1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 4

gen. nov., sp. nov., a novel taxon within the family isolated from sediment of Qiantang River No Access

Abstract

A Gram-stain-negative bacterium, designated LG-4, was isolated from sediment of Qiantang River in Zhejiang Province, PR China. Cells were strictly aerobic, non-spore-forming, non-motile and short-rod-shaped (1.0–1.2 µm long and 0.7–0.8 µm wide). Growth occurred at 15–42 °C (optimum, 30 °C), at pH 5.0–9.0 (pH 7.0) and at 0–2.0 % (w/v) NaCl (optimum, 0.5 % NaCl). Strain LG-4 showed 95.75–96.90 % 16S rRNA gene sequence similarity to various type strains of the genera , , , and of the family , and the most closely related strain was ZQBW (96.90 % similarity). The phylogenomic tree showed that strain LG-4 clustered in the family and was positioned outside of the clade composed of the genera and . The average nucleotide identity and digital DNA–DNA hybridization values between strain LG-4 and the related type strains were in the range of 74.19–77.56 % and 16.70–25.80 %, respectively. The average amino acid identity (AAI) values between strain LG-4 and related type strains of the family were 60.94–69.73 %, which are below the genus boundary (70 %). The evolutionary distance (ED) values between LG-4 and the related genera of the family were 0.21–0.34, which are within the recommended standard (≥0.21–0.23) for defining a novel genus in the family . The predominant cellular fatty acids were C ω7, C cyclo ω8, C and C, the isoprenoid quinone was Q-10, and the major polar lipids were phospholipid, phosphatidylglycerol, phosphatidylcholine, aminolipid and two unknown polar lipids. The genome size was 4.7 Mb with 68.6 mol% G+C content. On the basis of distinct phylogenetic relationships, low AAI values and high ED values, and differential phenotypic, physiological and biochemical characteristics, strain LG-4 represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain is LG-4 (=MCCC 1K08849=KCTC 8136)

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , AAI , ANI , dDDH , polyphasic taxonomy and Ruixingdingia sedimenti gen. nov., sp. nov.
Funding
This study was supported by the:
  • Science and Technology Program of Gansu Province (Award 22YF7FG188, 22JR5RG565)
    • Principle Award Recipient: luxu
  • Special Fund for Scientific Innovation Strategy-Construction of High-level Academy of Agriculture Science (Award BM2022019)
    • Principle Award Recipient: luxu
  • National Natural Science Foundation of China (Award 32170128)
    • Principle Award Recipient: NotApplicable
© 2024 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006350
2024-04-26
2024-05-07
Loading full text...

Full text loading...

References

  1. Garrity GM, Bell JA, Lilburn T. Family I. Rhodobacteraceae fam. nov.. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. eds Bergey’s Manual of Systematic Bacteriology, 2nd. edn New York: Springer; 2005 pp 164–167
     [Google Scholar]
  2. Liang KYH, Orata FD, Boucher YF et al. 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; 12:683109 [View Article] [PubMed]
     [Google Scholar]
  3. Göker M. Filling the gaps: missing taxon names at the ranks of class, order and family. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  4. Oren A, Göker M. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 72, part 12 of the IJSEM. Int J Syst Evol Microbiol 2023; 73:005799 [View Article]
     [Google Scholar]
  5. 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]
  6. Hu Q, Zhang L, Hang P, Zhou X-Y, Jia W-B et al. Xinfangfangia soli gen. nov., sp. nov., isolated from a diuron-polluted soil. Int J Syst Evol Microbiol 2018; 68:2622–2626 [View Article] [PubMed]
     [Google Scholar]
  7. Kämpfer P, Busse H-J, McInroy JA, Criscuolo A, Clermont D et al. Xinfangfangia humi sp. nov., isolated from soil amended with humic acid. Int J Syst Evol Microbiol 2019; 69:2070–2075 [View Article] [PubMed]
     [Google Scholar]
  8. Mu Y, Peng J-Y, Wang H-P, Song Y, Wang H-M et al. Xinfangfangia pollutisoli sp. nov., isolated from clopyralid-contaminated soil. Curr Microbiol 2022; 79:255 [View Article] [PubMed]
     [Google Scholar]
  9. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:73 [View Article] [PubMed]
     [Google Scholar]
  10. Liu Y, Xu C-J, Jiang J-T, Liu Y-H, Song X-F et al. Catellibacterium aquatile sp. nov., isolated from fresh water, and emended description of the genus Catellibacterium Tanaka et al. Int J Syst Evol Microbiol 2004; 60:2027–2031 [View Article] [PubMed]
     [Google Scholar]
  11. Zheng J-W, Chen Y-G, Zhang J, Ni Y-Y, Li W-J et al. Description of Catellibacterium caeni sp. nov., reclassification of Rhodobacter changlensis Anil Kumar et al. 2007 as Catellibacterium changlense comb. nov. and emended description of the genus Catellibacterium. Int J Syst Evol Microbiol 2011; 61:1921–1926 [View Article] [PubMed]
     [Google Scholar]
  12. Anil Kumar P, Srinivas TNR, Sasikala C, Ramana C. Rhodobacter changlensis sp. nov., a psychrotolerant, phototrophic alphaproteobacterium from the Himalayas of India. Int J Syst Evol Microbiol 2007; 57:2568–2571 [View Article] [PubMed]
     [Google Scholar]
  13. Ke Z, Wang S, Zhu W, Zhang F, Qiao W et al. Genetic bioaugmentation with triclocarban-catabolic plasmid effectively removes triclocarban from wastewater. Environ Res 2022; 214:113921 [View Article] [PubMed]
     [Google Scholar]
  14. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  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. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  18. Kimura M. Evolutionary rates models. J Mol Evol 1980; 16:111–120 [View Article]
     [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  20. Marmur J. A procedure for the isolation of deoxyribonucleic acid from 328 microorganisms. Method Enzymol 1963; 6:726–738
     [Google Scholar]
  21. 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]
  22. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article] [PubMed]
     [Google Scholar]
  23. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Zhang DF, He W, Shao ZZ et al. Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae. Int J Syst Evol Micr 2023; 73:006156
     [Google Scholar]
  26. Yoon S-H, Ha S-M, 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]
  27. 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]
  28. Hua Z-S, Qu Y-N, Zhu Q, Zhou E-M, Qi Y-L et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun 2018; 9:2832 [View Article] [PubMed]
     [Google Scholar]
  29. Huo Y-Y, Xu X-W, Cui H-L, Wu M. Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline-alkaline soil. Int J Syst Evol Microbiol 2010; 60:1383–1386 [View Article] [PubMed]
     [Google Scholar]
  30. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  31. Kates M. Techniques of Lipidology: isolation, analysis and identification of lipids (2nd Revised Edition). Biochem Soc Trans 1988; 16:906 [View Article]
     [Google Scholar]
  32. Hedlund BP, Chuvochina M, Hugenholtz P, Konstantinidis KT, Murray AE et al. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat Microbiol 2022; 7:1702–1708 [View Article] [PubMed]
     [Google Scholar]
  33. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  34. Jin C-Z, Jin L, Liu M-J, Lee J-M, Park D-J et al. Solihabitans fulvus gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from soil. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  35. Zhang J, Chen S-A, Zheng J-W, Cai S, Hang B-J et al. Catellibacterium nanjingense sp. nov., a propanil-degrading bacterium isolated from activated sludge, and emended description of the genus Catellibacterium. Int J Syst Evol Microbiol 2012; 62:495–499 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006350
Loading
Ruixingdingia sedimenti gen. nov., sp. nov., a novel taxon within the family Paracoccaceae isolated from sediment of Qiantang River
Int J Syst Evol Microbiol 74, 006350 (2024); https://doi.org/10.1099/ijsem.0.006350
/content/journal/ijsem/10.1099/ijsem.0.006350
/content/journal/ijsem/10.1099/ijsem.0.006350
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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