1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 64, Issue Pt_9

gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome Open Access

Abstract

A pure culture of an actinobacterium previously described as ‘ ’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8 represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8 is noticeable due to its unusually low values of cell size (0.05 µm), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8 is affiliated with the family with being its closest relative among the currently described species within this family. Strain MWH-Ta8 and the type strain of shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8 was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C (36.5 %), iso-C (16.5 %), iso-C (15.6 %) and iso-C (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8 represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8 ( = DSM 23834 = LMG 26932).

  • Published Online:
Funding
This study was supported by the:
  • Canadian Institutes for Health Research (Award MOP-4467)
  • Academy of Finland (Award 251665)
  • Austrian Science Fund (Award I482-B09)
© 2014 IUMS
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.065292-0
2014-09-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/9/3254.html?itemId=/content/journal/ijsem/10.1099/ijs.0.065292-0&mimeType=html&fmt=ahah

References

  1. Allgaier M., Grossart H. P. ( 2006 ). Diversity and seasonal dynamics of Actinobacteria populations in four lakes in northeastern Germany. . Appl Environ Microbiol 72, 3489–3497. [View Article] [PubMed]
    [Google Scholar]
  2. An S.-Y., Xiao T., Yokota A. ( 2008 ). Schumannella luteola gen. nov., sp. nov., a novel genus of the family Microbacteriaceae . . J Gen Appl Microbiol 54, 253–258. [View Article] [PubMed]
    [Google Scholar]
  3. Carini P., Steindler L., Beszteri S., Giovannoni S. J. ( 2013 ). Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium. . ISME J 7, 592–602. [View Article] [PubMed]
    [Google Scholar]
  4. DeSantis T. Z., Hugenholtz P., Larsen N., Rojas M., Brodie E. L., Keller K., Huber T., Dalevi D., Hu P., Andersen G. L. ( 2006 ). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with arb . . Appl Environ Microbiol 72, 5069–5072. [View Article] [PubMed]
    [Google Scholar]
  5. Duda V. I., Suzina N. E., Polivtseva V. N., Boronin A. M. ( 2012 ). [Ultramicrobacteria: Formation of the concept and contribution of ultramicrobacteria to biology]. . Mikrobiologiia 81, 415–427 (in Russian). [PubMed]
    [Google Scholar]
  6. Garcia S. L., McMahon K. D., Martinez-Garcia M., Srivastava A., Sczyrba A., Stepanauskas R., Grossart H. P., Woyke T., Warnecke F. ( 2013 ). Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. . ISME J 7, 137–147. [View Article] [PubMed]
    [Google Scholar]
  7. Giovannoni S. J., Bibbs L., Cho J. C., Stapels M. D., Desiderio R., Vergin K. L., Rappé M. S., Laney S., Wilhelm L. J. & other authors ( 2005a ). Proteorhodopsin in the ubiquitous marine bacterium SAR11. . Nature 438, 82–85. [View Article] [PubMed]
    [Google Scholar]
  8. Giovannoni S. J., Tripp H. J., Givan S., Podar M., Vergin K. L., Baptista D., Bibbs L., Eads J., Richardson T. H. & other authors ( 2005b ). Genome streamlining in a cosmopolitan oceanic bacterium. . Science 309, 1242–1245. [View Article] [PubMed]
    [Google Scholar]
  9. Glöckner F. O., Zaichikov E., Belkova N., Denissova L., Pernthaler J., Pernthaler A., Amann R. ( 2000 ). Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. . Appl Environ Microbiol 66, 5053–5065. [View Article] [PubMed]
    [Google Scholar]
  10. Hahn M. W. ( 2006 ). The microbial diversity of inland waters. . Curr Opin Biotechnol 17, 256–261. [View Article] [PubMed]
    [Google Scholar]
  11. Hahn M. W. ( 2009 ). Description of seven candidate species affiliated with the phylum Actinobacteria, representing planktonic freshwater bacteria. . Int J Syst Evol Microbiol 59, 112–117. [View Article] [PubMed]
    [Google Scholar]
  12. Hahn M. W., Lünsdorf H., Wu Q. L., Schauer M., Höfle M. G., Boenigk J., Stadler P. ( 2003 ). Isolation of novel ultramicrobacteria classified as Actinobacteria from five freshwater habitats in Europe and Asia. . Appl Environ Microbiol 69, 1442–1451. [View Article] [PubMed]
    [Google Scholar]
  13. Hahn M. W., Stadler P., Wu Q. L., Pöckl M. ( 2004 ). The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria. . J Microbiol Methods 57, 379–390. [View Article] [PubMed]
    [Google Scholar]
  14. Hahn M. W., Lang E., Brandt U., Wu Q. L., Scheuerl T. ( 2009 ). Emended description of the genus Polynucleobacter and the species Polynucleobacter necessarius and proposal of two subspecies, P. necessarius subsp. necessarius subsp. nov. and P. necessarius subsp. asymbioticus subsp. nov.. Int J Syst Evol Microbiol 59, 2002–2009. [View Article] [PubMed]
    [Google Scholar]
  15. Jang G. I., Cho Y., Cho B. C. ( 2013 ). Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern. . Int J Syst Evol Microbiol 63, 2124–2131. [View Article] [PubMed]
    [Google Scholar]
  16. Jezbera J., Sharma A. K., Brandt U., Doolittle W. F., Hahn M. W. ( 2009 ). ‘Candidatus Planktophila limnetica’, an actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton. . Int J Syst Evol Microbiol 59, 2864–2869. [View Article] [PubMed]
    [Google Scholar]
  17. Kang I., Lee K., Yang S.-J., Choi A., Kang D., Lee Y. K., Cho J.-C. ( 2012 ). Genome sequence of “Candidatus Aquiluna” sp. strain IMCC13023, a marine member of the Actinobacteria isolated from an arctic fjord. . J Bacteriol 194, 3550–3551. [View Article] [PubMed]
    [Google Scholar]
  18. Kumar Pinnaka A., Singh A., Ara S., Begum Z., Reddy G. S., Shivaji S. ( 2013 ). Draft genome sequence of Leifsonia rubra strain CMS 76RT, isolated from a cyanobacterial mat sample from a pond in Wright Valley, McMurdo, Antarctica. . Genome announcements. [View Article]
    [Google Scholar]
  19. Markowitz V. M., Chen I. M. A., Palaniappan K., Chu K., Szeto E., Grechkin Y., Ratner A., Jacob B., Huang J. H. & other authors ( 2012 ). IMG: the integrated microbial genomes database and comparative analysis system. . Nucleic Acids Res 40 (Database issue), D115–D122. [View Article] [PubMed]
    [Google Scholar]
  20. Meincke L., Copeland A., Lapidus A., Lucas S., Berry K. W., Del Rio T. G., Hammon N., Dalin E., Tice H. & other authors ( 2012 ). Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1T). . Stand Genomic Sci 6, 74–83. [View Article] [PubMed]
    [Google Scholar]
  21. Newton R. J., Jones S. E., Eiler A., McMahon K. D., Bertilsson S. ( 2011 ). A guide to the natural history of freshwater lake bacteria. . Microbiol Mol Biol Rev 75, 14–49. [View Article] [PubMed]
    [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. 4–20. Edited by Arts M. T., Wainman B. C. . New York:: Springer;. [View Article]
    [Google Scholar]
  23. Salcher M. M., Pernthaler J., Posch T. ( 2010 ). Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake. . Limnol Oceanogr 55, 846–856. [View Article]
    [Google Scholar]
  24. Schleifer K.-H., Kandler O. ( 1972 ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36, 407–477.[PubMed]
    [Google Scholar]
  25. Schumann P. ( 2011 ). Peptidoglycan structure. . Methods Microbiol 38, 101–129. [View Article]
    [Google Scholar]
  26. Schumann P., Kämpfer P., Busse H.-J., Evtushenko L. I. Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes ( 2009 ). Proposed minimal standards for describing new genera and species of the suborder Micrococcineae . . Int J Syst Evol Microbiol 59, 1823–1849. [View Article] [PubMed]
    [Google Scholar]
  27. Schumann P., Zhang D.-C., Redzic M., Margesin R. ( 2012 ). Alpinimonas psychrophila gen. nov., sp. nov., an actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite. . Int J Syst Evol Microbiol 62, 2724–2730. [View Article] [PubMed]
    [Google Scholar]
  28. Sharma A. K., Sommerfeld K., Bullerjahn G. S., Matteson A. R., Wilhelm S. W., Jezbera J., Brandt U., Doolittle W. F., Hahn M. W. ( 2009 ). Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria . . ISME J 3, 726–737. [View Article] [PubMed]
    [Google Scholar]
  29. Sun S., Mao R. ( 2008 ). Hydrography and drainage basin. . In Lake Taihu, China: Dynamics and Environmental Change, pp. 1–10. Edited by Qin B. . Springer: Berlin;. [View Article]
    [Google Scholar]
  30. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 2731–2739. [View Article] [PubMed]
    [Google Scholar]
  31. Zhang J.-Y., Liu X.-Y., Liu S.-J. ( 2010 ). Agrococcus terreus sp. nov. and Micrococcus terreus sp. nov., isolated from forest soil. . Int J Syst Evol Microbiol 60, 1897–1903. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.065292-0
Loading
Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome
Int J Syst Evol Microbiol 64, 3254 (2014); https://doi.org/10.1099/ijs.0.065292-0
/content/journal/ijsem/10.1099/ijs.0.065292-0
/content/journal/ijsem/10.1099/ijs.0.065292-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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