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Salimicrobium humidisoli sp. nov., Isolated from Saline–Alkaline Soil

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Abstract

A Gram-staining-positive, aerobic, non-endospore-forming, coccus-shaped, non-flagellated, and non-motile bacterium, designated WN024T, was isolated from the natural saline–alkali wetland soil of Binhai new district, Tianjin, China. Cells of strain WN024T were catalase- and oxidase-positive. The isolate was able to grow between 20 and 45 °C (optimal at 33–37 °C), pH 6.5–11.0 (optimal 7.5–8.0), and in the presence of 5.0–25.0% NaCl (optimal at 10.0–15.0%, w/v). The isolate could be affiliated to the genus Salimicrobium and the highest 16S rRNA gene sequence similarity of strain WN024T to its closest relative Salimicrobium salexigens DSM 22782T was 97.9%. The size of the genome was 2,622,223 bp in size with a G + C content of 47.1%. The sole respiratory quinone of strain WN024T was MK-7, the predominant fatty acids were iso-C15:0, anteiso-C15:0 and anteiso-C17:0. The major polar lipids were phosphatidylglycerol (PG), glycolipid (GL), phospholipid (PL) and diphosphatidylglycerol (DPG). The cell-wall diamino acid was meso-diaminopimelic acid. The DNA–DNA hybridization values between strain WN024T and the closest relative S. salexigens DSM 22782T was 47.3 ± 2.3%. The highest average nucleotide identity (ANI) value was 92.3% to S. salexigens DSM 22782T (GenBank Accession No. GCA_900156705.1). Therefore, we propose a novel species in the genus Salimicrobium to accommodate this novel isolate, named Salimicrobium humidisoli sp. nov. The type strain is WN024T (= ACCC 19979T = KCTC 33897T).

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References

  1. Yoon JH, Kang SJ, Oh TK (2007) Reclassification of Marinococcus albus Hao et al. 1985 as Salimicrobium album gen. nov., comb. nov. and Bacillus halophilus Ventosa et al. 1990 as Salimicrobium halophilum comb. nov., and description of Salimicrobium luteum sp. nov. Int J Syst Evol Microbiol 57:2406–2411

    Article  CAS  Google Scholar 

  2. Mo XQ, Xu N, Li HY, Meng WQ (2013) Study on soil seed bank in saline–alkali wetlands of Tianjin Binhai New Area. Adv Mat Res 610–613:3483–3487

    Google Scholar 

  3. Ostle AG, Holt JG (1982) Nile blue A as a fluorescent stain for poly-beta-hydroxybutyrate. Appl Environ Microbiol 44:238–241

    Article  CAS  Google Scholar 

  4. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general, molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  5. Dong XZ, Cai MY (eds) (2001) Chapter 14. Determination of biochemical characteristics. In Manual for the systematic identification of general bacteria, pp 370–398. Science Press, Beijing (in Chinese)

    Google Scholar 

  6. Fraser SL, Jorgensen JH (1997) Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 41:2738–2741

    Article  CAS  Google Scholar 

  7. Huang Y, Sun YJ, Ma SC, Chen L, Zhang H, Deng Y (2013) Isolation and characterization of Keratinibaculum paraultunense gen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity. FEMS Microbiol Lett 345:56–63

    Article  CAS  Google Scholar 

  8. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SH, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  CAS  Google Scholar 

  9. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  Google Scholar 

  10. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  Google Scholar 

  11. Fitch WM (1971) Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  12. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  Google Scholar 

  13. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  14. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477

    Article  CAS  Google Scholar 

  15. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Inc., Newark DE

    Google Scholar 

  16. Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917

    Article  CAS  Google Scholar 

  17. Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863–864

    Article  CAS  Google Scholar 

  18. Li RQ, Li YR, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714

    Article  CAS  Google Scholar 

  19. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272

    Article  CAS  Google Scholar 

  20. Liu B, Shi Y, Yuan J, Hu X, Zhang H, Li N, Li Z, Chen YX, Mu DS, Fan W (2013) Estimation of genomic characteristics byanalyzing k-mer frequency in de novo genome projects. arXiv:1308.2012

  21. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2014) Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055

    Article  Google Scholar 

  22. De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142

    Article  Google Scholar 

  23. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    Article  CAS  Google Scholar 

  24. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12

    Article  Google Scholar 

  25. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    Article  CAS  Google Scholar 

  26. Graham PH, Sadowsky MJ, Keyser HH, Barnet YM, Bradley RS (1991) Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. Int J Syst Bacteriol 41:582–587

    Article  Google Scholar 

  27. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  28. Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    Article  CAS  Google Scholar 

  29. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    Article  CAS  Google Scholar 

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Acknowledgments

This work was supported by the National Key Research and Development Program of China (2017YFD0201401), National Natural Science Foundation of China (NSFC No. 31670113). We would like to thank Prof. Aharon Oren for very valuable help in naming the organism. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA genes of strain WN024T was MF770264. The whole-genome has been deposited at DDBJ/EMBL/GenBank under the accession NSGH00000000. Thin-layer chromatograms of the polar lipids extracted from strain WN024T, additional phylogenetic trees, and the table containing the average nucleotide identity (ANI) values to closely related genomes are available as Supplementary Materials.

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  1. Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P.R. China

    Qin Xiong, Yunpeng Liu, Juanjuan Zhao & Guishan Zhang

  2. College of Life Science, Yangtze University, Jingzhou, 434023, Hubei, P.R. China

    Zhenjuan Fang

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Correspondence to Guishan Zhang.

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All of the authors of the manuscript entitled "Salimicrobium humidisoli sp. nov., isolated from saline–alkaline soil" declared that we have no conflicts of interest to this work. We declare that we do not have any commercial or any other associative interest that represents a conflict of interest in connection with the work submitted.

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Xiong, Q., Liu, Y., Zhao, J. et al. Salimicrobium humidisoli sp. nov., Isolated from Saline–Alkaline Soil. Curr Microbiol 78, 3292–3298 (2021). https://doi.org/10.1007/s00284-021-02551-4

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