1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 3

sp. nov. and sp. nov., ammonifying bacteria isolated from surface river water No Access

Abstract

Three aerobic, Gram-stain-negative, non-motile, rod-shaped bacteria, designated as strains SHINM13, GENT5 and GENT11 were isolated from surface river water (Saitama Prefecture, Japan). SHINM13 and GENT11 were positive for catalase, whereas GENT5 was negative. Phylogenetic analyses based on the 16S rRNA gene (1341 bp) or 40 marker gene (34,513 bp) sequences revealed that the strains formed distinct phylogenetic lineages within the genus . The three strains shared 99.3–99.6 % 16S rRNA gene sequence similarity among each other. The average nucleotide identity by orthology (OrthoANI) and digital DNA–DNA hybridization (dDDH) values between strains SHINM13 and GENT11 were 96.56 and 82.1 %, respectively, and those between SHINM13 and GENT5 were 83.46 % and 52.9 %, respectively. The major cellular fatty acids were Cω6, iso-C, iso-CG, anteiso-C and iso-C 3-OH. The major polar lipid was phosphatidylethanolamine. SHINM13 and GENT5 contained menaquinone-6 (MK-6) as the predominant respiratory quinone, and their DNA G+C contents were 34.4 and 35.1 mol%, respectively. Genome sequencing of the three isolates revealed a genome size of 2.26–2.40 Mbp. Furthermore, all three isolates converted dissolved organic nitrogen to ammonium during cell growth. On the basis of the results of phenotypic and phylogenetic analyses, strains SHINM13 and GENT11 and GENT5 represent two distinct novel species in the genus , for which the names sp. nov. (type strain SHINM13 =JCM 34684 =NCIMB 15379) and sp. nov. (type strain GENT5 =JCM 32249=NCIMB 15380) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ammonification , Bacterioplankton , Flavobacterium and surface river water
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005307
2022-03-28
2024-05-04
Loading full text...

Full text loading...

References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Genus II. Flavobacterium gen. nov. In Bergey’s Manual of Determinative Bacteriology, 1st ed. Baltimore, MD: Williams and Wilkins; 1923 pp 97–117
     [Google Scholar]
  2. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
     [Google Scholar]
  3. Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA et al. The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser 1983; 10:257 [View Article]
     [Google Scholar]
  4. 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. Aquat Microb Ecol 2002; 28:141–155 [View Article]
     [Google Scholar]
  5. Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S. A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 2011; 75:14–49 [View Article]
     [Google Scholar]
  6. Eiler A, Bertilsson S. Flavobacteria blooms in four eutrophic lakes: linking population dynamics of freshwater bacterioplankton to resource availability. Appl Environ Microbiol 2007; 73:3511–3518 [View Article] [PubMed]
     [Google Scholar]
  7. Zeder M, Peter S, Shabarova T, Pernthaler J. A small population of planktonic Flavobacteria with disproportionally high growth during the spring phytoplankton bloom in a prealpine lake. Environ Microbiol 2009; 11:2676–2686 [View Article] [PubMed]
     [Google Scholar]
  8. Rohwer RR, Hamilton JJ, Newton RJ, McMahon KD. TaxAss: leveraging a custom freshwater database achieves fine-scale taxonomic resolution. mSphere 2018; 3:e00327-18 [View Article] [PubMed]
     [Google Scholar]
  9. Watanabe K, Komatsu N, Kitamura T, Ishii Y, Park H-D et al. Ecological niche separation in the Polynucleobacter subclusters linked to quality of dissolved organic matter: a demonstration using a high sensitivity cultivation-based approach. Environ Microbiol 2012; 14:2511–2525 [View Article] [PubMed]
     [Google Scholar]
  10. 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]
  11. Watanabe K, Ishii Y, Komatsu N, Kitamura T, Watanabe M et al. Growth rates and tolerance to low water temperatures of freshwater bacterioplankton strains: ecological insights from shallow hypereutrophic lakes in Japan. Hydrobiologia 2016; 792:67–81 [View Article]
     [Google Scholar]
  12. Kim SW, Suda W, Kim S, Oshima K, Fukuda S et al. Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing. DNA Res 2013; 20:241–253 [View Article]
     [Google Scholar]
  13. Liu WT, Mirzabekov AD, Stahl DA. Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ Microbiol 2001; 3:619–629 [View Article]
     [Google Scholar]
  14. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
     [Google Scholar]
  15. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article]
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  17. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  19. Ogata Y, Suda W, Ikeyama N, Hattori M, Ohkuma M et al. Complete genome sequence of Phascolarctobacterium faecium JCM 30894, a succinate-utilizing bacterium isolated from human feces. Microbiol Resour Announc 2019; 8:e01487-18 [View Article] [PubMed]
     [Google Scholar]
  20. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  21. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article]
     [Google Scholar]
  22. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  23. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
     [Google Scholar]
  24. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article]
     [Google Scholar]
  25. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
     [Google Scholar]
  26. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  27. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article] [PubMed]
     [Google Scholar]
  28. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  29. Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods 2013; 10:1196–1199 [View Article] [PubMed]
     [Google Scholar]
  30. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. 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]
  33. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article] [PubMed]
     [Google Scholar]
  34. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
     [Google Scholar]
  35. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
     [Google Scholar]
  36. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  37. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note no. 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  38. Ekwe AP, Ahn J-H, Kim SB. Flavobacterium keumense sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2017; 67:2166–2170 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005307
Loading
Flavobacterium ammonificans sp. nov. and Flavobacterium ammoniigenes sp. nov., ammonifying bacteria isolated from surface river water
Int J Syst Evol Microbiol 72, 005307 (2022); https://doi.org/10.1099/ijsem.0.005307
/content/journal/ijsem/10.1099/ijsem.0.005307
/content/journal/ijsem/10.1099/ijsem.0.005307
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

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