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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 8

Polynucleobacter hirudinilacicola sp. nov. and Polynucleobacter campilacus sp. nov., both isolated from freshwater systems Free

Abstract

Strains MWH-EgelM1-30-B4 and MWH-Feld-100 were isolated from the water columns of two freshwater systems. Both strains represent delicate bacteria not easy to work with in laboratory experiments. Phylogenetic analyses of the 16S rRNA genes suggested that both strains were affiliated with the genus Polynucleobacter . Both strains share 16S rRNA gene sequence similarities of >99 % with eight free-living Polynucleobacter type strains, all affiliated with the cryptic species complex PnecC. The full-length 16S rRNA gene sequences of the two strains differ only in two and three positions, respectively, from the sequence of the closest related Polynucleobacter type strain. Genome sequencing of both strains revealed relatively small genome sizes of 2.0 Mbp and G+C contents of 45 mol%. Phylogenetic analyses based on nucleotide sequences of 319 shared protein-encoding genes consistently placed the two strains in taxon PnecC but did not suggest an affiliation with one of the previously described species. Pairwise analyses of whole genome average nucleotide identities (gANI) with representatives of all previously described Polynucleobacter species resulted in both cases throughout in values <80 %. Pairwise comparison of the genomes of the two new strains resulted in gANI values of 83.3 %. All gANI analyses clearly suggested that strains MWH-EgelM1-30-B4 and MWH-Feld-100 represent two novel Polynucleobacter species. We propose for these novel species the names Polynucleobacter hirudinilacicola sp. nov. and Polynucleobacter campilacus sp. nov. and strains MWH-EgelM1-30-B4 (=DSM 23911=LMG 30144) and MWH-Feld-100 (=DSM 24007=LMG 29705) as the type strains, respectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): average nucleotide identity , bacterioplankton , freshwater lake , genome , multi-locus phylogeny and Polynucleobacter
© 2018 IUMS
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2018-06-25
2024-04-19
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References

  1. Heckmann K, Schmidt HJ. Polynucleobacter necessarius gen. nov., sp. nov., an obligately endosymbiotic bacterium living in the cytoplasm of Euplotes aediculatus. Int J Syst Bacteriol 1987; 37:456–457 [View Article]
     [Google Scholar]
  2. Vannini C, Pöckl M, Petroni G, Wu QL, Lang E et al. Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria). Environ Microbiol 2007; 9:347–359 [View Article][PubMed]
     [Google Scholar]
  3. Hahn MW, Schmidt J, Pitt A, Taipale SJ, Lang E. Reclassification of four Polynucleobacter necessarius strains as representatives of Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., and emended description of Polynucleobacter necessarius. Int J Syst Evol Microbiol 2016; 66:2883–2892 [View Article][PubMed]
     [Google Scholar]
  4. Wu QL, Hahn MW. Differences in structure and dynamics of Polynucleobacter communities in a temperate and a subtropical lake, revealed at three phylogenetic levels. FEMS Microbiol Ecol 2006; 57:67–79 [View Article][PubMed]
     [Google Scholar]
  5. Zwart G, Crump BC, Kamst-van Agterveld MP, Hagen F, Han SK. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquatic Microbial Ecology 2002; 28:141–155 [View Article]
     [Google Scholar]
  6. Burkert U, Warnecke F, Babenzien D, Zwirnmann E, Pernthaler J. Members of a readily enriched beta-proteobacterial clade are common in surface waters of a humic lake. Appl Environ Microbiol 2003; 69:6550–6559 [View Article][PubMed]
     [Google Scholar]
  7. Watanabe K, Komatsu N, Ishii Y, Negishi M. Effective isolation of bacterioplankton genus Polynucleobacter from freshwater environments grown on photochemically degraded dissolved organic matter. FEMS Microbiol Ecol 2009; 67:57–68 [View Article][PubMed]
     [Google Scholar]
  8. Jezberová J, Jezbera J, Brandt U, Lindström ES, Langenheder S et al. Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogeneous 2000 km2 area. Environ Microbiol 2010; 12:658–669 [View Article][PubMed]
     [Google Scholar]
  9. Percent SF, Frischer ME, Vescio PA, Duffy EB, Milano V et al. Bacterial community structure of acid-impacted lakes: what controls diversity?. Appl Environ Microbiol 2008; 74:1856–1868 [View Article][PubMed]
     [Google Scholar]
  10. Crump BC, Kling GW, Bahr M, Hobbie JE. Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl Environ Microbiol 2003; 69:2253–2268 [View Article][PubMed]
     [Google Scholar]
  11. Allen MA, Cavicchioli R. Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data. Sci Rep 2017; 7:44480 [View Article][PubMed]
     [Google Scholar]
  12. Crevecoeur S, Vincent WF, Comte J, Lovejoy C. Bacterial community structure across environmental gradients in permafrost thaw ponds: methanotroph-rich ecosystems. Front Microbiol 2015; 6:192 [View Article][PubMed]
     [Google Scholar]
  13. Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R et al. Metagenomics of the water column in the pristine upper course of the Amazon river. PLoS One 2011; 6:e23785 [View Article][PubMed]
     [Google Scholar]
  14. Oloo F, Valverde A, Quiroga MV, Vikram S, Cowan D et al. Habitat heterogeneity and connectivity shape microbial communities in South American peatlands. Sci Rep 2016; 6:25712 [View Article][PubMed]
     [Google Scholar]
  15. Hahn MW, Koll U, Jezberová J, Camacho A. Global phylogeography of pelagic Polynucleobacter bacteria: restricted geographic distribution of subgroups, isolation by distance and influence of climate. Environ Microbiol 2015; 17:829–840 [View Article][PubMed]
     [Google Scholar]
  16. Hahn MW. Broad diversity of viable bacteria in 'sterile' (0.2 microm) filtered water. Res Microbiol 2004; 155:688–691 [View Article][PubMed]
     [Google Scholar]
  17. Hahn MW, Lang E, Brandt U, Wu QL, Scheuerl T. 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 2009; 59:2002–2009 [View Article][PubMed]
     [Google Scholar]
  18. Hahn MW, Huymann LR, Koll U, Schmidt J, Lang E et al. Polynucleobacter wuianus sp. nov., a free-living freshwater bacterium affiliated with the cryptic species complex PnecC. Int J Syst Evol Microbiol 2017; 67:379–385 [View Article][PubMed]
     [Google Scholar]
  19. Hahn MW, Jezberová J, Koll U, Saueressig-Beck T, Schmidt J. Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences. Isme J 2016; 10:1642–1655 [View Article][PubMed]
     [Google Scholar]
  20. Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D et al. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. Isme J 2012; 6:113–123 [View Article][PubMed]
     [Google Scholar]
  21. Hahn MW, Koll U, Karbon G, Schmidt J, Lang E. Polynucleobacter aenigmaticus sp. nov. isolated from the permanently anoxic monimolimnion of a temperate meromictic lake. Int J Syst Evol Microbiol 2017; 67:4646–4654 [View Article][PubMed]
     [Google Scholar]
  22. Pitt A, Schmidt J, Lang E, Whitman WB, Woyke T et al. Polynucleobacter meluiroseus sp. nov., a bacterium isolated from a lake located in the mountains of the Mediterranean island of Corsica. Int J Syst Evol Microbiol 2018; 68:1975–1985 [View Article][PubMed]
     [Google Scholar]
  23. Hahn MW. Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones. Appl Environ Microbiol 2003; 69:5248–5254 [View Article][PubMed]
     [Google Scholar]
  24. Hahn MW, Stadler P, Wu QL, Pöckl M. The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria. J Microbiol Methods 2004; 57:379–390 [View Article][PubMed]
     [Google Scholar]
  25. Hahn MW, Karbon G, Koll U, Schmidt J, Lang E. Polynucleobacter sphagniphilus sp. nov. a planktonic freshwater bacterium isolated from an acidic and humic freshwater habitat. Int J Syst Evol Microbiol 2017; 67:3261–3267 [View Article][PubMed]
     [Google Scholar]
  26. Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 2017 [View Article][PubMed]
     [Google Scholar]
  27. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article][PubMed]
     [Google Scholar]
  28. Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In Proceedings of the Gateway Computing Environments Workshop (GCE), 14 Nov 2010 New Orleans: 2010 pp. 1–8
     [Google Scholar]
  29. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  30. Chen IA, Markowitz VM, Chu K, Palaniappan K, Szeto E et al. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res 2017; 45:D507–D516 [View Article][PubMed]
     [Google Scholar]
  31. Hahn MW, Minasyan A, Lang E, Koll U, Spröer C. Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter. Int J Syst Evol Microbiol 2012; 62:376–383 [View Article][PubMed]
     [Google Scholar]
  32. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7[PubMed]
     [Google Scholar]
  33. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  34. Jezbera J, Jezberová J, Brandt U, Hahn MW. Ubiquity of Polynucleobacter necessarius subspecies asymbioticus results from ecological diversification. Environ Microbiol 2011; 13:922–931 [View Article][PubMed]
     [Google Scholar]
  35. Hoetzinger M, Schmidt J, Jezberová J, Koll U, Hahn MW. Microdiversification of a pelagic Polynucleobacter species is mainly driven by acquisition of genomic islands from a partially interspecific gene pool. Appl Environ Microbiol 2017; 83:e02266-16 [View Article][PubMed]
     [Google Scholar]
  36. Boscaro V, Felletti M, Vannini C, Ackerman MS, Chain PS et al. Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Proc Natl Acad Sci USA 2013; 110:18590–18595 [View Article][PubMed]
     [Google Scholar]
  37. Meincke L, Copeland A, Lapidus A, Lucas S, Berry KW et al. Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1T). Stand Genomic Sci 2012; 6:74–83 [View Article][PubMed]
     [Google Scholar]
  38. Hahn MW, Schmidt J, Asiyo GS, Kyrpides NC, Woyke T et al. Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov. Int J Syst Evol Microbiol 2017; 67:5087–5093 [View Article][PubMed]
     [Google Scholar]
  39. Janssen PJ, van Houdt R, Moors H, Monsieurs P, Morin N et al. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One 2010; 5:e10433 [View Article][PubMed]
     [Google Scholar]
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Polynucleobacter hirudinilacicola sp. nov. and Polynucleobacter campilacus sp. nov., both isolated from freshwater systems
Int J Syst Evol Microbiol 68, 2593 (2018); https://doi.org/10.1099/ijsem.0.002880
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