Desulfitobacterium hafniense

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

Desulfitobacterium hafniense
Scientific classification
Domain:
Bacteria
Phylum:
Bacillota
Class:
Clostridia
Order:
Clostridiales
Family:
Peptococcaceae
Genus:
Desulfitobacterium
Species:
D. hafniense
Binomial name
Desulfitobacterium hafniense
Christiansen and Ahring 1996

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-2T[1] Sewage sludge 10664
PCP-1[6] Sewage sludge 12420
TCP-A[7] River sediment 13557
GBFH[4] River sediment ---
Y51[8] Polluted soil ---
TCE1[9] Polluted soil ---
PCE-S[10] Polluted soil 14645
G2[11] Subsurface 16228
DP7[12] Human feces 13498
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 reductive

dehalogenases

 Genome described
Y51 5,7 1 2006[16]
DCB-2T 5,3 7 2012[15]
PCE-S 5,7 2 2015[17]
DH 5,4 0 2016[18]
TCE1 5,7 1 2017[19]
PCP-1 5,6 7 2017[19]
LBE 5,5 2 2017[19]
DP7 5,2 0 2017[19]
TCP-A 5 5 2017[19]


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. doi:10.1099/00207713-46-2-442.
  2. Kalan L, Ebert S, Kelly T, Wright GD (July 2009). "Noncanonical vancomycin resistance cluster from Desulfitobacterium hafniense Y51". Antimicrobial Agents and Chemotherapy. 53 (7): 2841–5. doi:10.1128/AAC.01408-08. PMC 2704641. PMID 19414574.
  3. Kruse T, Levisson M, de Vos WM, Smidt H (September 2014). "vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense". Microbial Biotechnology. 7 (5): 456–66. doi:10.1111/1751-7915.12139. PMC 4229326. PMID 25042042.
  4. Niggemyer A, Spring S, Stackebrandt E, Rosenzweig RF (December 2001). "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. doi:10.1128/AEM.67.12.5568-5580.2001. PMC 93345. PMID 11722908.
  5. Villemur R, Lanthier M, Beaudet R, Lépine F (September 2006). "The Desulfitobacterium genus". FEMS Microbiology Reviews. 30 (5): 706–33. doi:10.1111/j.1574-6976.2006.00029.x. PMID 16911041.
  6. Bouchard B, Beaudet R, Villemur R, McSween G, Lépine F, Bisaillon JG (October 1996). "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. doi:10.1099/00207713-46-4-1010. PMID 8863430.
  7. Breitenstein A, Saano A, Salkinoja-Salonen M, Andreesen JR, Lechner U (February 2001). "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. doi:10.1007/s002030000248. PMID 11285741. S2CID 25261490.
  8. Suyama A, Iwakiri R, Kai K, Tokunaga T, Sera N, Furukawa K (July 2001). "Isolation and characterization of Desulfitobacterium sp. strain Y51 capable of efficient dehalogenation of tetrachloroethene and polychloroethanes". Bioscience, Biotechnology, and Biochemistry. 65 (7): 1474–81. doi:10.1271/bbb.65.1474. PMID 11515528. S2CID 11762181.
  9. Gerritse J, Drzyzga O, Kloetstra G, Keijmel M, Wiersum LP, Hutson R, Collins MD, Gottschal JC (December 1999). "Influence of different electron donors and acceptors on dehalorespiration of tetrachloroethene by Desulfitobacterium frappieri TCE1". Applied and Environmental Microbiology. 65 (12): 5212–21. doi:10.1128/AEM.65.12.5212-5221.1999. PMC 91707. PMID 10583967.
  10. Miller E, Wohlfarth G, Diekert G (December 1997). "Comparative studies on tetrachloroethene reductive dechlorination mediated by Desulfitobacterium sp. strain PCE-S". Archives of Microbiology. 168 (6): 513–9. doi:10.1007/s002030050529. PMID 9385143. S2CID 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. 20 (2): 143–156. doi:10.1080/01490450303884. S2CID 93574898.
  12. van de Pas BA, Harmsen HJ, Raangs GC, de Vos WM, Schraa G, Stams AJ (June 2001). "A Desulfitobacterium strain isolated from human feces that does not dechlorinate chloroethenes or chlorophenols". Archives of Microbiology. 175 (6): 389–94. doi:10.1007/s002030100276. PMID 11491079. S2CID 35998991.
  13. Comensoli L, Maillard J, Albini M, Sandoz F, Junier P, Joseph E (May 2017). "Use of Bacteria To Stabilize Archaeological Iron". Applied and Environmental Microbiology. 83 (9). doi:10.1128/AEM.03478-16. PMC 5394308. PMID 28283522.
  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 (February 2012). "Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction". BMC Microbiology. 12: 21. doi:10.1186/1471-2180-12-21. PMC 3306737. PMID 22316246.
  16. Nonaka H, Keresztes G, Shinoda Y, Ikenaga Y, Abe M, Naito K, Inatomi K, Furukawa K, Inui M, Yukawa H (March 2006). "Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195". Journal of Bacteriology. 188 (6): 2262–74. doi:10.1128/JB.188.6.2262-2274.2006. PMC 1428132. PMID 16513756.
  17. Goris T, Hornung B, Kruse T, Reinhold A, Westermann M, Schaap PJ, Smidt H, Diekert G (2015). "Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S". Standards in Genomic Sciences. 10: 15. doi:10.1186/1944-3277-10-15. PMC 4511579. PMID 26203328.
  18. Zhang X, Li GX, Chen SC, Jia XY, Wu K, Cao CL, Bao P (February 2016). "Draft Genome Sequence of Desulfitobacterium hafniense Strain DH, a Sulfate-Reducing Bacterium Isolated from Paddy Soils". Genome Announcements. 4 (1). doi:10.1128/genomeA.01693-15. PMC 4751313. PMID 26868389.
  19. Kruse T, Goris T, Maillard J, Woyke T, Lechner U, de Vos W, Smidt H (December 2017). "Comparative genomics of the genus Desulfitobacterium". FEMS Microbiology Ecology. 93 (12). doi:10.1093/femsec/fix135. PMID 29040502.

Further reading
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