1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 1

sp. nov., isolated from saline-alkaline soil No Access

Abstract

A novel bacterium, designated TRT317, was isolated from saline-alkaline soil collected from the Pamir plateau in northwest China. Cells of this strain were Gram-stain-negative, aerobic rods and red-pink-coloured. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain TRT317 showed the highest sequence similarity to the type strains of (96.3 %) and (96.2 %). Growth was observed at 4–40 °C, pH 6.0–10.0 and in the presence of up to 7 % (w/v) NaCl. The major fatty acids were iso-C and summed feature 4 (iso-C I/anteiso-C B). The polar lipids included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified phospholipid, four unidentified glycolipids and five unidentified lipids. The whole-cell sugars of strain TRT317 were mannose, rhamnose, glucose, galactose, xylose, arabinose and four unidentified sugars. The sole respiratory quinone was MK-7. The genomic DNA G+C content of strain TRT317 was 47.7 mol%. The average nucleotide identity (ANI) value of strain TRT317 with was 88.3 %, which is below the standard ANI threshold for species identification (95–96 %). Combined results of physiological, genotypic, phylogenetic and chemotaxonomic analyses demonstrated that strain TRT317 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is TRT317 (=CGMCC1.18690=KCTC 82818).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Pamir plateau , polyphasic taxonomy , Pontibacter pamirensis sp. nov. and saline-alkaline soil
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31570109)
    • Principle Award Recipient: Deng-DiAn
  • Xinjiang Uygur Autonomous Region, regional coordinated Innovation Project and Shanghai Cooperation Organization Science and Technology Partnership Program (Award 2021E01018)
    • Principle Award Recipient: Wen-JunLi
  • the Open Subject of the Key Laboratory of the Autonomous Region (Award 2017D04008)
    • Principle Award Recipient: Deng-DiAn
  • Scientific Research Program of Higher Education Institution of Xinjiang (Award XJEDU2018I016)
    • Principle Award Recipient: Deng-DiAn
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005200
2022-01-25
2024-04-24
Loading full text...

Full text loading...

References

  1. Nedashkovskaya OI, Kim SB, Suzuki M, Shevchenko LS, Lee MS et al. Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum “Bacteroidetes”, and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003. Int J Syst Evol Microbiol 2005; 55:2583–2588 [View Article] [PubMed]
     [Google Scholar]
  2. Wang Y, Zhang K, Cai F, Zhang L, Tang Y et al. Pontibacter xinjiangensis sp. nov., in the phylum “Bacteroidetes”, and reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov. Int J Syst Evol Microbiol 2010; 60:99–103 [View Article]
     [Google Scholar]
  3. Xu L, Zeng X-C, Nie Y, Luo X, Zhou E et al. Pontibacter diazotrophicus sp. nov., a novel nitrogen-fixing bacterium of the family Cytophagaceae. PLoS One 2014; 9:e92294 [View Article] [PubMed]
     [Google Scholar]
  4. Zhang L, Zhang Q, Luo X, Tang Y, Dai J et al. Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 2008; 58:1210–1214 [View Article] [PubMed]
     [Google Scholar]
  5. Xu M, Wang Y, Dai J, Jiang F, Rahman E et al. Pontibacter populi sp. nov., isolated from the soil of a Euphrates poplar (Populus euphratica) forest. Int J Syst Evol Microbiol 2012; 62:665–670 [View Article] [PubMed]
     [Google Scholar]
  6. Subhash Y, Tushar L, Sasikala C, Ramana CV. Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from dry soil of a solar saltern. Int J Syst Evol Microbiol 2013; 63:4524–4532 [View Article]
     [Google Scholar]
  7. Cao H, Nie Y, Zeng X-C, Xu L, He Z et al. Pontibacter yuliensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:968–972 [View Article] [PubMed]
     [Google Scholar]
  8. Kang JY, Joung Y, Chun J, Kim H, Joh K et al. Pontibacter saemangeumensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:565–569 [View Article] [PubMed]
     [Google Scholar]
  9. Singh P, Kumari R, Nayyar N, Lal R. Pontibacter aurantiacus sp. nov. isolated from hexachlorocyclohexane (HCH) contaminated soil. Int J Syst Evol Microbiol 2017; 67:1400–1407 [View Article] [PubMed]
     [Google Scholar]
  10. Osman G, Zhang T, Lou K, Gao Y, Chang W et al. Pontibacter aydingkolensis sp. nov., isolated from soil of a salt lake. Int J Syst Evol Microbiol 2016; 66:5523–5528 [View Article] [PubMed]
     [Google Scholar]
  11. Smibert RM, Krieg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology Wiley; 1994 pp 607–654
     [Google Scholar]
  12. Tang S-K, Li W-J, Dong W, Zhang Y-G, Xu L-H et al. Studies of the biological characteristics of some halophilic and halotolerant actinomycetes isolated from saline and alkaline soils. Actinomycetologica 2003; 17:6–10 [View Article]
     [Google Scholar]
  13. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  14. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
     [Google Scholar]
  15. Narsing Rao MP, Dong Z-Y, Kan Y, Dong L, Li S et al. Description of Paenibacillus tepidiphilus sp. nov., isolated from a tepid spring. Int J Syst Evol Microbiol 2020; 70:1977–1981 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  21. 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]
  22. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  24. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016; 32:3047–3048 [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. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:1–15 [View Article] [PubMed]
     [Google Scholar]
  27. Blin K, Kim HU, Medema MH, Weber T. Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. Brief Bioinform 2019; 20:1103–1113 [View Article] [PubMed]
     [Google Scholar]
  28. Yoon S-H, Ha S-M, 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]
  29. 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] [PubMed]
     [Google Scholar]
  30. 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]
  31. Li Y, Shen Y. Chemical components of some microorganisms isolated from specific habitats and their antitumor activities. Chin J Org Chem 2013; 33:1135 [View Article]
     [Google Scholar]
  32. Azmi SA, Chatterjee S. Salt stress tolerant genes in halophilic and halotolerant bacteria: paradigm for salt stress adaptation and osmoprotection. Int J Curr Microbiol Appl Sci 2015; 4:642–658
     [Google Scholar]
  33. Subramani R, Aalbersberg W. Marine actinomycetes: an ongoing source of novel bioactive metabolites. Microbiol Res 2012; 167(10):571–580 [View Article] [PubMed]
     [Google Scholar]
  34. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  35. Tran PN, Tan NEH, Lee YP, Gan HM, Polter SJ et al. Whole-genome sequence and classification of 11 endophytic bacteria from poison ivy (Toxicodendron radicans). Genome Announc 2015; 3:e01319-15 [View Article] [PubMed]
     [Google Scholar]
  36. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Newark, DE: MIDI; 1990
  37. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  38. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 2006; 5:2359–2367 [View Article]
     [Google Scholar]
  39. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  40. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  41. 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 Meth 1984; 2:233–241 [View Article]
     [Google Scholar]
  42. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  43. Kim JH, Choi BH, Jo M, Kim SC, Lee PC. Flavobacterium faecale sp. nov., an agarase-producing species isolated from stools of Antarctic penguins. Int J Syst Evol Microbiol 2014; 64:2884–2890 [View Article] [PubMed]
     [Google Scholar]
  44. Heo J, Kim SH, Lee PC. New insight into the cleavage reaction of Nostoc sp. strain PCC 7120 carotenoid cleavage dioxygenase in natural and nonnatural carotenoids. Appl Environ Microbiol 2013; 79:3336–3345 [View Article] [PubMed]
     [Google Scholar]
  45. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article] [PubMed]
     [Google Scholar]
  46. Dilworth MJ. Acetylene reduction by nitrogen-fixing preparations from Clostridium pasteurianum. Biochim Biophys 1966; 127:285–294 [View Article]
     [Google Scholar]
  47. Fraser PD, Bramley PM. The biosynthesis and nutritional uses of carotenoids. Prog Lipid Res 2004; 43:228–265 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005200
Loading
Pontibacter pamirensis sp. nov., isolated from saline-alkaline soil
Int J Syst Evol Microbiol 72, 005200 (2022); https://doi.org/10.1099/ijsem.0.005200
/content/journal/ijsem/10.1099/ijsem.0.005200
/content/journal/ijsem/10.1099/ijsem.0.005200
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