A novel UV-resistant bacterium Sphingomonas endolithica sp. nov., and genomic analysis, isolated from the north slope of Mount Everest

• Published in: Antonie van Leeuwenhoek 2024-12, Vol.117 (1), p.5, Article 5
• Main Authors: Tian, Mao, Zhang, Wei, Zhang, Gaosen, Bahadur, Ali, Wu, Shiyu, Yu, Xue, Wu, Yujie, Jia, Puchao, Chen, Tuo, Liu, Guangxiu
• Format: Article
• Language: English
• Subjects: Amino acids; Bacteria; Biomedical and Life Sciences; Coenzyme Q10; Cold shock; Deoxyribonucleic acid; Detoxification; DNA; DNA sequencing; Ethanolamine; Fatty Acids; Galactose; Gene sequencing; Genes; Genomes; Genomic analysis; Genomics; Glycerol; Heat shock; Hybridization; Life Sciences; Lipids; Medical Microbiology; Microbiology; New species; Nucleotide sequence; Nucleotides; Original Paper; Peptidoglycans; Phospholipids; Phylogeny; Plant Sciences; Quinones; Ribose; RNA, Ribosomal, 16S - genetics; rRNA 16S; Similarity; Soil Science & Conservation; Sphingomonas; Sphingomonas - genetics; Strain; Subsystems
• ISSN: 0003-6072; 1572-9699; 1572-9699
• DOI: 10.1007/s10482-023-01903-3

Gram-stain-negative, aerobic, rod-shaped, non-motile bacterium strain ZFBP2030 T was isolated from a rock on the North slope of Mount Everest. This strain contained a unique ubiquinone-10 (Q-10) as a predominant respiratory quinone. Among the tested fatty acids, the strain contained summed feature 8, C 14:0 2OH, and C 16:0 , as major cellular fatty acids. The polar lipid profile contained phosphatidyl glycerol, phosphatidyl ethanolamine, three unidentified phospholipids, two unidentified aminolipids, and six unidentified lipids. The cell-wall peptidoglycan was a meso-diaminopimelic acid, and cell-wall sugars were ribose and galactose. Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain ZFBP2030 T was a member of the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas aliaeris DH-S5 T (97.9%), Sphingomonas alpina DSM 22537 T (97.3%) and Sphingomonas hylomeconis CCTCC AB 2013304 T (97.0%). The 16S rRNA gene sequence similarity between ZFBP2030 T and other typical strains was less than 97.0%. The average amino acid identity values, average nucleotide identity, and digital DNA–DNA hybridization values between strain ZFBP2030 T and its highest sequence similarity strains were 56.9–79.9%, 65.1–82.2%, and 19.3–25.8%, respectively. The whole-genome size of the novel strain ZFBP2030 T was 4.1 Mbp, annotated with 3838 protein-coding genes and 54 RNA genes. Moreover, DNA G + C content was 64.7 mol%. Stress-related functions predicted in the subsystem classification of the strain ZFBP2030 T genome included osmotic, oxidative, cold/heat shock, detoxification, and periplasmic stress responses. The overall results of this study clearly showed that strain ZFBP2030 T is a novel species of the genus Sphingomonas , for which the name Sphingomonas endolithica sp. nov. is proposed. The type of strain is ZFBP2030 T (= EE 013 T  = GDMCC 1.3123 T  = JCM 35386 T ).