1887

Abstract

A Gram-negative, filamentous aerobic bacterium designated as strain Mgbs1 was isolated on 12 April 2017 from the subsurface soil and leaf litter substrate at the base of a tree in a tropical peat swamp forest in the northern regions of the state of Selangor, Malaysia (3° 39′ 04.7′ N 101° 17′ 43.7′′ E). Phylogenetic analyses based on the full 16S rRNA sequence revealed that strain Mgbs1 belongs to the genus with the greatest sequence similarity to KP01 (97.65 %), DSM27406 (97.58 %), and DHOC24 (97.17 %). The major fatty acids of strain Mgbs1 (>10 %) are iso-C, C 5 and iso-C 3-OH while the predominant respiratory quinone is menaquinone-7. Strain Mgbs1 has a complete genome size of 8.03 Mb, with a G+C content of 48.5 mol%. The DNA–DNA hybridization (DDH) score between strain Mgbs1 and DSM27406 was 15.9 %, while DDH values of strain Mgbs1 against DHOC24 and KP01 were 20.0 and 19.10% respectively. Concurrently, Average Nucleotide Identity (ANI) scores between strain Mgbs1 against all three reference strains are 73.2 %. Based on the phenotypic, chemotaxonomic, and phylogenetic consensus, strain Mgbs1 represents a novel species of the genus , for which the name sp. nov. is proposed (=DSM 108835=JCM 33276).

  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004539
2020-11-04
2024-10-03
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/12/6355.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004539&mimeType=html&fmt=ahah

References

  1. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Bacteriol 1981; 31:285–293 [View Article]
    [Google Scholar]
  2. Glavina Del Rio T, Abt B, Spring S, Lapidus A, Nolan M et al. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand Genomic Sci 2010; 2:87–95 [View Article][PubMed]
    [Google Scholar]
  3. Parte AC. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article][PubMed]
    [Google Scholar]
  4. Whitman WB. Bergey’s Manual Trust Bergey’s Manual of Systematics of Archaea and Bacteria 2015 Wiley; 2015 In press
    [Google Scholar]
  5. Sungai Besar climate Sungai Besar climate: Average Temperature, weather by month, Sungai Besar weather averages - Climate-Data.org. https://en.climate-data.org/asia/malaysia/selangor/sungai-besar-765916/ accessed 20 October 2019
  6. Page SE, Rieley JO, Shotyk ØW, Weiss D. Interdependence of peat and vegetation in a tropical peat swamp forest. Philos Trans R Soc Lond B Biol Sci 1999; 354:1885–1897 [View Article]
    [Google Scholar]
  7. Nichols D, Cahoon N, Trakhtenberg EM, Pham L, Mehta A et al. Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species. Appl Environ Microbiol 2010; 76:2445–2450 [View Article][PubMed]
    [Google Scholar]
  8. Monciardini P, Sosio M, Cavaletti L, Chiocchini C, Donadio S. New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes. FEMS Microbiol Ecol 2002; 42:419–429 [View Article][PubMed]
    [Google Scholar]
  9. Yoon SH, 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]
  10. Huelsenbeck JP, Crandall KA. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Ecol Syst 1997; 28:437–466 [View Article]
    [Google Scholar]
  11. Bruno WJ, Socci ND, Halpern AL. Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 2000; 17:189–197 [View Article][PubMed]
    [Google Scholar]
  12. Sourdis J, Nei M. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol Biol Evol 1988; 5:298–311 [View Article][PubMed]
    [Google Scholar]
  13. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article][PubMed]
    [Google Scholar]
  14. Gronau I, Moran S. Optimal implementations of UPGMA and other common clustering algorithms. Inf Process Lett 2007; 104:205–210 [View Article]
    [Google Scholar]
  15. 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][PubMed]
    [Google Scholar]
  16. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article][PubMed]
    [Google Scholar]
  17. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–14 [View Article]
    [Google Scholar]
  18. Yoon SH, 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]
  19. Kim M, H-S O, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes.
  20. Kalim B, Ali NM. Optimization of fermentation media and growth conditions for microbial xylanase production. 3 Biotech 2016; 6:122 [View Article][PubMed]
    [Google Scholar]
  21. Güde H. Occurrence of cytophagas in sewage plants. Appl Environ Microbiol 1980; 39:756–763 [View Article][PubMed]
    [Google Scholar]
  22. Matuschek E, Brown DFJ, Kahlmeter G. Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories. Clin Microbiol Infect 2014; 20:O255–O266 [View Article][PubMed]
    [Google Scholar]
  23. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article][PubMed]
    [Google Scholar]
  24. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobiurn japonicum ; 1988
  25. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  26. Tindall BJ. Lipid composition of Halobacterium lacusprofundi ; 1990
  27. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  28. Kim MK, Jung HY. Chitinophaga terrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2007; 57:1721–1724 [View Article][PubMed]
    [Google Scholar]
  29. Lv YY, Wang J, You J, Qiu LH. Chitinophaga dinghuensis sp. nov, isolated from soil. Int J Syst Evol Microbiol 2015; 65:4816–4822 [View Article][PubMed]
    [Google Scholar]
  30. Wang Q, Cheng C, He LY, Huang Z, Sheng XF. Chitinophaga jiangningensis sp. nov., a mineral-weathering bacterium. Int J Syst Evol Microbiol 2014; 64:260–265 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004539
Loading
/content/journal/ijsem/10.1099/ijsem.0.004539
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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