1887

Abstract

Genome comparisons based on average nucleotide identity (ANI) values of four strains currently classified as subsp. resulted in ANI values of 75.7–78.4 %, suggesting that each of those strains represents a separate species. The species . was proposed by Heckmann and Schmidt in 1987 to accommodate obligate endosymbionts of ciliates affiliated with the genus . The required revision of this species is, however, hampered by the fact, that this species is based only on a description and lacks a type strain available as pure culture. Furthermore, the ciliate culture ATCC 30859, on which the description of the species was based, is no longer available. We found another culture (Ammermann) sharing the same origin with ATCC 30859 and proved the identity of the endosymbionts contained in the two cultures. A multilocus sequence comparison approach was used to estimate if the four strains currently classified as subsp. share ANI values with the endosymbiont in the Ammermann culture above or below the threshold for species demarcation. A significant correlation (R 0.98, <0.0001) between multilocus sequence similarity and ANI values of genome-sequenced strains enabled the prediction that it is highly unlikely that these four strains belong to the species . . We propose reclassification of strains QLW-P1DMWA-1 (=DSM 18221=CIP 109841), MWH-MoK4 (=DSM 21495=CIP 110977), MWH-JaK3 (=DSM 21493=CIP 110976) and MWH-HuW1 (=DSM 21492=CIP 110978) as comb. nov., sp. nov., sp. nov. and sp. nov., respectively.

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2016-08-01
2022-01-19
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References

  1. Ammermann D. 1971; Morphology and development of the macronuclei of the ciliates Stylonychia mytilus and Euplotes aediculatus. Chromosoma 33:209–238 [View Article][PubMed]
    [Google Scholar]
  2. Boscaro V., Felletti M., Vannini C., Ackerman M. S., Chain P. S., Malfatti S., Vergez L. M., Shin M., Doak T. G. et al. 2013; Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Proc Natl Acad Sci U S A 110:18590–18595 [View Article][PubMed]
    [Google Scholar]
  3. Hahn M. W. 2003; Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones. Appl Environ Microbiol 69:5248–5254 [View Article][PubMed]
    [Google Scholar]
  4. 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]
  5. Hahn M. W., Pöckl M., Wu Q. L. 2005; Low intraspecific diversity in a polynucleobacter subcluster population numerically dominating bacterioplankton of a freshwater pond. Appl Environ Microbiol 71:4539–4547 [View Article][PubMed]
    [Google Scholar]
  6. 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]
  7. Hahn M. W., Lang E., Brandt U., Lünsdorf H., Wu Q. L., Stackebrandt E. 2010; Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers. Int J Syst Evol Microbiol 60:166–173 [View Article][PubMed]
    [Google Scholar]
  8. Hahn M. W., Lang E., Tarao M., Brandt U. 2011a; Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake. Int J Syst Evol Microbiol 61:781–787 [View Article]
    [Google Scholar]
  9. Hahn M. W., Lang E., Brandt U., Sproer C. 2011b; Polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria. Int J Syst Evol Microbiol 61:788–794 [View Article]
    [Google Scholar]
  10. Hahn M. W., Minasyan A., Lang E., Koll U., Sproer C. 2012a; Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter. Int J Syst Evol Microbiol 62:376–383 [View Article]
    [Google Scholar]
  11. Hahn M. W., Scheuerl T., Jezberová J., Koll U., Jezbera J., Šimek K., Vannini C., Petroni G., Wu Q. L. 2012b; The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living Polynucleobacter population. PLoS One 7:e32772 [View Article]
    [Google Scholar]
  12. Hahn M. W., Jezberová J., Koll U., Saueressig-Beck T., Schmidt J. 2016; Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences. ISME J 10:1642–1655 [View Article][PubMed]
    [Google Scholar]
  13. Hao Z., Li L., Liu J., Ren Y., Wang L., Bartlam M., Egli T., Wang Y. 2013; Genome sequence of a freshwater low-nucleic-acid-content bacterium, Betaproteobacterium strain CB. Genome Announc 1:e0013513e0013513 [View Article][PubMed]
    [Google Scholar]
  14. Heckmann K., Schmidt H. J. 1987; Polynucleobacter necessarius gen. nov., sp. nov., an obligately endosymbiotic bacterium Living in the cytoplasm of Euplotes aediculatus. Int J Syst Bacteriol 37:456–457 [View Article]
    [Google Scholar]
  15. Jezbera J., Jezberová J., Brandt U., Hahn M. W. 2011; Ubiquity of Polynucleobacter necessarius subspecies asymbioticus results from ecological diversification. Environ Microbiol 13:922–931 [View Article][PubMed]
    [Google Scholar]
  16. Jezberová J., Jezbera J., Brandt U., Lindström E. S., Langenheder S., Hahn M. W. 2010; Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogeneous 2000 km area. Environ Microbiol 12:658–669 [View Article][PubMed]
    [Google Scholar]
  17. Kim M., Oh H. S., Park S. C., Chun J. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351 [View Article][PubMed]
    [Google Scholar]
  18. Konstantinidis K. T., Tiedje J. M. 2005; Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102:2567–2572 [View Article][PubMed]
    [Google Scholar]
  19. Konstantinidis K. T., Ramette A., Tiedje J. M. 2006; The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361:1929–1940 [View Article]
    [Google Scholar]
  20. Markowitz V. M., Chen I. M., Palaniappan K., Chu K., Szeto E., Grechkin Y., Ratner A., Jacob B., Huang J. et al. 2012; IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40:D115–D122 [View Article][PubMed]
    [Google Scholar]
  21. Meincke L., Copeland A., Lapidus A., Lucas S., Berry K. W., Del Rio T. G., Hammon N., Dalin E., Tice H. et al. 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]
  22. Petroni G., Dini F., Verni F., Rosati G. 2002; A molecular approach to the tangled intrageneric relationships underlying phylogeny in Euplotes (Ciliophora, Spirotrichea). Mol Phylogenet Evol 22:118–130 [View Article][PubMed]
    [Google Scholar]
  23. Rao M. V., Ammermann D. 1970; Polytene chromosomes and nucleic acid metabolism during macronuclear development in Euplotes. Chromosoma 29:246–254 [View Article][PubMed]
    [Google Scholar]
  24. Richter M., Rossello-Mora R. 2009; Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 106:19126–19131 [View Article]
    [Google Scholar]
  25. Vannini C., Pöckl M., Petroni G., Wu Q. L., Lang E., Stackebrandt E., Schrallhammer M., Richardson P. M., Hahn M. W. 2007; Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria). Environ Microbiol 9:347–359 [View Article][PubMed]
    [Google Scholar]
  26. Wang Y., Hammes F., Boon N., Chami M., Egli T. 2009; Isolation and characterization of low nucleic acid (LNA)-content bacteria. ISME J 3:889–902 [View Article][PubMed]
    [Google Scholar]
  27. Wu Q. L., Hahn M. W. 2006; Differences in structure and dynamics of Polynucleobacter communities in a temperate and a subtropical lake, revealed at three phylogenetic levels. FEMS Microbiol Ecol 57:67–79 [View Article][PubMed]
    [Google Scholar]
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