HyphomicrobiumDid we forget anything? Let us know

Genus nameHyphomicrobium
Alternative names
NCBI taxonomy ID81

Taxonomy (MiDAS 2.0)


16S gene copy number1

 In situOther
Hydrophobic cell surface214

FISH image of Hyphomicrobium in reactor sludge. Confocal laser scanning micrograph of reactor sludge triple hybridized with EUBMix (25 ng, fluorescein labelled), BET42a (25 ng, Cy5 labelled), and HYP1241 (25 ng, Cy3 labelled) probes. The yellow cell aggregates (arrow), composed of 1- to 2-micron diameter cells, comprise Hyphomicrobium cells since they are dual labelled with EUBMix (green) and HYP1241 (red) probes. - Source:7

Aerobic heterotroph
Nitrite reduction
Short-chain fatty acids
Proteins/Amino acids

POSNEGVariableNot assessed


Hyphomicrobium are aerobic, chemoorganotrophs 8 9 10 11 12. They are methylotrophic organisms that utilize one-carbon compounds e.g. methanol and methylamine 11 10 9 13 8, via the serine pathway 9 10 13. Denitrification is possible for some species 8 11. Often identified as major players in denitrification systems supplemented with methanol 16. Cells of Hyphomicrobium may be rod, coccus, or bean-shaped 9 10 13 and produce monopolar or bipolar filamentous outgrowths (hyphae or prosthecae) of varying length 17. No relevant in situ data has been determined for this genus.

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FISH probes

Hypho-1241 12


 In situOther
Aerobic Heterotroph89111315
Nitrite Reduction818
Sulfate Reduction
Short-chain Fatty Acids101213
Proteins/Amino Acids815

Abundance Information

 10 % percentileMedian90 % percentile
Activated Sludge0.71.12.1

Predominant InActivated sludge


[1] Tatusova, Ciufo, Fedorov, O'Neill, Tolstoy (2014): RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res. 42 (Database issue): D553-9. doi:10.1093/nar/gkt1274

[2] Guo, Zhang, Yu, Wei (2011): Variations of both bacterial community and extracellular polymers: the inducements of increase of cell hydrophobicity from biofloc to aerobic granule sludge. Bioresour. Technol. 102 (11): 6421-8. doi:10.1016/j.biortech.2011.03.046

[3] - NCBI genome database, NCBI id 81 -

[4] Venkatramanan, Prakash, Woyke, Chain, Goodwin, Watson, et al. (2013): Genome sequences for three denitrifying bacterial strains isolated from a uranium- and nitrate-contaminated subsurface environment. Genome Announc 1 (4): . doi:10.1128/genomeA.00449-13

[5] Martineau, Villeneuve, Mauffrey, Villemur (2014): Complete Genome Sequence of Hyphomicrobium nitrativorans Strain NL23, a Denitrifying Bacterium Isolated from Biofilm of a Methanol-Fed Denitrification System Treating Seawater at the Montreal Biodome. Genome Announc 2 (1): . doi:10.1128/genomeA.01165-13

[6] Badger, Hoover, Brun, Weiner, Laub, Alexandre, et al. (2006): Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus. J. Bacteriol. 188 (19): 6841-50. doi:10.1128/JB.00111-06

[7] Ginige, Hugenholtz, Daims, Wagner, Keller, Blackall, et al. (2004): Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Appl. Environ. Microbiol. 70 (1): 588-96.

[8] Oren, A., and Xu, X-W. (2014) The family Hyphomicrobiaceae. In: Rosenberg, E., De Long, E.F., Lory, S., Stackebrandt, E and Thompson, F. The Prokaryotes: Alphaproteobacteria and Beta-proteobacteria. Pp 247-281. Springer, Berlin, Heidelberg. - Oren Et Al 2014 -

[9] McDonald, Doronina, Trotsenko, McAnulla, Murrell (2001): Hyphomicrobium chloromethanicum sp. nov. and Methylobacterium chloromethanicum sp. nov., chloromethane-utilizing bacteria isolated from a polluted environment. Int. J. Syst. Evol. Microbiol. 51 (Pt 1): 119-22. doi:10.1099/00207713-51-1-119

[10] Urakami, T., Sasaki, J., Suzuki, K-I., and Komagata, K. (1995) Characterization and description of Hyphomicrobium denitrificans sp. nov. Int. J. Syst. Bacteriol. 45(3): 528-532. - Urakami Et Al 1995 -

[11] Martineau, Villeneuve, Mauffrey, Villemur (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 (Pt 10): 3777-81. doi:10.1099/ijs.0.048124-0

[12] Layton, Karanth, Lajoie, Meyers, Gregory, Stapleton, et al. (2000): Quantification of Hyphomicrobium populations in activated sludge from an industrial wastewater treatment system as determined by 16S rRNA analysis. Appl. Environ. Microbiol. 66 (3): 1167-74.

[13] Borodina, Kelly, Schumann, Rainey, Ward-Rainey, Wood, et al. (2002): 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. 177 (2): 173-83. doi:10.1007/s00203-001-0373-3

[14] Marshall, Cruickshank (1973): Cell surface hydrophobicity and the orientation of certain bacteria at interfaces. Arch Mikrobiol 91 (1): 29-40.

[15] LEIFSON (1964): HYPHOMICROBIUM NEPTUNIUM SP. N. Antonie Van Leeuwenhoek 30 (): 249-56.

[16] Baytshtok, Lu, Park, Kim, Yu, Chandran, et al. (2009): Impact of varying electron donors on the molecular microbial ecology and biokinetics of methylotrophic denitrifying bacteria. Biotechnol. Bioeng. 102 (6): 1527-36. doi:10.1002/bit.22213

[17] - -

[18] Martineau, Mauffrey, Villemur (2015): Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii. Appl. Environ. Microbiol. 81 (15): 5003-14. doi:10.1128/AEM.00848-15

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