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Volume 72, Issue 2

gen. nov., sp. nov., gen. nov., sp. nov. and sp. nov., three novel members isolated from deep-sea water in the southwest Indian ridge No Access

Abstract

Three Gram-staining-negative, aerobic and rod-shaped strains, designated as T40-1, T40-3 and JL-62, were isolated from the deep-sea water in the southwest Indian ridge. For strain T40-1, growth occurred at 15–37 °C (optimum, 28 °C), pH 6.0–9.0 (optimum, pH 7.5) and in the presence of 0.5–5.0 % NaCl (w/v; optimum, 2.0 %). Strain T40-3 could grow at 15–40 °C (optimum, 28 °C), with 0.5–11.0 % NaCl (optimum, 2.0 %, w/v) at pH 6.0–9.5 (optimum, 8.0). The temperature, pH and salinity ranges for growth of strain JL-62 were 15–40 °C (optimum, 30 °C), pH 5.5–9.0 (optimum, pH 7.5–8.0) and 0.5–9.0 % NaCl (w/v; optimum, 4.0 %). Ubiquinone-10 was the sole ubiquinone in all strains, the major fatty acids (>20 %) were summed feature 8 (C 7 / C 6). The major polar lipids of strains T40-1 and T40-3 were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain JL-62 contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sulfoquinovosyldiacylglycerol as major polar lipids. Phylogenetic trees based on 16S rRNA gene and core-genomic sequences revealed affiliation of strains T40-1and T40-3 to the family and formed two independent clades from other genera, and those two strains had average nucleotide identities of 62.0–72.0 % to their phylogenetically related species which fell into to the genus boundary range, indicating that they represent two novel genera. While strain JL-62 represents a novel species in the genus belonging to the family , which was supported by overall genomic relatedness index calculations. The DNA G+C contents of strains T40-1, T40-3 and JL-62 were 66.5, 60.1 and 62.1 mol %, respectively. Based on the polyphasic taxonomic data, strains T40-1 (=MCCC M24557=KCTC 82975) and T40-3 (=MCCC 1K05135=KCTC 82976) are classified as representing two novel genera belonging to the family with the names gen. nov., sp. nov. and gen. nov., sp. nov. are proposed, and strain JL-62 (=MCCC M24579=KCTC 82974) is proposed to represent a novel species within the genus with the name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Heliomarina baculiformis , Mesobacterium pallidum , Oricola indica , polyphasic taxonomy , the class Alphaproteobacteria and the southwest Indian ridge
Funding
This study was supported by the:
  • the China Postdoctoral Science Foundation (Award 2019M652042)
    • Principle Award Recipient: LinXu
  • the Scientific Research Fund of the Second Institute of Oceanography, MNR (Award JB2003)
    • Principle Award Recipient: LinXu
  • the Natural Science Foundation of China (Award 32000001)
    • Principle Award Recipient: LinXu
  • the Natural Science Foundation of China (Award 91851114)
    • Principle Award Recipient: Xue-WeiXu
  • the National Science and Technology Fundamental Resources Investigation Program of China (Award 2021FY100908)
    • Principle Award Recipient: PengZhou
  • the National Key R&D Program of China (Award 2018YFC0310704)
    • Principle Award Recipient: HongCheng
© 2022 The Authors
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2022-02-10
2024-04-27
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References

  1. Garrity GM, Bell JA, Lilburn T. Class I. Alphaproteobacteria class. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. eds Bergey’s Manual of Systematic Bacteriology, Volume 2. (The Proteobacteria), Part C New York: Springer; 2005a pp 1–574
     [Google Scholar]
  2. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold L-M et al. Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 2020; 11:468 [View Article] [PubMed]
     [Google Scholar]
  3. Liang KYH, Orata FD, Boucher YF, Case RJ. Roseobacters in a sea of poly- and paraphyly: whole genome-based taxonomy of the family Rhodobacteraceae and the Proposal for the Split of the “Roseobacter Clade” Into a Novel Family, Roseobacteraceae fam. nov. Front Microbiol 2021; 12:1635 [View Article] [PubMed]
     [Google Scholar]
  4. Brinkhoff T, Giebel HA, Simon M. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol 2008; 189:531–539 [View Article] [PubMed]
     [Google Scholar]
  5. Buchan A, González JM, Moran MA. Overview of the marine roseobacter lineage. Appl Environ Microbiol 2005; 71:5665–5677 [View Article] [PubMed]
     [Google Scholar]
  6. Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I et al. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J 2017; 11:1483–1499 [View Article] [PubMed]
     [Google Scholar]
  7. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC et al. The family Rhodobacteraceae. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. eds The Prokaryotes: Alphaproteobacteria and Betaproteobacteria Berlin, Heidelberg: Springer, Berlin Heidelberg; 2014 pp 439–512
     [Google Scholar]
  8. Choi YS, Oh JS, Roh DH. Pelagicola marinus sp. nov. isolated from deep-sea water. Int J Syst Evol Microbiol 2019; 69:3961–3966 [View Article] [PubMed]
     [Google Scholar]
  9. Lai Q-L, Liu X-P, Yuan J, Xie S-C, Shao Z-Z. Pararhodobacter marinus sp. nov., isolated from deep-sea water of the Indian Ocean. Int J Syst Evol Microbiol 2019; 69:932–936 [View Article] [PubMed]
     [Google Scholar]
  10. Chang Y-Q, Meng X, Du Z-Z, Du Z-J. Oceanibium sediminis gen. nov., sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2019; 69:249–254 [View Article]
     [Google Scholar]
  11. Zhang R, Wang C, Wang X-T, Mu D-S, Du Z-J. Jannaschia formosa sp. nov., isolated from marine saltern sediment. Int J Syst Evol Microbiol 2019; 69:2037–2042 [View Article] [PubMed]
     [Google Scholar]
  12. Jung HS, Jeong SE, Chun BH, Quan Z-X, Jeon CO. Rhodophyticola porphyridii gen. nov., sp. nov., isolated from a red alga, Porphyridium marinum. Int J Syst Evol Microbiol 2019; 69:1656–1661 [View Article]
     [Google Scholar]
  13. Kumari P, Bhattacharjee S, Poddar A, Das SK. Sulfitobacter faviae sp. nov., isolated from the coral Faviaveroni. Int J Syst Evol Microbiol 2016; 66:3786–3792 [View Article] [PubMed]
     [Google Scholar]
  14. Luo H, Moran MA. Evolutionary ecology of the marine Roseobacter clade. Microbiol Mol Biol Rev 2014; 78:573–587 [View Article] [PubMed]
     [Google Scholar]
  15. Hameed A, Shahina M, Lai W-A, Lin S-Y, Young L-S et al. Oricola cellulosilytica gen. nov., sp. nov., a cellulose-degrading bacterium of the family Phyllobacteriaceae isolated from surface seashore water, and emended descriptions of Mesorhizobium loti and Phyllobacterium myrsinacearum. Antonie van Leeuwenhoek 2015; 107:759–771 [View Article]
     [Google Scholar]
  16. Yang SH, Park MJ, Kwon KK. Oricola thermophila sp. nov., a marine bacterium isolated from tidal flat sediment and emended description of the genus Oricola Hameed et al. 2015. Int J Syst Evol Microbiol 2021; 71:004574 [View Article]
     [Google Scholar]
  17. Liao S, Tao C, Li H, Zhang G, Liang J et al. Surface sediment geochemistry and hydrothermal activity indicators in the Dragon Horn area on the Southwest Indian Ridge. Marine Geology 2018; 398:22–34 [View Article]
     [Google Scholar]
  18. Van Dover CL, Humphris SE, Fornari D, Cavanaugh CM, Collier R et al. Biogeography and ecological setting of Indian Ocean hydrothermal vents. Science 2001; 294:818–823 [View Article] [PubMed]
     [Google Scholar]
  19. Tao C, Lin J, Guo S, Chen YJ, Wu G et al. First active hydrothermal vents on an ultraslow-spreading center: Southwest Indian Ridge. Geology 2012; 40:47–50 [View Article]
     [Google Scholar]
  20. Zhang B-S. Study of Mineralization at the Longqi and Duanqiao Hydrothermal Fields, Southwest Indian Ridge. PhD dissertation China University of Geosciences (Beijing; 2019
     [Google Scholar]
  21. Lane DJ. Nucleic Acid Techniques in Bacterial Systematics Chichester: John Wiley and Sons; 1991 pp 115–175
     [Google Scholar]
  22. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
     [Google Scholar]
  23. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  24. Saitou NM, 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]
  25. 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] [PubMed]
     [Google Scholar]
  26. 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]
  27. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  28. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  29. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009; 19:1117–1123 [View Article] [PubMed]
     [Google Scholar]
  30. 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]
  31. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  32. Xu L, Wu Y-H, Zhou P, Cheng H, Liu Q et al. Investigation of the thermophilic mechanism in the genus Porphyrobacter by comparative genomic analysis. BMC Genomics 2018; 19:385 [View Article] [PubMed]
     [Google Scholar]
  33. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
     [Google Scholar]
  34. Wang X-J, Xu L, Wang N, Sun H-M, Chen X-L et al. Putridiphycobacter roseus gen. nov., sp. nov., isolated from Antarctic rotten seaweed. Int J Syst Evol Microbiol 2020; 70:648–655 [View Article]
     [Google Scholar]
  35. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  36. 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]
  37. 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]
  38. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
     [Google Scholar]
  39. Zobell CE. Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res 1941; 4:42–75
     [Google Scholar]
  40. Cai MY, Dong XZ. Determinative Manual for Routine Bacteriology BeiJing: Scientific Press; 2001
     [Google Scholar]
  41. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  42. Xu L, Huo Y-Y, Li Z-Y, Wang C-S, Oren A et al. Chryseobacterium profundimaris sp. nov., a new member of the family Flavobacteriaceae isolated from deep-sea sediment. Antonie Van Leeuwenhoek 2015; 107:979–989 [View Article] [PubMed]
     [Google Scholar]
  43. Xu X-W, Huo Y-Y, Bai X-D, Wang C-S, Oren A et al. Kordiimonas lacus sp. nov., isolated from a ballast water tank, and emended description of the genus Kordiimonas. Int J Syst Evol Microbiol 2011; 61:422–426 [View Article] [PubMed]
     [Google Scholar]
  44. Fang C, Wu Y-H, Xamxidin M, Wang C-S, Xu X-W. Maribacter cobaltidurans sp. nov., a heavy-metal-tolerant bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2017; 67:5261–5267 [View Article] [PubMed]
     [Google Scholar]
  45. Kamekura M, Kates M. Lipids of halophilic archaebacteria. In Halophilic Bacteria II 1988 pp 25–54
     [Google Scholar]
  46. Tindall BJ, Sikorski J, Simbert RA, Krieg NR. Phenotypic Characterization and the Principles of Comparative Systematics, Methods for General and Molecular Microbiology, 3rd edn. Washington, DC: American Society of Microbiology; 2007 pp 330–393
     [Google Scholar]
  47. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  48. 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]
  49. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
     [Google Scholar]
  50. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393–2411 [View Article] [PubMed]
     [Google Scholar]
  51. Lafay B, Ruimy R, de Traubenberg CR, Breittmayer V, Gauthier MJ et al. Roseobacter algicola sp. nov., a new marine bacterium isolated from the phycosphere of the toxin-producing dinoflagellate Prorocentrum lima. Int J Syst Bacteriol 1995; 45:290–296 [View Article] [PubMed]
     [Google Scholar]
  52. Baek J, Kim J-H, Yoon J-H, Lee J-S, Sukhoom A et al. Arenibacterium halophilum gen. nov., sp. nov., a halotolerant bacterium in the family Rhodobacteraceae isolated from a coastal sand dune. Int J Syst Evol Microbiol 2020; 70:6323–6330 [View Article] [PubMed]
     [Google Scholar]
  53. Zhang L, Wang K-L, Yin Q, Liang J-Y, Xu Y. Ruegeria kandeliae sp. nov., isolated from the rhizosphere soil of a mangrove plant Kandelia candel. Int J Syst Evol Microbiol 2018; 68:2653–2658 [View Article] [PubMed]
     [Google Scholar]
  54. Zhang G, Haroon MF, Zhang R, Dong X, Liu D et al. Ponticoccus marisrubri sp. nov., a moderately halophilic marine bacterium of the family Rhodobacteraceae. Int J Syst Evol Microbiol 2017; 67:4358–4364 [View Article] [PubMed]
     [Google Scholar]
  55. Park S, Park JM, Jung YT, Won SM, Yoon JH. Primorskyibacter insulae sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2015; 65:3971–3976 [View Article] [PubMed]
     [Google Scholar]
  56. Sass H, Köpke B, Rütters H, Feuerlein T, Dröge S et al. Tateyamaria pelophila sp. nov., a facultatively anaerobic alphaproteobacterium isolated from tidal-flat sediment, and emended descriptions of the genus Tateyamaria and of Tateyamaria omphalii. Int J Syst Evol Microbiol 2010; 60:1770–1777 [View Article] [PubMed]
     [Google Scholar]
  57. Sorokin DY, Tourova TP, Muyzer G. Citreicella thiooxidans gen. nov., sp. nov., a novel lithoheterotrophic sulfur-oxidizing bacterium from the Black Sea. Syst Appl Microbiol 2005; 28:679–687 [View Article]
     [Google Scholar]
  58. Yoon JH, Kang SJ, Oh TK. Roseovarius aestuarii sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2008; 58:1198–1202 [View Article] [PubMed]
     [Google Scholar]
  59. Ivanova EP, Gorshkova NM, Sawabe T, Zhukova NV, Hayashi K et al. Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina). Int J Syst Evol Microbiol 2004; 54:475–480 [View Article] [PubMed]
     [Google Scholar]
  60. Hwang CY, Bae GD, Yih W, Cho BC. Marivita cryptomonadis gen. nov., sp. nov. and Marivita litorea sp. nov., of the family Rhodobacteraceae, isolated from marine habitats. Int J Syst Evol Microbiol 2009; 59:1568–1575 [View Article]
     [Google Scholar]
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Mesobacterium pallidum gen. nov., sp. nov., Heliomarina baculiformis gen. nov., sp. nov. and Oricola indica sp. nov., three novel Alphaproteobacteria members isolated from deep-sea water in the southwest Indian ridge
Int J Syst Evol Microbiol 72, 005236 (2022); https://doi.org/10.1099/ijsem.0.005236
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