Microbiology 53: 153–163.

[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.

[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.

[ST03] Sorokin, D. Yu., T. P. Tourova, K. A. Sjollema & J. G. Kuenen. 2003. Thialkalivibrio nitratireducens sp. nov., a nitrate-reducing member of an autotrophic denitrifying consortium from a soda lake. International Journal of Systematic and Evolutionary Microbiology 53: 1779–1783.

Chromatiaceae

Colony of Thiocystis, copyright Patterson, David J.; Zettler Amaral, Linda; Edgcomb Virginia.

Belongs within: Chromatibacteria.

The Chromatiaceae are a group of anoxygenic phototrophic purple sulphur bacteria that, under the right growth conditions, deposit globules of elemental sulphur inside their cells (Imhoff 2001).

Characters (from Imhoff 2001): Photoautotrophic, anaerobic, using sulphide or elemental sulphur as an electron donor; major photosynthetic pigment bacteriochlorophyll a or b. Occasionally growing photoheterotrophically, chemoautotrophically or chemoheterotrophically. Usually possessing vesicular-type intracellular membranes; depositing globules of elemental sulphur inside cells. Flagella and/or gas vesicles may be present. Major type of cytochrome C c₅₅₁; major quinones MK-8/Q-8; major fatty acids C_16:0, C_16:1, C_18:1 (32–45%).

Chromatiaceae [Endothiorhodaceae, Thiorhodaceae]
    |--Thiospirillum jenense I01
    |--Lamprobacter modestohalophilus I01
    |--Thiopedia rosea I01
    |--Isochromatium buderi [=Chromatium buderi] I01
    |--Nitrosococcus oceanus GH01, PHK96
    |--Pfennigia GH01
    |--Rhabdochromatium marinum I01
    |--Thermochromatium tepidum [=Chromatium tepidum] I01
    |--Thiococcus pfennigii [=Thiocapsa pfennigii] I01
    |--Thiohalocapsa halophila [=Thiocapsa halophila] I01
    |--Thiolamprovum pedioforme [=Amoebobacter pedioforme] I01
    |--Lamprocystis I01
    |    |--L. purpurea (Eichler & Pfennig 1989) Imhoff 2001 JC08 [=Amoebobacter purpureus I01]
    |    `--L. roseopersicina I01
    |--Thiodictyon I01
    |    |--T. bacillosum I01
    |    `--T. elegans I01
    |--Marichromatium I01
    |    |--M. gracile [=Chromatium gracile] I01
    |    `--M. purpuratum [=Chromatium purpuratum] I01
    |--Chromatium I01
    |    |--C. okenii I01
    |    `--C. weissei I01
    |--Halochromatium I01
    |    |--H. glycolicum [=Chromatium glycolicum] I01
    |    `--H. salexigens [=Chromatium salexigens] I01
    |--Thiocapsa I01
    |    |--T. pendens [=Amoebobacter pendens] I01
    |    |--T. rosea [=Amoebobacter roseus] I01
    |    `--T. roseopersicina I01
    `--Thiocystis I01
         |--T. gelatinosa I01
         |--T. minor [=Chromatium minus] I01
         |--T. violacea I01
         `--T. violascens [=Chromatium violascens] I01

Nomen invalidum: Marichromatium marinum [=Rhodobacter marinus] I01

*Type species of generic name indicated

REFERENCES

[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.

[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.

[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.

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

Alteromonadaceae

Biofilm containing Alteromonas sp. and diatom Navicula incerta, from Rivas & Riquelme (2012).

Belongs within: Chromatibacteria.
Contains: Pseudoalteromonas.

The Alteromonadaceae are a group of marine gamma-Proteobacteria defined on phylogenetic grounds.

Characters (from Ivanova & Mikhailov 2001): Gram-negative, rod-shaped bacteria. Motile by single flagellum, sometimes sheathed, occasionally forming lateral flagella, fimbria or other sheath-like structure. Not forming endospores or microcysts; sometimes forming capsules. Requiring Na⁺-ions for growth; sometimes capable of growth in media containing 15% salts. Chemoorganotrophs; oxygen used as electron acceptor. Aerobic or facultatively anaerobic. Usually not denitrifying; arginine dehydrolase absent. Usually utilising glucose, fructose, not utilising mannose. Major isoprenoid quinone usually Q₈. Major fatty acids i15:0, 16:0, 16:1 (n-7). G+C content of DNA ranging from 35–50%.

Alteromonadaceae [Alteromonadales]
    |--+--Shewanella GH01
    |  |    |  i. s.: S. frigidimarina DH03
    |  |    |         S. violacea HH03
    |  |    |--S. algae RU03
    |  |    `--+--S. amazonensis RU03
    |  |       `--S. putrefaciens RU03
    |  `--+--Psychromonas DH03
    |     |    |--P. antarctica DH03
    |     |    `--P. kaikoi IT03
    |     `--Moritella RU03
    |          |--M. japonica DH03
    |          |--M. marina YH03
    |          `--M. yayanosii IT03
    `--+--+--+--‘Pseudoalteromonas’ bacteriolytica KI03
       |  |  `--‘Pseudoalteromonas’ sagamiensis Kobayashi, Imada et al. 2003 KI03
       |  `--+--Idiomarina KI03
       |     |    |--+--I. abyssalis DH03
       |     |    |  `--I. loihiensis Donachie, Hou et al. 2003 DH03
       |     |    `--+--I. baltica DH03
       |     |       `--I. zobellii DH03
       |     `--+--Thalassomonas viridans KI03
       |        `--Colwellia KI03
       |             |--C. demingiae IM01
       |             |--C. hadaliensis IM01
       |             |--C. hornerae KI03
       |             |--C. maris KI03
       |             |--C. psychrerythraea KI03
       |             |--C. psychrotropica IM01
       |             `--C. rossensis IM01
       `--+--Pseudoalteromonas KI03
          |--Glaciecola DH03
          |    |--G. pallidula KI03
          |    `--G. punicea KI03
          `--Alteromonas Baumann, Mandel & Allen 1972 KI03, IM01
               |--‘A. alvinellae’ KI03
               |--A. colwelliana IM01
               |--A. communis IM01
               |--A. fuliginea IM01
               |--A. hanedai IM01
               |--A. infernus IM01
               |--A. macleodii IM01
               |    |--A. m. ssp. macleodii IM01
               |    `--A. m. ssp. fijiensis IM01
               |--A. putrefaciens IM01
               `--A. vaga IM01

*Type species of generic name indicated

REFERENCES

[DH03] Donachie, S. P., S. Hou, T. S. Gregory, A. Malahoff & M. Alam. 2003. Idiomarina loihiensis sp. nov., a halophilic γ-proteobacterium from the Lo‘ihi submarine volcano, Hawai‘i. International Journal of Systematic and Evolutionary Microbiology 53: 1873–1879.

[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.

[HH03] Hugenholtz, P., & T. Huber. 2003. Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. International Journal of Systematic and Evolutionary Microbiology 53: 289–293.

[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.

[IM01] Ivanova, E. P., & V. V. Mikhaylov. 2001. A new famil, Alteromonadaceae fam. nov., including marine Proteobacteria of the genera Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia. Mikrobiologiya 70 (1): 15–23.

[KI03] Kobayashi, T., C. Imada, A. Hiraishi, H. Tsujibo, K. Miyamoto, N. Hamada & E. Watanabe. 2003. Pseudoalteromonas sagamiensis sp. nov., a marine bacterium that produces protease inhibitors. International Journal of Systematic and Evolutionary Microbiology 53: 1807–1811.

[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.

[YH03] Yumoto, I., K. Hirota, Y. Sogabe, Y. Nodasaka, Y. Yokota & T. Hoshino. 2003. Psychrobacter okhotskensis sp. nov., a lipase-producing facultative psychrophile isolated from the coast of the Okhotsk Sea. International Journal of Systematic and Evolutionary Microbiology 53: 1985–1989.