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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 10

sp. nov., isolated from mangrove sediment No Access

Abstract

A Gram-stain-negative, cream-coloured, aerobic, motile and ovoid- to rod-shaped bacterium, designated as FT325, was isolated from mangrove sediment collected in Shenzhen, PR China. The taxonomic position of strain FT325 was established by phylogenetic, physiological, biochemical and chemotaxonomic analyses. Strain FT325 grew optimally at 37–40 °C and pH 6.0 in the presence of 0 % (w/v) NaCl. Results of 16S rRNA gene sequence analysis showed that strain FT325 was most similarly related to CAU 1123 (96.2 %), DSM 18714 (93.9%) and HB 172011 (93.7 %). The major fatty acids (>10 %) were C 7 (60.0 %) and 11-methyl C 7 (16.7 %). The sole respiratory quinone was Q-10. The polar lipids were phosphatidylglycerol, one unidentified glycolipid, three unidentified aminolipids and three unidentified phospholipids. Its estimated genome size was 4 318 768 bp and the genomic DNA G+C content was 69.6 mol%. Based on its distinct phenotypic, chemotaxonomic and phylogenetic characteristics, strain FT325 represents a novel species of the genus , for which the name sp. nov. is proposed (=MCCC 1K07397=KCTC 92313).

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Keyword(s): Limibaculum sediminis , mangrove sediment , polyphasic taxonomy and Rhodobacteraceae
© 2022 The Authors
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2022-10-21
2024-05-18
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References

  1. Garrity GM, Bell JA, Lilburn T, Family I, Brenner DJ et al. Rhodobacteraceae fam. nov. In Krieg NR, Staley JT, Garrity GM. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 2 New York: Springer; 2005 p 161
     [Google Scholar]
  2. Feng T, Jeong SE, Kim KH, Park HY, Jeon CO. Aestuariicoccus marinus gen. nov., sp. nov., isolated from sea-tidal flat sediment. Int J Syst Evol Microbiol 2018; 68:260–265 [View Article]
     [Google Scholar]
  3. Park S, Choi J, Won SM, Park JM, Yoon JH. Aestuariibius insulae gen. nov., sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2018; 68:1350–1355 [View Article]
     [Google Scholar]
  4. Ren H, Ma H, Li H, Huang L, Luo Y. Acidimangrovimonas sediminis gen. nov., sp. nov., isolated from mangrove sediment and reclassification of Defluviimonas indica as Acidimangrovimonas indica comb nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov. Int J Syst Evol Microbiol 2019; 69:2445–2451 [View Article]
     [Google Scholar]
  5. Kim Y-O, Park I-S, Park S, Kim H, Nam B-H et al. Aliishimia ponticola gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2019; 69:3109–3115 [View Article]
     [Google Scholar]
  6. Wang G, Xu S, Su H, Chen B, Liang J et al. Histidinibacterium lentulum gen. nov., sp. nov., a marine bacterium from the culture broth of marine microalga Picochlorum sp. 122. Int J Syst Evol Microbiol 2019; 69:578–583 [View Article] [PubMed]
     [Google Scholar]
  7. Romanenko LA, Kurilenko VV, Chernysheva NY, Tekutyeva LA, Velansky PV et al. Harenicola maris gen. nov., sp. nov. isolated from the sea of Japan shallow sediments. Arch Microbiol 2021; 203:3973–3979 [View Article]
     [Google Scholar]
  8. Kong YH, Ren WT, Xu L, Cheng H, Zhou P et al. 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 2022; 72:5236 [View Article]
     [Google Scholar]
  9. Ren Y, Chen C, Ye Y, Wang R, Han S et al. Meridianimarinicoccus roseus gen. nov., sp. nov., a novel genus of the family Rhodobacteraceae isolated from seawater. Int J Syst Evol Microbiol 2019; 69:504–510 [View Article]
     [Google Scholar]
  10. Wang Y, Liu L, Yu M, Zhou S, Fu T et al. Carideicomes alvinocaridis gen. nov., sp. nov., a marine bacterium isolated from shrimp gill in a hydrothermal field of Okinawa Trough. Int J Syst Evol Microbiol 2020; 70:1777–1784 [View Article] [PubMed]
     [Google Scholar]
  11. Ren X-B, Cha Q-Q, Guo X-H, He X-Y, Su H-N et al. Pelagovum pacificum gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from surface seawater of the mariana trench. Int J Syst Evol Microbiol 2020; 70:6155–6162 [View Article]
     [Google Scholar]
  12. Shin YH, Kim J-H, Suckhoom A, Kantachote D, Kim W. Limibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae. Int J Syst Evol Microbiol 2017; 67:3812–3818 [View Article]
     [Google Scholar]
  13. Zhang C-J, Pan J, Duan C-H, Wang Y-M, Liu Y et al. Prokaryotic diversity in mangrove sediments across southeastern China fundamentally differs from that in other biomes. mSystems 2019; 4:e00442-19 [View Article]
     [Google Scholar]
  14. 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]
  15. 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]
  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]
     [Google Scholar]
  17. 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]
  18. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967 [View Article]
     [Google Scholar]
  19. 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]
     [Google Scholar]
  20. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 2004; 101:11030–11035 [View Article]
     [Google Scholar]
  21. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Curr Protoc Bioinformatics 2020; 70:e102 [View Article]
     [Google Scholar]
  22. 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]
  23. Yoon SH, Ha SM, Lim JM, Kwon SJ, 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]
  24. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
     [Google Scholar]
  25. Parks DH. CompareM; 2022 https://github.com/dparks1134/CompareM
  26. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article] [PubMed]
     [Google Scholar]
  27. Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 2021; 38:5825–5829 [View Article]
     [Google Scholar]
  28. 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]
     [Google Scholar]
  29. Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M. KEGG: integrating viruses and cellular organisms. Nucleic Acids Res 2021; 49:D545–D551 [View Article] [PubMed]
     [Google Scholar]
  30. Cowan ST. Cowan & Steel’s Manual for the Identification of Medical Bacteria, 2nd edn. Cambridge: Cambridge University Press; 1974 pp 148–162
     [Google Scholar]
  31. Lai QL, Liu XP, Yuan J, Xie SC, Shao ZZ. 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]
  32. Brenner DJ, Krieg NR, Garrity GM, Staley JT, Boone DR et al. Bergey’s Manual of Systematic Bacteriology, 2nd edn. New York: Springer; 2005 pp 161–167 [View Article]
     [Google Scholar]
  33. Srinivas TNR, Anil Kumar P, Sasikala C, Ramana CV, Imhoff JF. Rhodobacter vinaykumarii sp. nov., a marine phototrophic alphaproteobacterium from tidal waters, and emended description of the genus Rhodobacter. Int J Syst Evol Microbiol 2007; 57:1984–1987 [View Article]
     [Google Scholar]
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Limibaculum sediminis sp. nov., isolated from mangrove sediment
Int J Syst Evol Microbiol 72, 005580 (2022); https://doi.org/10.1099/ijsem.0.005580
/content/journal/ijsem/10.1099/ijsem.0.005580
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