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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 12

Proposal to reclassify into a novel genus as gen. nov., comb. nov., and description of sp. nov. and sp. nov., isolated from freshwater lakes on the Tibetan Plateau No Access

Abstract

Thousands of lakes harbouring different characteristics (pH, salinity, temperature) are located on the Tibetan Plateau, and the mining of microbial resources inhabited in these lakes has great value. Two Gram-stain-negative, aerobic, rod-shaped, non-motile strains (LQ15W and AIY15W) were isolated from freshwater lakes on the Tibetan Plateau. Comparisons based on the 16S rRNA gene sequences showed that both strains LQ15W and AIY15W share 16S rRNA gene sequence similarities 98.4 % with Z0201, but only about 95.0 % with DSM 16537. The 16S rRNA gene sequence similarity between strains LQ15W and AIY15W was 98.9 %. The phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that strains LQ15W and AIY15W take Z0201 as their closest neighbour and these three strains form a tight cluster. In the phylogenomic tree, the genus was splited into two clusters by . Strains LQ15W, AIY15W and Z0201 still formed a close cluster, and DSM 16537 and CUG 91378 formed another cluster. The calculated OrthoANIu, average amino acid identity and digital DNA–DNA hybridization values among strains LQ15W, AIY15W, Z0201, DSM 16537 and CUG 91378 were less than 91.0, 92.9 and 42.1 %, respectively. The major respiratory quinones of both strains LQ15W and AIY15W were MK-7 (32 %) and MK-8 (68 %), and their major fatty acids were iso-C, C 9, summed feature 3 and summed feature 9. The predominant polar lipids of both strains were phosphatidylethanolamine, unidentified aminophospholipids, unidentified phospholipids and lipids. Strain AIY15W also contained phosphatidylglycerol and unidentified glycolipid. Considering the distinct phylogenetic relationships and chemotaxonomic characteristics between strains Z0201 and DSM 16537, it is proposed to reclassify into a novel genus gen. nov. as comb. nov., and strains LQ15W and AIY15W should represent two independent novel species of the genus , for which the names sp. nov. (type strain: LQ15W=CICC 24711=JCM 34222) and sp. nov. (type strain: AIY15W=CICC 24708=JCM 34612) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Cognataquiflexum , freshwater lake and Tibetan Plateau
Funding
This study was supported by the:
  • Youth Innovation Promotion Association of the Chinese Academy of Sciences (Award 2014273)
    • Principle Award Recipient: PengXing
  • Yunnan Provincial Minister of Science and Technology (Award 202005AF150005)
    • Principle Award Recipient: HuibinLu
  • National Natural Science Foundation of China (Award 31670505; 31722008)
    • Principle Award Recipient: PengXing
  • the Second Tibetan Plateau Scientific Expedition and Research Program (Award 2019QZKK0503)
    • Principle Award Recipient: PengXing
© 2022 The Authors
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2022-12-20
2024-05-09
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References

  1. Brettar I, Christen R, Höfle MG. Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the Cytophaga-Flavobacterium-Bacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 2004; 54:2335–2341 [View Article] [PubMed]
     [Google Scholar]
  2. Bhumika V, Srinivas TNR, Ravinder K, Anil Kumar P. Mariniradius saccharolyticus gen. nov., sp. nov., a member of the family Cyclobacteriaceae isolated from marine aquaculture pond water, and emended descriptions of the genus Aquiflexum and Aquiflexum balticum. Int J Syst Evol Microbiol 2013; 63:2088–2094 [View Article] [PubMed]
     [Google Scholar]
  3. Wang XT, Wang XM, Zheng WS, Zhang XK, Du ZJ. Aquiflexum aquatile sp. nov., isolated from lake water. Int J Syst Evol Microbiol 2019; 69:1947–1952 [View Article] [PubMed]
     [Google Scholar]
  4. Huang J, Han M, Fang B, Yang J, Xiao H et al. Aquiflexum lacus sp. nov., isolated from a lake sediment sample. Arch Microbiol 2021; 203:2911–2917 [View Article] [PubMed]
     [Google Scholar]
  5. Zhang R, Wu Q, Piceno YM, Desantis TZ, Saunders FM et al. Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high-density microarray and clone library analysis. FEMS Microbiol Ecol 2013; 86:277–287 [View Article] [PubMed]
     [Google Scholar]
  6. Xing P, Hahn MW, Wu QL. Low taxon richness of bacterioplankton in high-altitude lakes of the eastern tibetan plateau, with a predominance of Bacteroidetes and Synechococcus spp. Appl Environ Microbiol 2009; 75:7017–7025 [View Article]
     [Google Scholar]
  7. Misal SA, Lingojwar DP, Gawai KR. Properties of NAD (P) H azoreductase from alkaliphilic red bacteria Aquiflexum sp. DL6. Protein J 2013; 32:601–608 [View Article]
     [Google Scholar]
  8. Misal SA, Bajoria VD, Lingojwar DP, Gawai KR. Purification and characterization of nitroreductase from red alkaliphilic bacterium Aquiflexum sp. DL6. Prikl Biokhim Mikrobiol 2013; 49:249–254 [View Article]
     [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Sequencing Techniques in Bacterial Systematics New York, USA: Wiley; 1991 pp 115–175
     [Google Scholar]
  10. 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]
     [Google Scholar]
  11. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
  15. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1 [View Article]
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  17. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [Google Scholar]
  18. Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S et al. ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Genome Res 2017; 27:768–777 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. 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]
  21. 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]
     [Google Scholar]
  22. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article]
     [Google Scholar]
  23. Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M. New approach for understanding genome variations in KEGG. Nucleic Acids Res 2019; 47:D590–D595 [View Article] [PubMed]
     [Google Scholar]
  24. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article] [PubMed]
     [Google Scholar]
  25. Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Front Microbiol 2018; 9:771 [View Article]
     [Google Scholar]
  26. Zhu XF. Modern Experimental Techniques of Microbiology Hangzhou, China: Zhejiang University Press; 2011
     [Google Scholar]
  27. Lu HB, Xing P, Phurbu D, Tang Q, Wu QL. Pelagibacterium montanilacus sp. nov., an alkaliphilic bacterium isolated from Lake Cuochuolong on the Tibetan Plateau. Int J Syst Evol Microbiol 2018; 68:2220–2225 [View Article] [PubMed]
     [Google Scholar]
  28. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  29. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. eds Methods in Phytobacteriology Budapest, Hungary: Akademiai Kaido; 1990 pp 199–204
     [Google Scholar]
  30. 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]
  31. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202
     [Google Scholar]
  32. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  33. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article]
     [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. Bowman JP, Nichols CM, Gibson JAE. Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 2003; 53:1343–1355 [View Article]
     [Google Scholar]
  36. Brettar I, Christen R, Höfle MG. Belliella baltica gen. nov., sp. nov., a novel marine bacterium of the Cytophaga-Flavobacterium-Bacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 2004; 54:65–70 [View Article] [PubMed]
     [Google Scholar]
  37. Kumar PA, Srinivas TNR, Madhu S, Kumar RS, Singh S et al. Retraction. Cecembia lonarensis gen. nov., sp. nov., a novel haloalkalitolerant bacterium of the family Cyclobacteriaceae, isolated from a haloalkaline lake and emended descriptions of the genera Indibacter, Nitritalea, Belliella and Aquiflexum. Int J Syst Evol Microbiol 2010; 61:2252–2258 [View Article]
     [Google Scholar]
  38. Albuquerque L, Tiago I, Nobre MF, Veríssimo A, da Costa MS. Cecembia calidifontis sp. nov., isolated from a hot spring runoff, and emended description of the genus Cecembia. Int J Syst Evol Microbiol 2013; 63:1431–1436 [View Article] [PubMed]
     [Google Scholar]
  39. Kämpfer P, Young C-C, Chen W-M, Rekha PD, Fallschissel K et al. Fontibacter flavus gen. nov., sp. nov., a member of the family “Cyclobacteriaceae”, isolated from a hot spring. Int J Syst Evol Microbiol 2010; 60:2066–2070 [View Article]
     [Google Scholar]
  40. Srinivas TNR, Aditya S, Bhumika V, Kumar PA. Lunatimonas lonarensis gen. nov., sp. nov., a haloalkaline bacterium of the family Cyclobacteriaceae with nitrate reducing activity. Syst Appl Microbiol 2014; 37:10–16 [View Article] [PubMed]
     [Google Scholar]
  41. Han M-X, Huang J-R, Jiang H-C, Fang B-Z, Xie Y-G et al. Lunatibacter salilacus gen. nov., sp. nov., a member of the family Cyclobacteriaceae, isolated from a saline and alkaline lake sediment. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  42. Wang YX, Liu YP, Huo QQ, Li YP, Feng FY et al. Mongoliibacter ruber gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae isolated from a haloalkaline lake. Int J Syst Evol Microbiol 2016; 66:1088–1094 [View Article]
     [Google Scholar]
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Proposal to reclassify Aquiflexum aquatile into a novel genus as Cognataquiflexum aquatile gen. nov., comb. nov., and description of Cognataquiflexum nitidum sp. nov. and Cognataquiflexum rubidum sp. nov., isolated from freshwater lakes on the Tibetan Plateau
Int J Syst Evol Microbiol 72, 005653 (2023); https://doi.org/10.1099/ijsem.0.005653
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