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Genus Hyphomicrobium

Warning: In the List of Prokaryotic names with Standing in Nomenclature, an arrow () only indicates the sequence of valid publication of names and does not mean that the last name in the sequence must be used (see: Introduction).

Number of species cited in this file: 13
Number of subspecies cited in this file: 3

Classification (Warning: see also the file "Classification of prokaryotes: Introduction").


For a detailed description of this taxon see Bergey’s Manual of Systematics of Archaea and Bacteria (BMSAB).


 

Hyphomicrobium Stutzer and Hartleb 1899, genus. (Type genus of the order ¤ Hyphomicrobiales Douglas 1957 [Approved Lists 1980]; type genus of the family ¤ Hyphomicrobiaceae Babudieri 1950 [Approved Lists 1980]).
Type species: ¤ Hyphomicrobium vulgare Stutzer and Hartleb 1899 (Approved Lists 1980).
Etymology: Gr. n. huphê, a web, thread; Gr. adj. mikros, small; Gr. masc. n. bios, life; N.L. neut. n. Hyphomicrobium, thread-producing microbe.
Approved Lists reference: SKERMAN (V.B.D.), McGOWAN (V.) and SNEATH (P.H.A.) (editors): Approved Lists of Bacterial Names. Int. J. Syst. Bacteriol., 1980, 30, 225-420 (Approved Lists of Bacterial Names in IJSEM Online - Approved Lists of Bacterial Names Amended edition).
Original publication: STUTZER (A.) and HARTLEB (R.): Untersuchungen über die bei der Bildung von Salpeter beobachteten Mikroorganismen. Mitteilungen des Landwirtschaftlichen Institutes der Kaiserlichen Universitat Breslau, 1899, 1, 75-100.

Note: According to P. Hirsch, the first description of Hyphomicrobium vulgare was published in 1898 (not in 1899).
References:
1 HIRSCH (P.): Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL In: J.T. STALEY, M.P. BRYANT, N. PFENNIG and J.G. HOLT (editors), Bergey's Manual of Systematic Bacteriology, first edition, vol. 3, The Williams & Wilkins Co., Baltimore, 1989, pp. 1895-1904.
2 HIRSCH (P.): Personal communication (December 13, 2004).

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Hyphomicrobium aestuarii Hirsch 1989, sp. nov.
Type strain: (see also StrainInfo.net) ATCC 27483= IFAM NQ-521Gr = NCIMB 11052.
Sequence accession no. (16S rRNA gene) for the type strain: not found.
Etymology: L. n. aestuarium, channel extending inland from the sea, and only filled with water at floodtide, an estuary; L. gen. n. aestuarii, of the estuary.
Valid publication: Validation List no. 31. Int. J. Syst. Bacteriol., 1989, 39, 495-497.
Effective publication: HIRSCH (P.): Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In: J.T. STALEY, M.P. BRYANT, N. PFENNIG and J.G. HOLT (editors), Bergey's Manual of Systematic Bacteriology, first edition, vol. 3, The Williams & Wilkins Co., Baltimore, 1989, pp. 1895-1904.
Validation List no. 31 in IJSEM Online

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Hyphomicrobium chloromethanicum McDonald et al. 2001, sp. nov.
Type strain: (see also StrainInfo.net) CM2 = NCIMB 13687 = VKM B-2176.
Sequence accession no. (16S rRNA gene) for the type strain: AF198623.
Etymology: Gr. adj. chlôros, green; N.L. pref. chloro, referring to the chlorine radical; N.L. n. methanum, methane: L. masc. suff. -icus, suffix used with the sense of pertaining to; N.L. adj. methanicus, pertaining to methane, intended to mean methane (utilizing); N.L. neut. n. chloromethanicum, chloromethane (utilizing).
Valid publication: McDONALD (I.R.), DORONINA (N.V.), TROTSENKO (Y.A.), McANULLA (C.) and MURRELL (J.C.): Hyphomicrobium chloromethanicum sp. nov. and Methylobacterium chloromethanicum sp. nov., chloromethane-utilizing bacteria isolated from a polluted environment. Int. J. Syst. Evol. Microbiol., 2001, 51, 119-122.
Original article in IJSEM Online

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Hyphomicrobium coagulans (ex Takada 1975) Hirsch 1989, sp. nov., nom. rev.
Type strain: (see also StrainInfo.net) Takada 10-2.
Sequence accession no. (16S rRNA gene) for the type strain: not found.
Synonym: "Hyphomicrobium coagulans" Takada 1975.
Etymology: L. part. adj. coagulans, curdling, coagulating.
Valid publication: Validation List no. 31. Int. J. Syst. Bacteriol., 1989, 39, 495-497.
Effective publication: HIRSCH (P.): Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In: J.T. STALEY, M.P. BRYANT, N. PFENNIG and J.G. HOLT (editors), Bergey's Manual of Systematic Bacteriology, first edition, vol. 3, The Williams & Wilkins Co., Baltimore, 1989, pp. 1895-1904.
Validation List no. 31 in IJSEM Online

Note: The type strain is currently not available from a recognized culture collection.
Reference: YARZA (P.), SPRÖER (C.), SWIDERSKI (J.), MROTZEK (N.), SPRING (S.), TINDALL (B.J.), GRONOW (S.), PUKALL (R.), KLENK (H.P.), LANG (E.), VERBARG (S.), CROUCH (A.), LILBURN (T.), BECK (B.), UNOSSON (C.), CARDEW (S.), MOORE (E.R.B.), GOMILA (M.), NAKAGAWA (Y.), JANSSENS (D.), DE VOS (P.), PEIREN (J.), SUTTELS (T.), CLERMONT (D.), BIZET (C.), SAKAMOTO (M.), IIDA (T.), KUDO (T.), KOSAKO (Y.), OSHIDA (Y.), OHKUMA (M.), ARAHAL (D.R.), SPIECK (E.), POMMERENING ROESER (A.), FIGGE (M.), PARK (D.), BUCHANAN (P.), CIFUENTES (A.), MUNOZ (R.), EUZEBY (J.P.), SCHLEIFER (K.H.), LUDWIG (W.), AMANN (R.), GLÖCKNER (F.O.) and RÓSSELLO-MÓRA (R.): Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names. Syst. Appl. Microbiol., 2013, 36, 69-73.
Publication online

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Hyphomicrobium denitrificans Urakami et al. 1995, sp. nov.
Type strain: (see also StrainInfo.net) TK 0415 = Attwood and Harder strain X = ATCC 51888= DSM 1869 = NCIB (now NCIMB) 11706.
Sequence accession no. (16S rRNA gene) for the type strain: CP002083 (complete genome).
Etymology: N.L. part. adj. denitrificans, denitrifying.
Valid publication: URAKAMI (T.), SASAKI (J.), SUZUKI (K.I.) and KOMAGATA (K.): Characterization and description of Hyphomicrobium denitrificans sp. nov. Int. J. Syst. Bacteriol., 1995, 45, 528-532.
Original article in IJSEM Online

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Hyphomicrobium facile corrig. Hirsch 1989, sp. nov.
Type strain: (see also StrainInfo.net) ATCC 27485= DSM 1565 = IFAM H-526.
Sequence accession no. (16S rRNA gene) for the type strain: Y14309.
Etymology: L. neut. adj. facile, ready, quick.
Valid publication: Validation List no. 31. Int. J. Syst. Bacteriol., 1989, 39, 495-497.
Effective publication: HIRSCH (P.): Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In: J.T. STALEY, M.P. BRYANT, N. PFENNIG and J.G. HOLT (editors), Bergey's manual of systematic bacteriology, first edition, vol. 3, The Williams & Wilkins Co., Baltimore, 1989, pp. 1895-1904.
Validation List no. 31 in IJSEM Online

Notes:
1 The original spelling of the specific epithet, facilis (sic), has been corrected by Euzéby 1998.
Reference: EUZÉBY (J.P.): Taxonomic note: necessary correction of specific and subspecific epithets according to Rules 12c and 13b of the International Code of Nomenclature of Bacteria (1990 Revision). Int. J. Syst. Bacteriol., 1998, 48, 1073-1075.
Original article in IJSEM Online
2 Subsequently, this species has been divided into subspecies (see: below).

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Hyphomicrobium facile subsp. facile corrig. Hirsch 1989, subsp. nov.
Type strain: (see also StrainInfo.net) ATCC 27485= DSM 1565 = IFAM H-526.
Sequence accession no. (16S rRNA gene) for the type strain: Y14309.
Etymology: L. neut. adj. facile, ready, quick.
Valid publication: HOWEY (R.T.), LOCK (C.M.) and MOORE (L.V.H.): Subspecies names automatically created by Rule 46. Int. J. Syst. Bacteriol., 1990, 40, 317-319.
Original article in IJSEM Online

Notes:
1 The subspecies name Hyphomicrobium facile subsp. facile corrig. Hirsch 1989 is automatically created by the valid publication of Hyphomicrobium facile subsp. tolerans corrig. Hirsch 1989 and the valid publication of Hyphomicrobium facile subsp. ureaphilum corrig. Hirsch 1989 [Rule 40d (formerly Rule 46)].
2 The original spelling Hyphomicrobium facilis subsp. facilis (sic), has been corrected by Euzéby 1998.
Reference: EUZÉBY (J.P.): Taxonomic note: necessary correction of specific and subspecific epithets according to Rules 12c and 13b of the International Code of Nomenclature of Bacteria (1990 Revision). Int. J. Syst. Bacteriol., 1998, 48, 1073-1075.
Original article in IJSEM Online

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Hyphomicrobium facile subsp. tolerans corrig. Hirsch 1989, subsp. nov.
Type strain: (see also StrainInfo.net) ATCC 27489= IFAM I-551.
Sequence accession no. (16S rRNA gene) for the type strain: Y14311.
Etymology: L. part. adj. tolerans, tolerating; pertaining to the tolerance of high CO concentrations.
Valid publication: Validation List no. 31. Int. J. Syst. Bacteriol., 1989, 39, 495-497.
Effective publication: HIRSCH (P.): Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In: J.T. STALEY, M.P. BRYANT, N. PFENNIG and J.G. HOLT (editors), Bergey's Manual of Systematic Bacteriology, first edition, vol. 3, The Williams & Wilkins Co., Baltimore, 1989, pp. 1895-1904.
Validation List no. 31 in IJSEM Online

Note: The original spelling Hyphomicrobium facilis subsp. tolerans (sic), has been corrected by Euzéby 1998.
Reference: EUZÉBY (J.P.): Taxonomic note: necessary correction of specific and subspecific epithets according to Rules 12c and 13b of the International Code of Nomenclature of Bacteria (1990 Revision). Int. J. Syst. Bacteriol., 1998, 48, 1073-1075.
Original article in IJSEM Online

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Hyphomicrobium facile subsp. ureaphilum corrig. Hirsch 1989, subsp. nov.
Type strain: (see also StrainInfo.net) ATCC 27492= IFAM CO-582.
Sequence accession no. (16S rRNA gene) for the type strain: Y14310.
Etymology: N.L. n. urea, urea; N.L. adj. philus -a -um (from Gr. adj. philos -ê -on), friend, loving; N.L. neut. adj. ureaphilum, loving urea.
Valid publication: Validation List no. 31. Int. J. Syst. Bacteriol., 1989, 39, 495-497.
Effective publication: HIRSCH (P.): Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In: J.T. STALEY, M.P. BRYANT, N. PFENNIG and J.G. HOLT (editors), Bergey's Manual of Systematic Bacteriology, first edition, vol. 3, The Williams & Wilkins Co., Baltimore, 1989, pp. 1895-1904.
Validation List no. 31 in IJSEM Online

Note: The original spelling Hyphomicrobium facilis subsp. ureaphilum (sic), has been corrected by Euzéby 1998.
Reference: EUZÉBY (J.P.): Taxonomic note: necessary correction of specific and subspecific epithets according to Rules 12c and 13b of the International Code of Nomenclature of Bacteria (1990 Revision). Int. J. Syst. Bacteriol., 1998, 48, 1073-1075.
Original article in IJSEM Online

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Hyphomicrobium hollandicum Hirsch 1989, sp. nov.
Type strain: (see also StrainInfo.net) ATCC 27498= IFAM KB-677.
Sequence accession no. (16S rRNA gene) for the type strain: Y14303.
Etymology: N.L. neut. adj. hollandicum, pertaining to Holland, referring to the isolation from the Netherlands.
Valid publication: Validation List no. 31. Int. J. Syst. Bacteriol., 1989, 39, 495-497.
Effective publication: HIRSCH (P.): Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In: J.T. STALEY, M.P. BRYANT, N. PFENNIG and J.G. HOLT (editors), Bergey's Manual of Systematic Bacteriology, first edition, vol. 3, The Williams & Wilkins Co., Baltimore, 1989, pp. 1895-1904.
Validation List no. 31 in IJSEM Online

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Hyphomicrobium indicum Johnson and Weisrock 1969, species.
Type strain: (see also StrainInfo.net) ATCC 19614= DSM 5151 = IFO (now NBRC) 14233.
Sequence accession no. (16S rRNA gene) for the type strain: AB016982.
Synonym: "Hyphomicrobium indium" (sic) Johnson and Weisrock 1966.
Etymology: L. neut. adj. indicum, of India, Indian (isolated from the Indian Ocean).
Approved Lists reference: SKERMAN (V.B.D.), McGOWAN (V.) and SNEATH (P.H.A.) (editors): Approved Lists of Bacterial Names. Int. J. Syst. Bacteriol., 1980, 30, 225-420 (Approved Lists of Bacterial Names in IJSEM Online - Approved Lists of Bacterial Names Amended edition).
Original publication: JOHNSON (R.M.) and WEISROCK (W.P.): Hyphomicrobium indicum sp. nov. (Hyphomicrobiaceae Douglas). International Journal of Systematic Bacteriology, 1969, 19, 295-307.

¤ Photobacterium indicum (Johnson and Weisrock 1969) Ivanova et al. 2004, comb. nov.

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Hyphomicrobium methylovorum Izumi et al. 1983, sp. nov.
Type strain: (see also StrainInfo.net) KM 146 = ATCC 35216= DSM 5458 = IFO (now NBRC) 14180 = JCM 6890.
Sequence accession no. (16S rRNA gene) for the type strain: Y14307.
Etymology: N.L. n. methylum (from French méthyle, back-formation from French méthylène, coined from Gr. n. methu, wine and Gr. n. hulê, wood), the methyl radical; N.L. pref. methylo-, pertaining to the methyl radical; N.L. pref. methylo-, pertaining to the methyl radical;  L. v. voro, to eat, devour; N.L. neut. adj. methylovorum, methyl devouring.
Valid publication: Validation List no. 10. Int. J. Syst. Bacteriol., 1983, 33, 438-440.
Effective publication: IZUMI (Y.), TAKIZAWA (M.), TANI (Y.) and YAMADA (H.): An obligate methylotrophic Hyphomicrobium strain, identification, growth characteristics and cell composition. J. Ferm. Technol., 1982, 60, 371-375.
Validation List no. 10 in IJSEM Online

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Hyphomicrobium neptunium Leifson 1964, species.
Type strain: (see also StrainInfo.net) LE670 = ATCC 15444= DSM 5154 = IFAM LE670 = IFO (now NBRC) 14232.
Sequence accession no. (16S rRNA gene) for the type strain: CP000158.
Etymology: L. neut. adj. neptunium, of Neptunus, pertaining to Neptunus, god of the sea.
Approved Lists reference: SKERMAN (V.B.D.), McGOWAN (V.) and SNEATH (P.H.A.) (editors): Approved Lists of Bacterial Names. Int. J. Syst. Bacteriol., 1980, 30, 225-420 (Approved Lists of Bacterial Names in IJSEM Online - Approved Lists of Bacterial Names Amended edition).
Original publication: LEIFSON (E.): Hyphomicrobium neptunium sp. n. Antonie van Leeuwenhoek Journal of Microbiology and Serology, 1964, 30, 249-256.

¤ Hyphomonas neptunium (Leifson 1964) Moore et al. 1984, comb. nov.

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Hyphomicrobium nitrativorans Martineau et al. 2013, sp. nov.
Type strain: (see also StrainInfo.net) NL23=ATCC BAA-2476=LMG 27277.
Sequence accession no. (16S rRNA) for the type strain: JX131369.
Etymology: N.L. n. nitras -atis, nitrate; L. part. adj. vorans, devouring, consuming; N.L. part adj. nitrativorans, nitrate-consuming.
Source: Industrial.
Valid publication: MARTINEAU, C., VILLENEUVE, C., MAUFFREY, F. and VILLEMUR, R. 2013. Hyphomicrobium nitrativorans sp. nov., isolated from the biofilm of a methanol-fed denitrification system treating seawater at the Montreal Biodome. Int. J. Syst. Evol. Microbiol., 63, 3777-3781.
Original article in IJSEM Online

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Hyphomicrobium sulfonivorans Borodina et al. 2002, sp. nov.
Type strain: (see also StrainInfo.net) S1 = ATCC BAA-113 = DSM 13863.
Sequence accession no. (16S rRNA gene) for the type strain: AF235089.
Etymology: N.L. n. sulfonum, sulfone; L. part. adj. vorans, eating, devouring; N.L. part. adj. sulfonivorans, sulfone-devouring.
Valid publication: Validation List no. 85. Int. J. Syst. Evol. Microbiol., 2002, 52, 685-690.
Effective publication: BORODINA (E.), KELLY (D.P.), SCHUMANN (P.), RAINEY (F.A.), WARD-RAINEY (N.L.) and WOOD (A.P.): Enzymes of dimethylsulfone metabolism and the phylogenetic characterization of the facultative methylotrophs Arthrobacter sulfonivorans sp. nov., Arthrobacter methylotrophus sp. nov., and Hyphomicrobium sulfonivorans sp. nov. Arch. Microbiol., 2002, 177, 173-183.
Validation List no. 85 in IJSEM Online - Effective publication Online

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Hyphomicrobium vulgare Stutzer and Hartleb 1899, species. (Type species of the genus.)
Type strain: (see also StrainInfo.net) ATCC 33404= JCM 6889 = NCIB 9698.
Sequence accession no. (16S rRNA gene) for the type strain: AB543807.
Etymology: L. neut. adj. vulgare, usual, common.
Approved Lists reference: SKERMAN (V.B.D.), McGOWAN (V.) and SNEATH (P.H.A.) (editors): Approved Lists of Bacterial Names. Int. J. Syst. Bacteriol., 1980, 30, 225-420 (Approved Lists of Bacterial Names in IJSEM Online - Approved Lists of Bacterial Names Amended edition).
Original publication: STUTZER (A.) and HARTLEB (R.): Untersuchungen über die bei der Bildung von Salpeter beobachteten Mikroorganismen. Mitteilungen des Landwirtschaftlichen Institutes der Kaiserlichen Universitat Breslau, 1899, 1, 75-100.

Notes:
1 According to P. Hirsch, the first description of Hyphomicrobium vulgare was published in 1898 (not in 1899).
References:
1 HIRSCH (P.): Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL In: J.T. STALEY, M.P. BRYANT, N. PFENNIG and J.G. HOLT (editors), Bergey's Manual of Systematic Bacteriology, first edition, vol. 3, The Williams & Wilkins Co., Baltimore, 1989, pp. 1895-1904.
2 HIRSCH (P.): Personal communication (December 13, 2004).
2 In the Approved Lists, the type strain is incorrectly designated as NCIB 8698.
3 In the Bergey's Manual of Systematic Bacteriology (first edition), P. Hirsch wrote "the original type strain no longer exists; a neotype culture is being proposed: IFAM MC-750 (ATCC 27500". However, this proposal was never published in the IJSB or in the IJSEM (see Rule 18c). Moreover, the strain NCIB 9698 = ATCC 33404= JCM 6889 is available from culture collections.
Reference: HIRSCH (P.): Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In: J.T. STALEY, M.P. BRYANT, N. PFENNIG and J.G. HOLT (editors), Bergey's Manual of Systematic Bacteriology, first edition, vol. 3, The Williams & Wilkins Co., Baltimore, 1989, pp. 1895-1904.

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Hyphomicrobium zavarzinii Hirsch 1989, sp. nov.
Type strain: (see also StrainInfo.net) ATCC 27496= IFAM ZV-622 = VKM B-2174.
Sequence accession no. (16S rRNA gene) for the type strain: Y14305.
Etymology: N.L. gen. n. zavarzinii, of Zavarzin, named for G.A. Zavarzin, the Russian microbiologist who isolated these bacteria.
Valid publication: Validation List no. 31. Int. J. Syst. Bacteriol., 1989, 39, 495-497.
Effective publication: HIRSCH (P.): Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In: J.T. STALEY, M.P. BRYANT, N. PFENNIG and J.G. HOLT (editors), Bergey's Manual of Systematic Bacteriology, first edition, vol. 3, The Williams & Wilkins Co., Baltimore, 1989, pp. 1895-1904.
Validation List no. 31 in IJSEM Online

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