1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 10

sp. nov., a novel strain isolated from desert soil No Access

Abstract

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16 grew at pH 6.0–11.0 (optimum, pH 8.0–9.0), 4–40 °C (optimum, 30–35 °C) and in the presence of 0–8 % (w/v) NaCl (optimum, 0–2 %). The strain was negative for catalase and positive for oxidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SJ-16 clustered with 100111 and THG-MD21, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains 100111, THG-MD21, B9 and all other type strains of the genus , respectively. The major cellular fatty acids were iso-C, iso-C, summed feature 3 (C 7 and/or C 6) and summed feature 9 (C 10-methyl and/or iso-C 9). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids, and ubiquinone-8 was the only respiratory quinone. The genomic DNA G+C content was 69.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values of strain SJ-16 to 100111, THG-MD21, 4-12 and B9 were 36.9, 37.5, 24.0 and 21.1 %, and 80.9, 80.6, 80.7 and 76.3 %, respectively. Based on phenotypic, physiological and phylogenetic results, strain SJ-16 represents a novel species of the genus , for which the name is proposed. The type strain is SJ-16 (=CGMCC 1.17694=KCTC 82207).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): desert soil , genome comparison , Luteimonas and polyphasic taxonomy
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31960020)
    • Principle Award Recipient: Ji-QuanSun
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005048
2021-10-11
2024-05-13
Loading full text...

Full text loading...

References

  1. Finkmann W, Altendorf K, Stackebrandt E, Lipski A. Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp nov., Luteimonas mephitis gen. nov., sp nov and Pseudoxanthomonas broegbernensis gen. nov., sp nov. Int J Syst Evol Microbiol 50:273–282 [View Article] [PubMed]
     [Google Scholar]
  2. Xiong L, An L, Zong Y, Wang M, Wang G et al. Luteimonas gilva sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2020; 70:3462–3467 [View Article] [PubMed]
     [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. Zhang H, Zhao H-Z, Liu J, Qin W, Huang X. Luteimonas weifangensis sp. nov., isolated from bensulfuron-methyl contaminated watermelon soil. Curr Microbiol 2020; 77:3787–3792 [View Article] [PubMed]
     [Google Scholar]
  5. Siddiqi MZ, Yeon JM, Choi H, Lee JH, Kim SY et al. Luteimonas granuli sp. nov., isolated from granules of the wastewater treatment plaIsolated from Granules of the Wastewater Treatment Plant. Curr Microbiol 2020; 77:2002–2007 [View Article] [PubMed]
     [Google Scholar]
  6. Lin P, Yan ZF, Li CT. Luteimonas cellulosilyticus sp. nov., Cellulose-degrading bacterium isolated from soil in Changguangxi National Wetland Park, China. Curr Microbiol 2020; 77:1341–1347 [View Article] [PubMed]
     [Google Scholar]
  7. Zhang G, Lai X-H, Yang J, Jin D, Pu J et al. Luteimonas chenhongjianii, a novel species isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae. Int J Syst Evol Microbiol 2020; 70:3186–3193 [View Article] [PubMed]
     [Google Scholar]
  8. Zhang SH, Wang XX, Yang J, Lu S, Lai XH et al. Luteimonas yindakuii sp. nov. isolated from the leaves of dandelion Dandelion (Taraxacum officinale) on the Qinghai-Tibetan Plateau. Int J Syst Evol Microbiol 2020; 70:1007–1014 [View Article] [PubMed]
     [Google Scholar]
  9. Cha Q-Y, Zhou X-K, Zhang X-F, Li M, Wei Y-Q et al. Luteimonas lumbrici sp. nov., a novel bacterium isolated from wormcast. Int J Syst Evol Microbiol 2020; 70:604–610 [View Article] [PubMed]
     [Google Scholar]
  10. Zhao GY, Shao F, Zhang M, Zhang XJ, Wang JY et al. Luteimonas rhizosphaerae sp. nov., isolated from the rhizosphere of Triticum aestivum L. Int J Syst Evol Microbiol 2018; 68:1197–1203 [View Article] [PubMed]
     [Google Scholar]
  11. Roh SW, Kim K-H, Nam Y-D, Chang H-W, Kim M-S et al. Luteimonas aestuarii sp nov., isolated from tidal flat sedimentTidal Flat Sediment. J Microbiol 2008; 46:525–529 [View Article] [PubMed]
     [Google Scholar]
  12. Zhang D-C, Liu H-C, Xin Y-H, Zhou Y-G, Schinner F et al. Luteimonas terricola sp nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2010; 60:1581–1584 [View Article] [PubMed]
     [Google Scholar]
  13. Young C-C, Kaempfer P, Chen W-M, Yen W-S, Arun AB et al. Luteimonas composti sp nov, a moderately thermophilic bacterium isolated from food waste. Int J Syst Evol Microbiol 2007; 57:741–744 [View Article] [PubMed]
     [Google Scholar]
  14. Chou J-H, Cho N-T, Arun AB, Young C-C, Chen W-M. Luteimonas aquatica sp nov., isolated from fresh water from Southern Taiwan. Int J Syst Evol Microbiol 2008; 58:2051–2055 [View Article] [PubMed]
     [Google Scholar]
  15. Fan XY, Yu T, Li Z, Zhang XH. Luteimonas abyssi sp nova, isolated from deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:668–674 [View Article] [PubMed]
     [Google Scholar]
  16. Ke CY, Sun WJ, Li YB, GM L, Zhang QZ et al. Microbial enhanced oil recovery in Baolige Oilfield using an indigenous facultative anaerobic strain Luteimonas huabeiensis sp nov. J Pet Sci Eng 2018; 167:160–167
     [Google Scholar]
  17. Koshlaf E, Shahsavari E, Haleyur N, Osborn AM, Ball AS. Impact of necrophytoremediation on petroleum hydrocarbon degradation, ecotoxicity and soil bacterial community composition in diesel-contaminated soil. Environ Sci Pollut Res 2020; 27:31171–31183 [View Article]
     [Google Scholar]
  18. Mu Y, Pan YF, Shi WX, Liu L, Jiang Z et al. Luteimonas arsenica sp nov., an arsenic-tolerant bacterium isolated from arsenic-contaminated soil. Int J Syst Evol Microbiol 2016; 66:2291–2296 [View Article] [PubMed]
     [Google Scholar]
  19. Sun J-Q, Xu L, Guo Y, Li W-L, Shao Z-Q et al. Kribbella deserti sp nov., isolated from rhizosphere soil of Ammopiptanthus mongolicus. Int J Syst Evol Microbiol 2017; 67:692–696 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Edwards AWF. The origin and early development of the method of minimum evolution for the reconstruction of phylogenetic trees. Syst Biol 1996; 45:79–91 [View Article]
     [Google Scholar]
  22. von Haeseler A. Maximum likelihood tree reconstruction. Zool-Anal Complex Syst 2000; 102:101–110
     [Google Scholar]
  23. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article] [PubMed]
     [Google Scholar]
  24. Felsenstein J. Confidence on phylogenies - an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  25. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. troducing 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]
  26. Ma J-P, Wang Z, Lu P, Wang H-J, Ali SW et al. Biodegradation of the sulfonylurea herbicide chlorimuron-ethyl by the strain Pseudomonas sp. LW3. FEMS Microbiol Lett 2010; 296:203–209
     [Google Scholar]
  27. Sun J-Q, Xu L, Wang L-J, Wu X-L. Draft genome sequence of a Rhodococcus strain isolated from tannery wastewater treatment sludge. Microbiol Resour Announc 2015; 3:e01463–14
     [Google Scholar]
  28. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  29. Auch AF, Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridizationfor microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117 [View Article] [PubMed]
     [Google Scholar]
  30. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PEER J 2016; 4:e1900v1
     [Google Scholar]
  31. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
  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. Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  35. Xu L, Dong ZB, Fang L, Luo YJ, Wei ZY et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article] [PubMed]
     [Google Scholar]
  36. Smibert RM, Krieg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  37. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press;
     [Google Scholar]
  38. Fraser SL, Jorgensen JH. Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 1997; 41:2738–2741 [View Article]
     [Google Scholar]
  39. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  40. Oren A. Characterization of pigments of Prokaryotes and their use in taxonomy and classification. Method Microbiol 2011; 38:261–282
     [Google Scholar]
  41. Akhwale JK, Göker M, Rohde M, Schumann P, Klenk H-P et al. Belliella kenyensis sp. nov., isolated from an alkaline lake. Int J Syst Evol Microbiol 2015; 65:457–462 [View Article] [PubMed]
     [Google Scholar]
  42. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  43. Kates M. Techniques of Lipidology: Isolation, Analysis, and Identification of Lipids Ottawa: Newport Somerville Innovation; 1986
     [Google Scholar]
  44. Komagata K, Suzuki K-I. Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 1988; 19:161–207
     [Google Scholar]
  45. Ngo HTT, Yin CS. Luteimonas terrae sp nov., isolated from rhizosphere soil of Radix ophiopogonis. Int J Syst Evol Microbiol 2016; 66:1920–1925 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005048
Loading
Luteimonas deserti sp. nov., a novel strain isolated from desert soil
Int J Syst Evol Microbiol 71, 005048 (2021); https://doi.org/10.1099/ijsem.0.005048
/content/journal/ijsem/10.1099/ijsem.0.005048
/content/journal/ijsem/10.1099/ijsem.0.005048
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