1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 5

Isolation of sp. nov., a novel bacterium in the family from marine mangrove sediment No Access

Abstract

A Gram-stain-negative, strictly aerobic and oval-shaped bacterial strain with a flagellum, designated GS-10, was isolated from mangrove wetland sediment. GS-10 grew at 20–40 °C (optimum, 37 °C), in the pH range of 5.0–11.0 (optimum, 6.0–8.0) and under various NaCl concentrations from 1 to 11 % (w/v) (optimum, 5–6 %). The respiratory quinone was ubiquinone-10, and the predominant polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids (>10 % of the total fatty acids) were summed feature 4 (Ciso I/anteiso B) and summed feature 8 (Cω7 and/or Cω6). The G+C content of the genomic DNA was 63.71 %. On the basis of the results from comparative analysis of the 16S rRNA gene sequence, GS-10 represents a member of the family and had the highest sequence similarity to CECT 4357 (97.47 %), followed by W11-2B (97.03 %), CL-SK44 (96.83 %), CECT 5118 (96.75 %) and CECT 5383 (96.68 %). Phylogenetic trees based on 16S rRNA gene sequences, multilocus sequence analysis (MLSA) and whole genome sequences revealed that GS-10 clustered with species within the genus . The average nucleotide identity (ANI) and the average amino acid identity (AAI) values were calculated from complete genome sequences and indicated that GS-10 represented a novel species of the genus , and the name sp. nov. is proposed for this species. The type strain of is GS-10 (=MCCC 1K03624=KCTC 82131).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): mangrove wetland sediment and Thalassobius mangrovi
Funding
This study was supported by the:
  • Natural Science Foundation of Fujian Province (Award 2019J01023)
    • Principle Award Recipient: HongXu
  • National Natural Science Foundation of China (Award U20B2037, 41676101 and 41476095)
    • Principle Award Recipient: HongXu
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004801
2021-05-11
2023-09-25
Loading full text...

Full text loading...

References

  1. Garrity GM, Bell JA, Lilburn T. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006; 56:1–6 [View Article][PubMed]
     [Google Scholar]
  2. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC. The Family Rhodobacteraceae. The Prokaryotes: Alphaproteobacteria and Betaproteobacteria Berlin Heidelberg: Springer; 2014 pp 439–512
     [Google Scholar]
  3. 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]
  4. Moran MA, González JM, Kiene RP. Linking a bacterial taxon to sulfur cycling in the sea: studies of the marine Roseobacter group. Geomicrobiol J 2003; 20:375–388 [View Article]
     [Google Scholar]
  5. Zafiriou OC, Andrews SS, Wang W. Concordant estimates of oceanic carbon monoxide source and sink processes in the Pacific yield a balanced global “blue-water” CO budget. Global Biogeochem Cycles 2003; 17:1015 [View Article]
     [Google Scholar]
  6. Liu Z-X, Dorji P, Liu H-C, Li A-H, Zhou Y-G. Tabrizicola sediminis sp. nov., one aerobic anoxygenic photoheterotrophic bacteria from sediment of saline lake. Int J Syst Evol Microbiol 2019; 69:2565–2570 [View Article][PubMed]
     [Google Scholar]
  7. Arahal DR, Lucena T, Rodrigo-Torres L, Pujalte MJ. Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis. Int J Syst Evol Microbiol 2018; 68:2515–2522 [View Article][PubMed]
     [Google Scholar]
  8. Verméglio A, Joliot P. The photosynthetic apparatus of Rhodobacter sphaeroides. Trends Microbiol 1999; 7:435–440 [View Article][PubMed]
     [Google Scholar]
  9. Buchan A, González JM, Moran MA. Overview of the marine Roseobacter lineage. Appl Environ Microbiol 2005; 71:5665–5677 [View Article][PubMed]
     [Google Scholar]
  10. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
     [Google Scholar]
  11. 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]
  12. 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]
  13. 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]
  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. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
     [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. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  18. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
     [Google Scholar]
  19. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
     [Google Scholar]
  20. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold L-M et al. Analysis of 1000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 2020; 11:468 [View Article][PubMed]
     [Google Scholar]
  21. Rivas R, Martens M, de Lajudie P, Willems A. Multilocus sequence analysis of the genus Bradyrhizobium. Syst Appl Microbiol 2009; 32:101–110 [View Article][PubMed]
     [Google Scholar]
  22. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
     [Google Scholar]
  23. Zhang D, Gao F, Jakovlić I, Zou H, Zhang J et al. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour 2020; 20:348–355 [View Article][PubMed]
     [Google Scholar]
  24. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL et al. KBase: the United States department of energy systems biology knowledgebase. Nat Biotechnol 2018; 36:566–569 [View Article][PubMed]
     [Google Scholar]
  25. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4:e1900v1
     [Google Scholar]
  26. 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]
  27. 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]
  28. Zheng S, Zhang D, Gui J, Wang J, Zhu X et al. Thalassotalea mangrovi sp. nov., a bacterium isolated from marine mangrove sediment. Int J Syst Evol Microbiol 2019; 69:3644–3649 [View Article][PubMed]
     [Google Scholar]
  29. Du Z-J, Wang Y, Dunlap C, Rooney AP, Chen G-J. Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov. Int J Syst Evol Microbiol 2014; 64:1690–1696 [View Article][PubMed]
     [Google Scholar]
  30. Lanyi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67
     [Google Scholar]
  31. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [View Article][PubMed]
     [Google Scholar]
  32. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of bradyrhizobium japonicum. Int J System Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  33. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
     [Google Scholar]
  34. 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]
  35. Han S-B, Su Y, Hu J, Wang R-J, Sun C et al. Terasakiella brassicae sp. nov., isolated from the wastewater of a pickle-processing factory, and emended descriptions of Terasakiella pusilla and the genus Terasakiella. Int J Syst Evol Microbiol 2016; 66:1807–1812 [View Article][PubMed]
     [Google Scholar]
  36. Rüger HJ, Höfle MG. Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev. Int J Syst Bacteriol 1992; 42:133–143 [View Article][PubMed]
     [Google Scholar]
  37. Arahal DR, Macián MC, Garay E, Pujalte MJ. Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov. Int J Syst Evol Microbiol 2005; 55:2371–2376 [View Article][PubMed]
     [Google Scholar]
  38. Iwaki H, Yasukawa N, Fujioka M, Takada K, Hasegawa Y. Isolation and characterization of a marine cyclohexylacetate-degrading bacterium Lutimaribacter litoralis sp. nov., and reclassification of Oceanicola pacificus as Lutimaribacter pacificus comb. nov. Curr Microbiol 2013; 66:588–593 [View Article][PubMed]
     [Google Scholar]
  39. Yuan J, Lai Q, Wang B, Sun F, Liu X et al. Oceanicola pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium. Int J Syst Evol Microbiol 2009; 59:1158–1161 [View Article][PubMed]
     [Google Scholar]
  40. 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][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004801
Loading
Isolation of Thalassobius mangrovi sp. nov., a novel bacterium in the family Rhodobacteraceae, from marine mangrove sediment
Int J Syst Evol Microbiol 71, 004801 (2021); https://doi.org/10.1099/ijsem.0.004801
/content/journal/ijsem/10.1099/ijsem.0.004801
/content/journal/ijsem/10.1099/ijsem.0.004801
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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