1887

Abstract

Three strains of methylotrophic (FAM1, RZ18-153 and RZ94) isolated from Lake Washington sediment samples were characterized. Based on phylogenetic analysis of 16S rRNA gene sequences the strains should be assigned to the genus . Similarly to other members of the family, the strains show broad metabolic capabilities and are able to utilize a number of organic acids, alcohols and aromatic compounds in addition to methanol and methylamine. The main fatty acids were 16:1ω7 (49–59 %) and 16:0 (32–29 %). Genomes of all isolates were sequenced, assembled and annotated in collaboration with the DOE Joint Genome Institute (JGI). Genome comparison revealed that the strains FAM1, RZ18-153 and RZ94 are closely related to each other and almost equally distant from two previously described species of the genus , and . Like other methylotrophic species of the genus , all three strains possess one-subunit PQQ-dependent ethanol/methanol dehydrogenase (Mdh-2), the -methylglutamate pathway and the serine cycle (isocitrate lyase/malate synthase, Icl/ms variant). Like , strains FAM1, RZ18-153 and RZ94 have a quinohemoprotein amine dehydrogenase, a tungsten-containing formaldehyde ferredoxin oxidoreductase, phenol hydroxylase, and the complete Calvin cycle. Similarly to , the three strains possess two-subunit methanol dehydrogenase (MxaFI), monoamine oxidase (MAO) and nitrogenase. Based on the phenotypic and genomic data, the strains FAM1, RZ18-153 and RZ94 represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is FAM1 ( = JCM 30542 = VKM = B-2888).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000190
2015-07-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/7/2227.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000190&mimeType=html&fmt=ahah

References

  1. Anthony C. ( 1982). The Biochemistry of Methylotrophs New York: Academic Press;.
    [Google Scholar]
  2. Baytshtok V., Lu H., Park H., Kim S., Yu R., Chandran K. ( 2009;). Impact of varying electron donors on the molecular microbial ecology and biokinetics of methylotrophic denitrifying bacteria. Biotechnol Bioeng 102 15271536 [View Article] [PubMed].
    [Google Scholar]
  3. Bennett S. ( 2004;). Solexa Ltd. Pharmacogenomics 5 433438 [View Article] [PubMed].
    [Google Scholar]
  4. Butler J., MacCallum I., Kleber M., Shlyakhter I.A., Belmonte M.K., Lander E.S., Nusbaum C., Jaffe D.B. ( 2008;). ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 18 810820 [View Article] [PubMed].
    [Google Scholar]
  5. Cai T., Qian L., Cai S., Chen L. ( 2011;). Biodegradation of benazolin-ethyl by strain Methyloversatilis sp. cd-1 isolated from activated sludge. Curr Microbiol 62 570577 [View Article] [PubMed].
    [Google Scholar]
  6. Crowther G.J., Kosály G., Lidstrom M.E. ( 2008;). Formate as the main branch point for methylotrophic metabolism in Methylobacterium extorquens AM1. J Bacteriol 190 50575062 [View Article] [PubMed].
    [Google Scholar]
  7. Dawson R.M.C., Elliott D.C., Elliott W.H., Jones K.M. ( 1986). Data for Biochemical Research Oxford: Clarendon Press;.
    [Google Scholar]
  8. Doronina N.V., Kaparullina E.N., Trotsenko Y.A. ( 2014;). Methyloversatilis thermotolerans sp. nov., a novel thermotolerant facultative methylotroph isolated from a hot spring. Int J Syst Evol Microbiol 64 158164 [View Article] [PubMed].
    [Google Scholar]
  9. Eichhorn E., van der Ploeg J.R., Leisinger T. ( 1999;). Characterization of a two-component alkanesulfonate monooxygenase from Escherichia coli.. J Biol Chem 274 2663926646 [View Article] [PubMed].
    [Google Scholar]
  10. Ewing B., Green P. ( 1998;). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8 186194 [PubMed]. [CrossRef]
    [Google Scholar]
  11. Ewing B., Hillier L., Wendl M.C., Green P. ( 1998;). Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8 175185 [View Article] [PubMed].
    [Google Scholar]
  12. Goldfarb K.C., Karaoz U., Hanson C.A., Santee C.A., Bradford M.A., Treseder K.K., Wallenstein M.D., Brodie E.L. ( 2011;). Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol 2 94 [View Article] [PubMed].
    [Google Scholar]
  13. Gordon D., Abajian C., Green P. ( 1998;). Consed: a graphical tool for sequence finishing. Genome Res 8 195202 [View Article] [PubMed].
    [Google Scholar]
  14. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M. ( 2007;). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57 8191 [View Article] [PubMed].
    [Google Scholar]
  15. Harder W., Attwood M.M., Quayle J.R. ( 1973;). Methanol assimilation by Hyphomicrobium sp. J Gen Microbiol 78 155163 [View Article].
    [Google Scholar]
  16. Kalyuzhnaya M.G., De Marco P., Bowerman S., Pacheco C.C., Lara J.C., Lidstrom M.E., Chistoserdova L. ( 2006;). Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates. Int J Syst Evol Microbiol 56 25172522 [View Article] [PubMed].
    [Google Scholar]
  17. Kalyuzhnaya M.G., Hristova K.R., Lidstrom M.E., Chistoserdova L. ( 2008;). Characterization of a novel methanol dehydrogenase in representatives of Burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolution. J Bacteriol 190 38173823 [View Article] [PubMed].
    [Google Scholar]
  18. Kittichotirat W., Good N.M., Hall R., Bringel F., Lajus A., Médigue C., Smalley N.E., Beck D., Bumgarner R., other authors. ( 2011;). Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales . J Bacteriol 193 45414542 [View Article] [PubMed].
    [Google Scholar]
  19. Kong Y., Nielsen J.L., Nielsen P.H. ( 2004;). Microautoradiographic study of Rhodocyclus-related polyphosphate-accumulating bacteria in full-scale enhanced biological phosphorus removal plants. Appl Environ Microbiol 70 53835390 [View Article] [PubMed].
    [Google Scholar]
  20. Latypova E., Yang S., Wang Y.-S., Wang T., Chavkin T.A., Hackett M., Schäfer H., Kalyuzhnaya. M.G. 2010;;. Genetics of the glutamate-mediated methylamine utilization pathway in the facultative methylotrophic beta-proteobacterium Methyloversatilis universalis FAM5. Mol. Microbiol. 75:426439. [CrossRef]
    [Google Scholar]
  21. Nichols P.D., Guckert J.B., White D.C. ( 1986;). Determination of monounsaturated fatty acid double-bond position and geometry for microbial monocultures and complex consortia by capillary GC-MS of their dimethyl disulphide adducts. J Microbiol Methods 5 4955 [View Article].
    [Google Scholar]
  22. Parrish C.C. ( 1999;). Determination of total lipid, lipid classes, and fatty acids in aquatic samples. . In Lipids in Freshwater Ecosystems, pp. 420. Edited by Arts M. T., Wainman B. C. New York: Springer; [View Article] .
    [Google Scholar]
  23. Sambrook J., Fritsch E.F., Maniatis T. ( 1989). Molecular Cloning: a Laboratory Manual , 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;.
    [Google Scholar]
  24. Smibert R.M., Krieg N.R. ( 1994;). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  25. Zerbino D.R., Birney E. ( 2008;). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18 821829 [View Article] [PubMed].
    [Google Scholar]
  26. Zilles J.L., Peccia J., Kim M.W., Hung C.H., Noguera D.R. ( 2002;). Involvement of Rhodocyclus-related organisms in phosphorus removal in full-scale wastewater treatment plants. Appl Environ Microbiol 68 27632769 [View Article] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.000190
Loading
/content/journal/ijsem/10.1099/ijs.0.000190
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error