1887

Abstract

A Gram-negative, aerobic, rod-shaped, non-spore-forming, motile bacterium, designated strain RPE64, was isolated from the gut symbiotic organ of the bean bug , collected in Tsukuba, Japan, in 2007. 16S rRNA gene sequencing showed that this strain belongs to the clade, exhibiting the highest sequence similarity to LMG 29314 (100 %), LMG 29316 (99.52 %) and LMG 29326 (99.04 %). Phylogenomic analyses based on 107 single-copy core genes and Genome Distance Phylogeny confirmed LMG 29314 LMG 29326 and several uncultivated, endophytic species as its nearest phylogenetic neighbours. Digital DNA–DNA hybridization experiments unambiguously demonstrated that strain RPE64 represents a novel species in this lineage. The G+C content of its genome was 63.2 mol%. The isoprenoid quinone was ubiquinone 8 and the predominant fatty acid components were C, C 7 and C cyclo. The absence of nitrate reduction and the capacity to grow at pH 8 clearly differentiated strain RPE64 from related species. Based on these genotypic and phenotypic characteristics, strain RPE64 is classified as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is RPE64 (=NCIMB 15023=JCM 31142).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002848
2018-07-01
2024-11-12
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/7/2370.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002848&mimeType=html&fmt=ahah

References

  1. Kikuchi Y, Meng XY, Fukatsu T. Gut symbiotic bacteria of the genus Burkholderia in the broad-headed bugs Riptortus clavatus and Leptocorisa chinensis (Heteroptera: Alydidae). Appl Environ Microbiol 2005; 71:4035–4043 [View Article][PubMed]
    [Google Scholar]
  2. Takeshita K, Kikuchi Y. Riptortus pedestris and Burkholderia symbiont: an ideal model system for insect-microbe symbiotic associations. Res Microbiol 2017; 168:175–187 [View Article][PubMed]
    [Google Scholar]
  3. Kikuchi Y, Hosokawa T, Fukatsu T. Insect-microbe mutualism without vertical transmission: a stinkbug acquires a beneficial gut symbiont from the environment every generation. Appl Environ Microbiol 2007; 73:4308–4316 [View Article][PubMed]
    [Google Scholar]
  4. Kikuchi Y, Fukatsu T. Live imaging of symbiosis: spatiotemporal infection dynamics of a GFP-labelled Burkholderia symbiont in the bean bug Riptortus pedestris. Mol Ecol 2014; 23:1445–1456 [View Article][PubMed]
    [Google Scholar]
  5. Peeters C, Meier-Kolthoff JP, Verheyde B, de Brandt E, Cooper VS et al. Phylogenomic study of Burkholderia glathei-like organisms, proposal of 13 novel Burkholderia species and emended descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae. Front Microbiol 2016; 7:877 [View Article][PubMed]
    [Google Scholar]
  6. Dobritsa AP, Samadpour M. Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia. Int J Syst Evol Microbiol 2016; 66:2836–2846 [View Article][PubMed]
    [Google Scholar]
  7. Vandamme P, Peeters C, de Smet B, Price EP, Sarovich DS et al. Comparative genomics of Burkholderia singularis sp. nov., a low G+C content, free-living bacterium that defies taxonomic dissection of the genus Burkholderia. Front Microbiol 2017; 8:1679 [View Article][PubMed]
    [Google Scholar]
  8. Depoorter E, Bull MJ, Peeters C, Coenye T, Vandamme P et al. Burkholderia: an update on taxonomy and biotechnological potential as antibiotic producers. Appl Microbiol Biotechnol 2016; 100:5215–5229 [View Article][PubMed]
    [Google Scholar]
  9. Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR et al. Genome data provides high support for generic boundaries in Burkholderia sensu lato. Front Microbiol 2017; 8:1154 [View Article][PubMed]
    [Google Scholar]
  10. Wong YC, Abd El Ghany M, Naeem R, Lee KW, Tan YC et al. Candidate essential genes in Burkholderia cenocepacia J2315 identified by genome-wide TraDIS. Front Microbiol 2016; 7:1288 [View Article][PubMed]
    [Google Scholar]
  11. Kikuchi Y, Hosokawa T, Fukatsu T. An ancient but promiscuous host-symbiont association between Burkholderia gut symbionts and their heteropteran hosts. ISME J 2011; 5:446–460 [View Article][PubMed]
    [Google Scholar]
  12. Draghi WO, Peeters C, Cnockaert M, Snauwaert C, Wall LG et al. Burkholderia cordobensis sp. nov., from agricultural soils. Int J Syst Evol Microbiol 2014; 64:2003–2008 [View Article][PubMed]
    [Google Scholar]
  13. Vandamme P, de Brandt E, Houf K, Salles JF, Dirk van Elsas J et al. Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil. Int J Syst Evol Microbiol 2013; 63:4707–4718 [View Article][PubMed]
    [Google Scholar]
  14. Tian Y, Kong BH, Liu SL, Li CL, Yu R et al. Burkholderia grimmiae sp. nov., isolated from a xerophilous moss (Grimmia montana). Int J Syst Evol Microbiol 2013; 63:2108–2113 [View Article][PubMed]
    [Google Scholar]
  15. Shibata TF, Maeda T, Nikoh N, Yamaguchi K, Oshima K et al. Complete genome sequence of Burkholderia sp. strain RPE64, bacterial symbiont of the bean bug Riptortus pedestris. Genome Announc 2013; 1:e0044113 [View Article][PubMed]
    [Google Scholar]
  16. Yoon SH, Ha SM, 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]
  17. Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA et al. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J 2012; 6:1186–1199 [View Article][PubMed]
    [Google Scholar]
  18. Ankenbrand MJ, Keller A. bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome 2016; 59:783–791 [View Article][PubMed]
    [Google Scholar]
  19. van Oevelen S, de Wachter R, Vandamme P, Robbrecht E, Prinsen E. Identification of the bacterial endosymbionts in leaf galls of Psychotria (Rubiaceae, angiosperms) and proposal of 'Candidatus Burkholderia kirkii' sp. nov. Int J Syst Evol Microbiol 2002; 52:2023–2027 [View Article][PubMed]
    [Google Scholar]
  20. Lemaire B, van Oevelen S, de Block P, Verstraete B, Smets E et al. Identification of the bacterial endosymbionts in leaf nodules of Pavetta (Rubiaceae). Int J Syst Evol Microbiol 2012; 62:202–209 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. Tamaki H, Tanaka Y, Matsuzawa H, Muramatsu M, Meng XY et al. Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. Int J Syst Evol Microbiol 2011; 61:1442–1447 [View Article][PubMed]
    [Google Scholar]
  23. Kinosita Y, Kikuchi Y, Mikami N, Nakane D, Nishizaka T. Unforeseen swimming and gliding mode of an insect gut symbiont, Burkholderia sp. RPE64, with wrapping of the flagella around its cell body. ISME J 2018; 12:838–848 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.002848
Loading
/content/journal/ijsem/10.1099/ijsem.0.002848
Loading

Data & Media loading...

Supplements

Supplementary File 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