1887

Abstract

A novel Gram-stain-negative strain, designated JM10B15, was isolated from pond water for collected from Jiangmen City, Guangdong province, south PR China. Cells of the strain were aerobic, rod-shaped, and motile by lateral flagella. JM10B15 could grow at 15–40 °C, pH 6.0–9.5, and in 0–3.0 % NaCl, with optimal growth at 25–35 °C, pH 7.5–8.5, and in 0 % NaCl, respectively. Furthermore, this strain grew well on Reasoner's 2A agar but not on nutrient broth agar or Luria–Bertani agar. JM10B15 was a denitrifying bacterium capable of removing nitrites and nitrates, and three key functional genes, , , and , were identified in its genome. The results of phylogenetic analyses based on the 16S rRNA gene and genome sequences indicated that JM10B15 belonged to the genus . JM10B15 showed the highest 16S rRNA sequence similarity to YJ-T1-11 (98.8 %), followed by IFAM 1031 (98.6 %) and HB-1 (98.1 %). The average nucleotide identity and digital DNA–DNA hybridization values between JM10B15 and the other type strains of genus were 78.1–82.1 % and 18.4–22.1 %, respectively. The major fatty acids of strain JM10B15 were summed feature 8 (C 6 and/or C 7) and C 7 11-methyl. In addition, the major respiratory quinone of this novel strain was Q-10, and the predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, four unidentified phospholipids, three unidentified lipids, and an unidentified aminophospholipid. Results of analyses of the phylogenetic, genomic, physiological, and biochemical characteristics indicated that JM10B15 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is JM10B15 (=GDMCC 1.4148=KCTC 8140).

Funding
This study was supported by the:
  • Guangdong Strategic Special Fund for Rural Revitalization (Award 2023-WBH-00-001)
    • Principle Award Recipient: HonghuiZhu
  • Guangdong Special Support Program (Award 2021JC06N628)
    • Principle Award Recipient: HonghuiZhu
  • GDAS’ Project of Science and Technology Development (Award 2022GDASZH-2022010101)
    • Principle Award Recipient: MingxiaZhang
  • GDAS’ Project of Science and Technology Development (Award 2022GDASZH-2022010202)
    • Principle Award Recipient: YulianZhang
  • National Natural Science Foundation of China (Award 32200086)
    • Principle Award Recipient: MingxiaZhang
  • National Natural Science Foundation of China (Award 32070115)
    • Principle Award Recipient: MingxiaZhang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006430
2024-06-17
2024-07-15
Loading full text...

Full text loading...

References

  1. Rothe B, Fischer A, Hirsch P, Sittig M, Stackebrandt E. The phylogenetic position of the budding bacteria Blastobacter aggregatus and Gemmobacter aquatilis gen., nov. sp. nov. Arch Microbiol 1987; 147:92–99 [View Article]
    [Google Scholar]
  2. Chen W-M, Cho N-T, Huang W-C, Young C-C, Sheu S-Y. Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilumas Gemmobacter nectariphilus comb. nov., Catellibacterium changlenseas Gemmobacter changlensis comb. nov., Catellibacterium aquatileas Gemmobacter aquaticus nom. nov., Catellibacterium caenias Gemmobacter caeni comb. nov., Catellibacterium nanjingenseas Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis. Int J Syst Evol Microbiol 2013; 63:470–478 [View Article]
    [Google Scholar]
  3. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic Names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  4. Kang JY, Kim MJ, Chun J, Son KP, Jahng KY. Gemmobacter straminiformis sp. nov., isolated from an artificial fountain. Int J Syst Evol Microbiol 2017; 67:5019–5025 [View Article] [PubMed]
    [Google Scholar]
  5. Yoo Y, Lee DW, Lee H, Kwon B-O, Khim JS et al. Gemmobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2019; 69:1676–1681 [View Article] [PubMed]
    [Google Scholar]
  6. Kämpfer P, Jerzak L, Wilharm G, Golke J, Busse H-J et al. Gemmobacter intermedius sp. nov., isolated from a white stork (Ciconia ciconia). Int J Syst Evol Microbiol 2015; 65:778–783 [View Article]
    [Google Scholar]
  7. Lim K, Kannan AD, Shobnam N, Mahmood M, Lee J et al. Gemmobacter serpentinus sp. nov., isolated from conserved forages. Int J Syst Evol Microbiol 2020; 70:4224–4232 [View Article] [PubMed]
    [Google Scholar]
  8. Suman J, Zubrova A, Rojikova K, Pechar R, Svec P et al. Pseudogemmobacter bohemicus gen. nov., sp. nov., a novel taxon from the Rhodobacteraceae family isolated from heavy-metal-contaminated sludge. Int J Syst Evol Microbiol 2019; 69:2401–2407 [View Article] [PubMed]
    [Google Scholar]
  9. Li G, Jiang Y, Li Q, Chen X, Jiang L et al. Falsigemmobacter faecalis gen. nov. sp. nov., isolated from faeces of Rhinopithecus roxellanae, and reclassification of Gemmobacter intermedius as Falsigemmobacter intermedius comb. nov. Arch Microbiol 2020; 202:2599–2606 [View Article] [PubMed]
    [Google Scholar]
  10. Bu X, Li Y, Lai W, Yao C, Liu Y et al. Innovation and development of the aquaculture nutrition research and feed industry in China. Rev Aquacult 2024; 16:759–774 [View Article]
    [Google Scholar]
  11. Zhang M, Zhang Y, Yao Q, Yang F, Zhu H. Marivirga aurantiaca sp. nov., a halophilic nitrite-reducing bacterium, isolated from intertidal surface sediments. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
    [Google Scholar]
  12. Huang F, Pan L, He Z, Zhang M, Zhang M. Identification, interactions, nitrogen removal pathways and performances of culturable heterotrophic nitrification-aerobic denitrification bacteria from mariculture water by using cell culture and metagenomics. Sci Total Environ 2020; 732:139268 [View Article] [PubMed]
    [Google Scholar]
  13. Zhang M, Li A, Yao Q, Xiao B, Zhu H. Pseudomonas oligotrophica sp. nov., a novel denitrifying bacterium possessing nitrogen removal capability under low carbon-nitrogen ratio condition. Front Microbiol 2022; 13:882890 [View Article] [PubMed]
    [Google Scholar]
  14. Zhang M, Li A, Xu S, Chen M, Yao Q et al. Sphingobacterium micropteri sp. nov. and Sphingobacterium litopenaei sp. nov., isolated from aquaculture water. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  15. 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] [PubMed]
    [Google Scholar]
  16. Katoh K, Standley DM. MAFFT: iterative refinement and additional methods. Methods Mol Biol 2014; 1079:131–146 [View Article] [PubMed]
    [Google Scholar]
  17. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
    [Google Scholar]
  18. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
    [Google Scholar]
  19. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2018; 35:518–522 [View Article] [PubMed]
    [Google Scholar]
  20. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
    [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  22. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Bacteriology, 3rd edn. Washington, DC: American Society of Microbiology; 2007 pp 330–393 [View Article]
    [Google Scholar]
  23. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1988; 19:1–67
    [Google Scholar]
  24. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the Taxonomy of Flavobacterium and Cytophaga-like Bacteria of the International Committee On Systematics Of Prokaryotes 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]
  25. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  26. 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] [PubMed]
    [Google Scholar]
  27. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  28. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
    [Google Scholar]
  31. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  32. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genom 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  33. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article] [PubMed]
    [Google Scholar]
  34. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
    [Google Scholar]
  35. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [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. Collins MD, Jones D. A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 1981; 51:129–134 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006430
Loading
/content/journal/ijsem/10.1099/ijsem.0.006430
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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