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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 4

gen. nov., sp. nov., isolated from the Kumtag Desert soil No Access

Abstract

A novel orange-coloured bacterium, designated strain SYSU D00508, was isolated from a sandy soil sampled from the Kumtag Desert in China. Strain SYSU D00508 was aerobic, Gram-stain-negative, oxidase-positive, catalase-positive and non-motile. Growth occurred at 4–45°C (optimum 28–30°C), pH 6.0–9.0 (optimum pH 7.0–8.0) and with 0–2.5 % NaCl (w/v, optimum 0–1.0 %). The major polar lipids consisted of phosphatidylethanolamine (PE), unidentified aminolipids (AL1-3) and unidentified polar lipids (L1-5) were also detected. The major respiratory quinone was MK-7 and the major fatty acids (>10 %) were iso-C 3-OH, iso-C and iso-C G. The genomic DNA G+C content was 42.6 %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU D00508 belonged to the family and showed 93.9 % ( DSM18137), 92.9 % ( NBRC 106135), 93.0 % ( JCM 32095) and 92.8 % ( JCM 19942) similarities. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain SYSU D00508 is proposed to represent a novel species of a new genus, named gen. nov., sp. nov., within the family . The type strain is SYSU D00508 (=KCTC 82286=CGMCC 1.18648=MCCC 1K05005).

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  • Accepted:
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Keyword(s): Aridibaculum aurantiacum gen. nov., sp. nov., , Kumtag Desert and polyphasic taxonomy
Funding
This study was supported by the:
  • Xinjiang Uygur Autonomous Region regional coordinated innovation project (Shanghai cooperation organization science and technology partnership program) (Award 2021E01018)
    • Principle Award Recipient: Wen-JunLi
  • the Fundamental Research Funds for the Central Universities, Sun Yat-Sen University (Award 2021qntd26)
    • Principle Award Recipient: LeiDong
  • National Natural Science Foundation of China (Award 32061143043)
    • Principle Award Recipient: Wen-JunLi
  • National Natural Science Foundation of China (Award 32000005)
    • Principle Award Recipient: LeiDong
  • the Third Xinjiang Scientific Expedition Program (Award 2022xjkk1200)
    • Principle Award Recipient: DongLei
© 2023 Sun Yat-Sen University
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References

  1. Kämpfer P, Lodders N, Falsen E. Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 2011; 61:518–523 [View Article] [PubMed]
     [Google Scholar]
  2. An D-S, Lee H-G, Im W-T, Liu Q-M, Lee S-T. Segetibacter koreensis gen. nov., sp. nov., a novel member of the phylum bacteroidetes, isolated from the soil of a ginseng field in south korea. Int J Syst Evol Microbiol 2007; 57:1828–1833 [View Article] [PubMed]
     [Google Scholar]
  3. Kim S-J, Ahn J-H, Weon H-Y, Hong S-B, Seok S-J et al. Parasegetibacter terrae sp. nov., isolated from paddy soil and emended description of the genus Parasegetibacter. Int J Syst Evol Microbiol 2015; 65:113–116 [View Article] [PubMed]
     [Google Scholar]
  4. Zhang K, Tang Y, Zhang L, Dai J, Wang Y et al. Parasegetibacter luojiensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from a forest soil. Int J Syst Evol Microbiol 2009; 59:3058–3062 [View Article] [PubMed]
     [Google Scholar]
  5. Weon H-Y, Kwon S-W, Son J-A, Kim S-J, Kim Y-S et al. Adhaeribacter aerophilus sp. nov., Adhaeribacter aerolatus sp. nov. and Segetibacter aerophilus sp. nov., isolated from air samples. Int J Syst Evol Microbiol 2010; 60:2424–2429 [View Article] [PubMed]
     [Google Scholar]
  6. Kim WH, Lee S, Ahn TY. Flavihumibacter cheonanensis sp. nov., isolated from sediment of a shallow stream. Int J Syst Evol Microbiol 2014; 64:3235–3239 [View Article] [PubMed]
     [Google Scholar]
  7. Jiang W-K, Lu M-Y, Cui M-D, Wang X, Wang H et al. Terrimonas soli sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2018; 68:819–823 [View Article] [PubMed]
     [Google Scholar]
  8. Weon H-Y, Kim B-Y, Yoo S-H, Lee S-Y, Kwon S-W et al. Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 2006; 56:1777–1782 [View Article] [PubMed]
     [Google Scholar]
  9. Li S, Dong L, Han JR et al. Longitalea arenae gen. nov., sp. nov. and Longitalea luteola sp. nov.,two new members of the family Chitinophagaceae isolated from desert soil. Arch Microbiol 2022; 204:1–10 [PubMed]
     [Google Scholar]
  10. Kämpfer P. Chitinophagaceae fam. nov. In Bergey’s Manual of Systematics of Archaea and Bacteria 2015 pp 1–2
     [Google Scholar]
  11. Li S, Dong L, Lian W-H, Lin Z-L, Lu C-Y et al. Exploring untapped potential of Streptomyces spp. in Gurbantunggut Desert by use of highly selective culture strategy. Sci Total Environ 2021; 790:148235 [View Article] [PubMed]
     [Google Scholar]
  12. Lian W-H, Li S, Lin Z-L, Han J-R, Mohamad OAA et al. Sabulibacter ruber gen. nov., sp. nov., a novel bacterium in the family Hymenobacteraceae, isolated from desert soil. Int J Syst Evol Microbiol 2022; 72:005248 [View Article] [PubMed]
     [Google Scholar]
  13. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article] [PubMed]
     [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] [PubMed]
     [Google Scholar]
  15. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. 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]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  19. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  20. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article] [PubMed]
     [Google Scholar]
  21. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Felsenstein J. Confidencelimits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  24. Harrison PG, Strulo B. SPADES - a process algebra for discrete event simulation. J Log Comput 2000; 10:3–42 [View Article]
     [Google Scholar]
  25. 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]
  26. Shi W, Sun Q, Fan G, Hideaki S, Moriya O et al. gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. Nucleic Acids Res 2021; 49:D694–D705 [View Article] [PubMed]
     [Google Scholar]
  27. 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] [PubMed]
     [Google Scholar]
  28. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
     [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk HP, 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. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  31. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article] [PubMed]
     [Google Scholar]
  32. Dong L, Li S, Lian W-H, Wei Q-C, Mohamad OAA et al. Sphingomonas arenae sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2022; 72:005195 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. 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]
  35. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  36. Leifson E. Atlas of Bacterial Flagellation New York: Academic Press; 1960 [View Article]
     [Google Scholar]
  37. Narsing Rao MP, Dong Z-Y, Kan Y, Zhang K, Fang B-Z et al. Description of Paenibacillus antri sp. nov. and Paenibacillus mesophilus sp. nov., isolated from cave soil. Int J Syst Evol Microbiol 2020; 70:1048–1054 [View Article] [PubMed]
     [Google Scholar]
  38. Dong L, Ming H, Zhou E-M, Yin Y-R, Liu L et al. Crenobacter luteus gen. nov., sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2015; 65:214–219 [View Article] [PubMed]
     [Google Scholar]
  39. 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]
  40. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  41. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
     [Google Scholar]
  42. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  43. 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]
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Aridibaculum aurantiacum gen. nov., sp. nov., isolated from the Kumtag Desert soil
Int J Syst Evol Microbiol 73, 005823 (2023); https://doi.org/10.1099/ijsem.0.005823
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