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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 5

sp. nov., a novel denitrifying bacteria isolated from the Yellow Sea and transfer of and to the genus as comb. nov. and nom. nov. No Access

Abstract

A Gram-stain-negative and rod-shaped bacterium, designated strain CY04, was isolated from a sediment sample collected from the Yellow Sea. CY04 exhibited the highest 16S rRNA gene sequence similarity of 98.7 % to CY05, followed by the similarities of 98.6 %, 98.0 and 98.0 % to DSW4-44, W43 and QS115 respectively. Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on genome sequences revealed that CY04 formed a robust cluster with CY05, DSW4-44, W43 and QS115. Calculated digital DNA–DNA hybridisation and average nucleotide identity values between CY04 and its closely related species were 22.2–23.7 % and 79.0–81.2 % respectively. Cells of CY04 were strictly aerobic, non-motile and positive for catalase, oxidase and denitrification. CY04 harboured a set of genes encoding the enzymes involved in denitrification. Growth occurred at 10–30 °C (optimum, 20 °C), at pH 6.5–9.5 (optimum, pH 8.0) and with 1–6 % (w/v) (optimum, 2.5 %,) NaCl. The major component of the fatty acids was summed feature 8 (Cω7 and/or Cω6). The isoprenoid quinone was Q-10. Results of the phenotypic, chemotaxonomic and molecular study indicate that strain CY04 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CY04 (=MCCC 1K08635=KCTC 62199). It is also proposed that and should be reclassified as comb. nov. and nom. nov. An emended description of the genus is also proposed.

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Keyword(s): denitrification , Parasedimentitalea denitrificans sp. nov. , Parasedimentitalea huanghaiensis comb. nov. , Parasedimentitalea maritima nom. nov. and Zongyanglinia
Funding
This study was supported by the:
  • Projects of Medical and Health Technology Development Program in Shandong Province (Award 202202040316)
    • Principle Award Recipient: CaixingShi
  • Lin He's New Medicine and Clinical Translation Academician Workstation Research Fund (Award JYHL2022MS12)
    • Principle Award Recipient: AngLiu
© 2024 The Authors
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2024-05-20
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References

  1. Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol 2018; 16:263–276 [View Article] [PubMed]
     [Google Scholar]
  2. Sun Y, Li A, Zhang X, Ma F. Regulation of dissolved oxygen from accumulated nitrite during the heterotrophic nitrification and aerobic denitrification of Pseudomonas stutzeri T13. Appl Microbiol Biotechnol 2015; 99:3243–3248 [View Article] [PubMed]
     [Google Scholar]
  3. Ozeki S, Baba I, Takaya N, Shoun H. A novel C1-using denitrifier Alcaligenes sp. STC1 and its genes for copper-containing nitrite reductase and azurin. Biosci Biotechnol Biochem 2001; 65:1206–1210 [View Article] [PubMed]
     [Google Scholar]
  4. Patureau D, Bernet N, Delgenès JP, Moletta R. Effect of dissolved oxygen and carbon-nitrogen loads on denitrification by an aerobic consortium. Appl Microbiol Biotechnol 2000; 54:535–542 [View Article] [PubMed]
     [Google Scholar]
  5. Ding W, Liu P, Xu Y, Fang J, Cao J. Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench. FEMS Microbiol Lett 2019; 366:fnaa004 [View Article] [PubMed]
     [Google Scholar]
  6. Li A-Q, Zhang C, Li D-H, Qi X-Q, Meng L et al. Parasedimentitalea psychrophila sp. nov., a psychrophilic bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
     [Google Scholar]
  7. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  8. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform 2004; 5:113 [View Article] [PubMed]
     [Google Scholar]
  9. 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]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  12. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983 [View Article]
     [Google Scholar]
  13. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  14. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  15. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  16. Li M, Hou L-Z, Xu X-H, Wang X-X, Zheng M-C et al. Phylogenomic analyses of a clade within the family Flavobacteriaceae suggest taxonomic reassignments of species of the genera Algibacter, Hyunsoonleella, Jejuia, and Flavivirga, and the proposal of Pseudalgibacter gen. nov. and Pseudalgibacter alginicilyticus comb. nov. Curr Microbiol 2021; 78:3277–3284 [View Article]
     [Google Scholar]
  17. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
     [Google Scholar]
  18. Liu A, Dong X, Wang W, Qin J, Leng H et al. Reclassification of Sabulilitoribacter multivorans and Sabulilitoribacter arenilitoris as Flaviramulus multivorans comb. nov. and Wocania arenilitoris comb. nov., respectively, based on genome sequence analysis. Int J Syst Evol Microbiol 2023; 73: [View Article]
     [Google Scholar]
  19. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
     [Google Scholar]
  20. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
     [Google Scholar]
  21. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432–4450 [View Article] [PubMed]
     [Google Scholar]
  22. Liu A, Zhang Y-J, Cheng P, Peng Y-J, Blom J et al. Whole genome analysis calls for a taxonomic rearrangement of the genus Colwellia. Antonie van Leeuwenhoek 2020; 113:919–931 [View Article] [PubMed]
     [Google Scholar]
  23. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393–2411 [View Article] [PubMed]
     [Google Scholar]
  24. Simpson PJL, Richardson DJ, Codd R. The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB. Microbiology 2010; 156:302–312 [View Article] [PubMed]
     [Google Scholar]
  25. Sánchez C, Minamisawa K. Redundant roles of Bradyrhizobium oligotrophicum Cu-type (NirK) and cd1-type (NirS) nitrite reductase genes under denitrifying conditions. FEMS Microbiol Lett 2018; 365: [View Article] [PubMed]
     [Google Scholar]
  26. Müller C, Zhang L, Zipfel S, Topitsch A, Lutz M et al. Molecular interplay of an assembly machinery for nitrous oxide reductase. Nature 2022; 608:626–631 [View Article] [PubMed]
     [Google Scholar]
  27. Liu A, Zhang X-Y, Chen C-X, Xie B-B, Qin Q-L et al. Neptunomonas qingdaonensis sp. nov., isolated from intertidal sand. Int J Syst Evol Microbiol 2013; 63:1673–1677 [View Article] [PubMed]
     [Google Scholar]
  28. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  29. Farmer JⅢ, Janda JM, Brenner FW, Cameron DN, Birkhead KM. Genus 1. Vibrio Pacini 1854, 411AL. In Brenner DJ, Krieg NR, Staley JT. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. New York: Springer; 2005 pp 494–546
     [Google Scholar]
  30. Wu Y-H, Xu L, Zhou P, Wang C-S, Oren A et al. Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field. Int J Syst Evol Microbiol 2015; 65:3645–3651 [View Article] [PubMed]
     [Google Scholar]
  31. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207 [View Article]
     [Google Scholar]
  32. Xu L, Liu A, Zhang YJ. Zongyanglinia huanghaiensis gen. nov., sp. nov., a novel denitrifying bacterium isolated from the yellow sea, and transfer of Pelagicola marinus to Zongyanglinia gen. nov. as Zongyanglinia marinus comb. nov. Antonie van Leeuwenhoek 2021; 114:137–149 [View Article] [PubMed]
     [Google Scholar]
  33. Choi YS, Oh JS, Roh DH. Pelagicola marinus sp. nov. isolated from deep-sea water. Int J Syst Evol Microbiol 2019; 69:3961–3966 [View Article] [PubMed]
     [Google Scholar]
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Parasedimentitalea denitrificans sp. nov., a novel denitrifying bacteria isolated from the Yellow Sea and transfer of Zongyanglinia huanghaiensis and Zongyanglinia marina to the genus Parasedimentitalea as Parasedimentitalea huanghaiensis comb. nov. and Parasedimentitalea maritima nom. nov.
Int J Syst Evol Microbiol 74, 006377 (2024); https://doi.org/10.1099/ijsem.0.006377
/content/journal/ijsem/10.1099/ijsem.0.006377
/content/journal/ijsem/10.1099/ijsem.0.006377
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