Desulfitobacterium hafniense explained

Desulfitobacterium hafniense is a species of gram positive bacteria, its type strain is DCB-2T.[1] (NCBI taxonomy ID 272564; DSM 10664).

D. hafniense are anaerobic spore-forming bacteria. The majority of the described isolates are facultatively organohalide respiring bacteria capable of reductive dechlorination of organohalides such as chlorophenols, and tetrachloroethene. The cells of D. hafniense are rod-shaped and 3.3 to 6 μm long by 0.6 to 0.7 μm wide, they are motile, each cell having one or two terminal flagella. All tested strains are resistant to the antibiotic vancomycin.[2] [3]

Over the years several additional strains belonging to the hafniense species has been described from a diverse range of environments. Strains PCP-1, TCE1, DP7, TCP-A and G2 were originally published as members of a separate species Frappieri, but all are today considered as belonging to the hafniense species.[4] [5]

D. hafniense isolates!Strain!Source!DSM
DCB-2TSewage sludge 10664
PCP-1[6] Sewage sludge12420
TCP-A[7] River sediment13557
GBFHRiver sediment---|-|Y51[8] |Polluted soil|---|-|TCE1[9] |Polluted soil|---
PCE-S[10] Polluted soil14645
G2[11] Subsurface16228
DP7[12] Human feces13498
LBE[13] not described---|}

Genomes

The genome of D. hafniense contains the machinery for both pyrrolysine and selenocysteine, making it the only known organism that potentially utilizes 22 amino acids in protein translation. [14] Desulfitobacterium hafniense strain DCB-2T has a single circular genome that contains 5.78 Mbp encoding 5,045 genes. The genome of Desulfitobacterium hafniense strain DCB-2T harbors seven genes encoding reductive dehalogenases, five of these seems to be functional and two are disrupted by mutations.[15]

Full genome sequence information is available for nine desulfitobacterium hafniense strains. They all have genome sizes ranging from 5 to 5,7 Mbp, none of the sequenced strains contains any plasmids. The genomes encodes only limited numbers of reductive dehalogenases, in addition to genes for utilizing a wide range of electron donors and acceptors.

!Strain!Genome size (Mbp)!Number of reductivedehalogenases!Genome described
Y515,712006[16]
DCB-2T5,372012
PCE-S5,722015[17]
DH5,402016[18]
TCE15,712017[19]
PCP-15,672017
LBE5,522017
DP75,202017
TCP-A552017

Further reading

  • Villemur R, Lanthier M, Beaudet R, Lépine F . The Desulfitobacterium genus . FEMS Microbiology Reviews . 30 . 5 . 706–33 . September 2006 . 16911041 . 10.1111/j.1574-6976.2006.00029.x . free .
  • Nonaka H, Keresztes G, Shinoda Y, Ikenaga Y, Abe M, Naito K, Inatomi K, Furukawa K, Inui M, Yukawa H . Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195 . Journal of Bacteriology . 188 . 6 . 2262–74 . March 2006 . 16513756 . 1428132 . 10.1128/JB.188.6.2262-2274.2006 . etal .
  • Kim SH, Harzman C, Davis JK, Hutcheson R, Broderick JB, Marsh TL, Tiedje JM . Joan B. Broderick. Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction . BMC Microbiology . 12 . 1 . 21 . February 2012 . 22316246 . 3306737 . 10.1186/1471-2180-12-21 . free.
  • Lanthier M, Juteau P, Lépine F, Beaudet R, Villemur R . Desulfitobacterium hafniense is present in a high proportion within the biofilms of a high-performance pentachlorophenol-degrading, methanogenic fixed-film reactor . Applied and Environmental Microbiology . 71 . 2 . 1058–65 . February 2005 . 15691966 . 546785 . 10.1128/AEM.71.2.1058-1065.2005 .
  • Villemur R . The pentachlorophenol-dehalogenating Desulfitobacterium hafniense strain PCP-1 . Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences . 368 . 1616 . 20120319 . April 2013 . 23479749 . 3638460 . 10.1098/rstb.2012.0319 .

External links

Notes and References

  1. Christiansen N, Ahring BK . 1996. Desulfitobacterium hafniense sp. nov., an Anaerobic, Reductively Dechlorinating Bacterium. International Journal of Systematic Bacteriology. 46. 2. 442–448. 10.1099/00207713-46-2-442 . free.
  2. Kalan L, Ebert S, Kelly T, Wright GD . Noncanonical vancomycin resistance cluster from Desulfitobacterium hafniense Y51 . Antimicrobial Agents and Chemotherapy . 53 . 7 . 2841–5 . July 2009 . 19414574 . 2704641 . 10.1128/AAC.01408-08 .
  3. Kruse T, Levisson M, de Vos WM, Smidt H . vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense . Microbial Biotechnology . 7 . 5 . 456–66 . September 2014 . 25042042 . 4229326 . 10.1111/1751-7915.12139 .
  4. Niggemyer A, Spring S, Stackebrandt E, Rosenzweig RF . Isolation and characterization of a novel As(V)-reducing bacterium: implications for arsenic mobilization and the genus Desulfitobacterium . Applied and Environmental Microbiology . 67 . 12 . 5568–80 . December 2001 . 11722908 . 93345 . 10.1128/AEM.67.12.5568-5580.2001 .
  5. Villemur R, Lanthier M, Beaudet R, Lépine F . The Desulfitobacterium genus . FEMS Microbiology Reviews . 30 . 5 . 706–33 . September 2006 . 16911041 . 10.1111/j.1574-6976.2006.00029.x . free .
  6. Bouchard B, Beaudet R, Villemur R, McSween G, Lépine F, Bisaillon JG . Isolation and characterization of Desulfitobacterium frappieri sp. nov., an anaerobic bacterium which reductively dechlorinates pentachlorophenol to 3-chlorophenol . International Journal of Systematic Bacteriology . 46 . 4 . 1010–5 . October 1996 . 8863430 . 10.1099/00207713-46-4-1010 . free .
  7. Breitenstein A, Saano A, Salkinoja-Salonen M, Andreesen JR, Lechner U . Analysis of a 2,4,6-trichlorophenol-dehalogenating enrichment culture and isolation of the dehalogenating member Desulfitobacterium frappieri strain TCP-A . Archives of Microbiology . 175 . 2 . 133–42 . February 2001 . 11285741 . 10.1007/s002030000248. 25261490 .
  8. Suyama A, Iwakiri R, Kai K, Tokunaga T, Sera N, Furukawa K . Isolation and characterization of Desulfitobacterium sp. strain Y51 capable of efficient dehalogenation of tetrachloroethene and polychloroethanes . Bioscience, Biotechnology, and Biochemistry . 65 . 7 . 1474–81 . July 2001 . 11515528 . 10.1271/bbb.65.1474 . 11762181 . free .
  9. Gerritse J, Drzyzga O, Kloetstra G, Keijmel M, Wiersum LP, Hutson R, Collins MD, Gottschal JC . Influence of different electron donors and acceptors on dehalorespiration of tetrachloroethene by Desulfitobacterium frappieri TCE1 . Applied and Environmental Microbiology . 65 . 12 . 5212–21 . December 1999 . 10.1128/AEM.65.12.5212-5221.1999 . 10583967 . 91707 .
  10. Miller E, Wohlfarth G, Diekert G . Comparative studies on tetrachloroethene reductive dechlorination mediated by Desulfitobacterium sp. strain PCE-S . Archives of Microbiology . 168 . 6 . 513–9 . December 1997 . 9385143 . 10.1007/s002030050529. 11883954 .
  11. Shelobolina ES, VanPraagh CG, Lovley DR . March 2003 . Use of Ferric and Ferrous Iron Containing Minerals for Respiration by Desulfitobacterium frappieri . Geomicrobiology Journal. en. 20. 2. 143–156. 10.1080/01490450303884 . 93574898 .
  12. van de Pas BA, Harmsen HJ, Raangs GC, de Vos WM, Schraa G, Stams AJ . A Desulfitobacterium strain isolated from human feces that does not dechlorinate chloroethenes or chlorophenols . Archives of Microbiology . 175 . 6 . 389–94 . June 2001 . 11491079 . 10.1007/s002030100276. 35998991 .
  13. Comensoli L, Maillard J, Albini M, Sandoz F, Junier P, Joseph E . Use of Bacteria To Stabilize Archaeological Iron . Applied and Environmental Microbiology . 83 . 9 . May 2017 . 28283522 . 5394308 . 10.1128/AEM.03478-16 .
  14. Herring, S.; Ambrogelly, A.; Polycarpo, C. R.; Soll, D. Recognition of Pyrrolysine TRNA by the Desulfitobacterium Hafniense Pyrrolysyl-TRNA Synthetase. Nucleic Acids Research 2007, 35 (4), 1270–1278. https://doi.org/10.1093/nar/gkl1151.
  15. Kim SH, Harzman C, Davis JK, Hutcheson R, Broderick JB, Marsh TL, Tiedje JM . Joan B. Broderick. Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction . BMC Microbiology . 12 . 21 . February 2012 . 22316246 . 3306737 . 10.1186/1471-2180-12-21 . free .
  16. Nonaka H, Keresztes G, Shinoda Y, Ikenaga Y, Abe M, Naito K, Inatomi K, Furukawa K, Inui M, Yukawa H . Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195 . Journal of Bacteriology . 188 . 6 . 2262–74 . March 2006 . 16513756 . 1428132 . 10.1128/JB.188.6.2262-2274.2006 .
  17. Goris T, Hornung B, Kruse T, Reinhold A, Westermann M, Schaap PJ, Smidt H, Diekert G . Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S . Standards in Genomic Sciences . 10 . 15 . 2015 . 26203328 . 4511579 . 10.1186/1944-3277-10-15 . free .
  18. Zhang X, Li GX, Chen SC, Jia XY, Wu K, Cao CL, Bao P . Draft Genome Sequence of Desulfitobacterium hafniense Strain DH, a Sulfate-Reducing Bacterium Isolated from Paddy Soils . Genome Announcements . 4 . 1 . February 2016 . 26868389 . 4751313 . 10.1128/genomeA.01693-15 .
  19. Kruse T, Goris T, Maillard J, Woyke T, Lechner U, de Vos W, Smidt H . Comparative genomics of the genus Desulfitobacterium . FEMS Microbiology Ecology . 93 . 12 . December 2017 . 29040502 . 10.1093/femsec/fix135 . free .

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