Location of Repository

Novel methylotrophic bacteria isolated from the River Thames (London, UK)

By Rich Boden, Elizabeth Thomas, Parita Savani, Donovan P. Kelly and Ann P. Wood

Abstract

Enrichment and elective culture for methylotrophs from sediment of the River Thames in central London yielded a diversity of pure cultures representing several genera of Gram-negative and Gram-positive bacteria, which were mainly of organisms not generally regarded as typically methylotrophic. Substrates leading to successful isolations included methanol, monomethylamine, dimethylamine, trimethylamine, methanesulfonate and dimethylsulfone. Several isolates were studied in detail and shown by their biochemical and morphological properties and 16S rRNA gene sequencing to be Sphingomonas melonis strain ET35, Mycobacterium fluoranthenivorans strain DSQ3, Rhodococcus erythropolis strain DSQ4, Brevibacterium casei strain MSQ5, Klebsiella oxytoca strains MMA/F and MMA/1, Pseudomonas mendocina strain TSQ4, and Flavobacterium sp. strains MSA/1 and MMA/2. The results show that facultative methylotrophy is present across a wide range of Bacteria, suggesting that turnover of diverse C1-compounds is of much greater microbiological and environmental significance than is generally thought. The origins of the genes encoding the enzymes of methylotrophy in diverse heterotrophs need further study, and could further our understanding of the phylogeny and antiquity of methylotrophic systems. \u

Topics: QR
Publisher: Blackwell
Year: 2008
OAI identifier: oai:wrap.warwick.ac.uk:327

Suggested articles

Preview

Citations

  1. (1898) Some Thames bacteria.
  2. (1899) Microorganisms in water. In Our Secret Friends and Foes.
  3. (1899) Thames bacteria,
  4. (2005a) Isolation and properties of MSA-degrading Afipia felis from Antarctica and comparison with other strains of A. felis. doi
  5. (1939). 12. Bacterium methylicum (Loew) Migula. (Bacillus methylicus Loew). In Bergey’s Manual of Determinative Bacteriology.
  6. (1988). 3-Hexulose phosphate synthase from a new facultative methylotroph, Mycobacterium gastri MB19. doi
  7. (1981). A facultatively anaerobic methylotrophic bacterium, Brevibacterium rufescens comb. nov., from oil reservoirs.
  8. (2004). A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land.
  9. (2000). A novel operon encoding formaldehyde fixation: the ribulose monophosphate pathway in the gram-positive facultative methylotrophic bacterium Mycobacterium gastri MB19. doi
  10. (2003). A reconstruction of Archaean biological diversity based on molecular fossils from the 2.78 to 2.45-billionyear-old Mount Bruce Supergroup, Hammersley Basin, doi
  11. (1933). A simplified method of staining endospores. doi
  12. (1978). Aerobic and anaerobic growth of Paracoccus denitrificans on methanol. doi
  13. (2006). Aerobic methylotrophic prokaryotes. doi
  14. (1981). Arthrobacter P1, a fast growing versatile methylotroph with amine oxidase as a key enzyme in the metabolism of methylated amines. doi
  15. (1992). Bacillus methanolicus sp. nov., a new species of thermotolerant, methanolutilizing, endospore-forming bacteria. doi
  16. (1999). Bacillus subtilis yckG and yckF encode two key enzymes of the ribulose monophosphate pathway used by methylotrophs, and yckH is required for their expression.
  17. (2005). Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lake. doi
  18. (1900). Bacterium methylicum (Loew) Migula.
  19. (1968). Base composition of deoxyribonucleic acids isolated from mycobacteria.
  20. (2006). Cloning of formate dehydrogenase gene from a methanol-degrading actinomycete. doi
  21. (2003). Cometabolism of methyl tertiary butyl ether and gaseous n-alkanes by Pseudomonas mendocina KR-1 grown on C5 to C8 nalkanes. doi
  22. (1995). Cowan and Steel’s Manual for the identification of Medical Bacteria. doi
  23. (1987). Degradation of substituted thiophenes by bacteria isolated from activated sludge. doi
  24. (2001). Different physiological roles of ATP- and PPi-dependent phosphofructokinase isoenzymes in the methylotrophic actinomycete Amycolatopsis methanolica. doi
  25. (1970). Enrichment, isolation and some properties of methane-utilizing bacteria. doi
  26. (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. doi
  27. (1977). Examination of obligate and facultative methylotrophs for plasmid DNA. doi
  28. (2005). Genus I. Pseudomonas Migula. In Bergey’s Manual of Systematic Bacteriology.
  29. (2005). Genus I. Sphingomonas. doi
  30. (2008). Gram positive and Gram negative plasmid. doi
  31. (2002). Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing.
  32. (1997). Is the ribulose monophosphate pathway widely distributed in bacteria? doi
  33. (1988). Isolation and initial characterization of thermotolerant methylotrophic Bacillus strains. doi
  34. (2005). Isolation and molecular detection of methylotrophic bacteria occurring in the human mouth. doi
  35. (1975). Isolation of methanol-utilizing bacteria and its vitamin B12 production. doi
  36. (2007). Isolation of Methylophaga spp. from marine dimethylsulfide-degrading enrichment cultures and identification of polypeptides induced during growth on dimethylsulfide. doi
  37. (2003). Lateral gene transfer and the origins of prokaryotic groups.
  38. (2008). List of prokaryotic names with standing in nomenclature - Genus Flavobacterium. http://www.bacterio.cict.fr/f/flavobacterium.html 504 Frankland, P.F. (1885) The removal of microorganisms from water. Proc Roy Soc Lond
  39. (1989). Methanol-utilizing Mycobacterium strains isolated from soil. doi
  40. (2006). Methylobacterium. In The doi
  41. (2005). Methylocella species are facultatively methanotrophic. doi
  42. (2005). Methylotrophic autotrophy in Beijerinckia mobilis. doi
  43. (2006). Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates. doi
  44. (1998). Microbes of the sulfur cycle.
  45. (2004). Molecular analysis of shower curtain biofilm microbes. doi
  46. (2005). Molecular detection and isolation from Antarctica of methylotrophic bacteria able to grow with methylated sulfur compounds. doi
  47. (2004). Molecular detection and isolation of facultatively methylotrophic bacteria, including Methylobacterium podarium sp. nov., from the human foot microflora. doi
  48. (2004). Molecular phylogeny of methylotrophs in a deep-sea sediment from a tropical west Pacific warm pool. doi
  49. (2004). Mycobacterium fluoranthenivorans sp. nov., a fluoranthene and aflatoxin B degrading bacterium from contaminated soil of a former coal gas plant. doi
  50. (1999). Nature, nomenclature and taxonomy of obligate methanol utilizing strains.
  51. (2004). Plasmid-dependent methylotrophy in themotolerant Bacillus methanolicus. doi
  52. (1984). Plasmids in methanotrophic bacteria: isolation, characterization and DNA hybridization analysis. doi
  53. (1982). Practical procedure for demonstrating bacterial flagella.
  54. (1979). Production of vitamin B12 by gram-variable methanol-utilizing bacteria. doi
  55. (2002). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. doi
  56. (2006). Sphingomonas dokdonensis sp. nov., isolated from soil. doi
  57. (2002). Sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow Spanish melon fruits. doi
  58. (2005). Stable isotope probing of nucleic acids in methanotrophs and methylotrophs: a review. doi
  59. (2000). Stable-isotope probing as a tool in microbial ecology. doi
  60. (2007). Study of methanol-induced phenotypic changes in a novel strain of Acinetobacter lwoffii. doi
  61. (1987). The determination of nitrate in soil solution by ultraviolet spectrophotometry. doi
  62. (2006). The Genus Flavobacterium. doi
  63. (2006). The Genus Mycobacteriumnonmedical. doi
  64. (2006). The Genus Paracoccus. doi
  65. (1997). The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs.
  66. (2006). The physiological role of the ribulose monophosphate pathway in bacteria and Archaea. doi
  67. (1992). The physiology and biochemistry of aerobic methanol-utilizing Gram-negative and Gram-positive bacteria. doi
  68. (2002). The ribulose monophosphate pathway operon encoding formaldehyde fixation in a thermotolerant methylotroph, Bacillus brevis S1. doi
  69. (2006). The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the Archaeon Thermococcus kodakaraensis. doi
  70. (1961). The ultraviolet spectrum of deoxyribonucleic acids and their constituents. doi
  71. (1991). Transformation of a new gram-positive methylotroph, Brevibacterium methylicum, by plasmid DNA. doi
  72. (1892). Ueber einen Bacillus, welcher Ameisensäure und Formaldehyd assimilieren kann.
  73. (2006). Upregulated transcription of plasmid and chromosomal ribulose monophosphate pathway genes is critical for methanol assimilation rate and methanol tolerance in the methylotrophic bacterium Bacillus methanolicus. doi
  74. (2005). Use of DNA-stable isotope probing and functional gene probes to investigate the diversity of methyl chlorideutilizing bacteria in soil. doi
  75. (2004). Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. doi
  76. (1997). Xanthobacter tagetidis sp. nov., an organism associated with Tagetes species and able to grow on substituted thiophenes. doi

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.