1887

Abstract

is a symbiotic group of bacteria associated with entomopathogenic nematodes of the family Steinernematidae. Although the described species list is extensive, not all their symbiotic bacteria have been identified. One single motile, Gram-negative and non-spore-forming rod-shaped symbiotic bacterium, strain VLS, was isolated from the entomopathogenic nematode . Analyses of the 16S rRNA gene determined that the VLS isolate belongs to the genus , and its closest related species is DSM 16338 (98.2 %). Deeper analyses using the whole genome for phylogenetic reconstruction indicate that VLS exhibits a unique clade in the genus. Genomic comparisons considering digital DNA–DNA hybridization (dDDH) values confirms this result, showing that the VLS values are distant enough from the 70 % threshold suggested for new species, sharing 30.7, 30.5 and 30.3 % dDDH with MCB, DSM 18168 and DSM 18168, respectively, as the closest species. Detailed physiological, biochemical and chemotaxonomic tests of the VLS isolate reveal consistent differences from previously described species. Phylogenetic, physiological, biochemical and chemotaxonomic approaches show that VLS represents a new species of the genus , for which the name sp. nov. (type strain VLS=CCCT 20.04=DSM 111583) is proposed.

Funding
This study was supported by the:
  • agencia nacional de investigación y desarrollo (anid), cl (Award 2021-21210687)
    • Principle Award Recipient: CarlosCastaneda-Alvarez
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2021-12-13
2024-05-11
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References

  1. Bird AF, Akhurst RJ. The nature of the intestinal vesicle in nematodes of the family Steinernematidae. Int J Parasitol 1983; 13:599–606 [View Article]
    [Google Scholar]
  2. Forst S, Nealson K. Molecular biology of the symbiotic-pathogenic bacteria Xenorhabdus spp. and Photorhabdus spp. Microbiol Rev 1996; 60:21–43 [View Article] [PubMed]
    [Google Scholar]
  3. Kämpfer P, Tobias NJ, Ke LP, Bode HB, Glaeser SP. Xenorhabdus thuongxuanensis sp. nov. and Xenorhabdus eapokensis sp. nov., isolated from Steinernema species. Int J Syst Evol Microbiol 2017; 67:1107–1114 [View Article] [PubMed]
    [Google Scholar]
  4. Hunt DJ, Nguyen KB. Advances in Entomopathogenic Nematode Taxonomy and Phylogeny Brill; 2016
    [Google Scholar]
  5. Edgington S, Buddie AG, Tymo LM, France A, Merino L et al. Steinernema unicornum sp. n. (Panagrolaimomorpha: Steinernematidae), a new entomopathogenic nematode from Tierra del Fuego, Chile. J Nematode Morphol Syst 2009; 12:113–131
    [Google Scholar]
  6. Tailliez P, Laroui C, Ginibre N, Paule A, Pagès S et al. Phylogeny of Photorhabdus and Xenorhabdus based on universally conserved protein-coding sequences and implications for the taxonomy of these two genera. Proposal of new taxa: X. vietnamensis sp. nov., P. luminescens subsp. caribbeanensis subsp. nov., P. l. Int J Syst Evol Microbiol 2010; 60:1921–1937
    [Google Scholar]
  7. Tailliez P, Pagès S, Edgington S, Tymo LM, Buddie AG. Description of Xenorhabdus magdalenensis sp. nov., the symbiotic bacterium associated with Steinernema australe. Int J Syst Evol Microbiol 2012; 62:1761–1765 [View Article] [PubMed]
    [Google Scholar]
  8. Machado RAR, Muller A, Ghazal SM, Thanwisai A, Pagès S et al. Photorhabdus heterorhabditis subsp. aluminescens subsp. nov., Photorhabdus heterorhabditis subsp. heterorhabditis subsp. nov., Photorhabdus australis subsp. thailandensis subsp. nov., Photorhabdus australis subsp. australis subsp. nov., and Photorhabdus aegyptia sp. nov. isolated from Heterorhabditis entomopathogenic nematodes. Int J Syst Evol Microbiol 2021; 71:1–9 [View Article]
    [Google Scholar]
  9. Machado RAR, Bruno P, Arce CCM, Liechti N, Köhler A et al. Photorhabdus khanii subsp. guanajuatensis subsp. nov., isolated from Heterorhabditis atacamensis, and Photorhabdus luminescens subsp. mexicana subsp. nov., isolated from Heterorhabditis mexicana entomopathogenic nematodes. Int J Syst Evol Microbiol 2019; 69:652–661 [View Article] [PubMed]
    [Google Scholar]
  10. Nguyen KB, Maruniak J, Adams BJ. Diagnostic and phylogenetic utility of the rDNA internal transcribed spacer sequences of Steinernema. J Nematol 2001; 33:73–82 [PubMed]
    [Google Scholar]
  11. Stock SP, Campbell JF, Nadler SA. Phylogeny of Steinernema Travassos, 1927 (Cephalobina: Steinernematidae) inferred from ribosomal DNA sequences and morphological characters. J Parasitol 2001; 87:877–889 [View Article] [PubMed]
    [Google Scholar]
  12. Uluğ D, Hazir C, Hazir S. A new and simple technique for the isolation of symbiotic bacteria associated with entomopathogenic nematodes (Heterorhabditidae and Steinernematidae). Turk J Zool 2015; 39:365–367 [View Article]
    [Google Scholar]
  13. Akhurst RJ. Morphological and functional dimorphism in Xenorhabdus spp., bacteria symbiotically associated with the insect pathogenic nematodes Neoaplectana and Heterorhabditis. Microbiology 1980; 121:303–309 [View Article]
    [Google Scholar]
  14. 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]
  15. Jukes TH, Cantor CR. Evolution of protein molecules. In Mammalian Protein Metabolism Amsterdam: Elsevier; pp 21–132
    [Google Scholar]
  16. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  17. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Bioinformatics 1992; 8:275–282 [View Article]
    [Google Scholar]
  18. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article] [PubMed]
    [Google Scholar]
  19. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article] [PubMed]
    [Google Scholar]
  20. Price MN, Dehal PS, Arkin AP. FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article] [PubMed]
    [Google Scholar]
  21. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [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. 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]
  24. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article] [PubMed]
    [Google Scholar]
  25. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995; 61:3756–3758 [View Article] [PubMed]
    [Google Scholar]
  26. Sierra G. A simple method for the detection of lipolytic activity of micro-organisms and some observations on the influence of the contact between cells and fatty substrates. Antonie van Leeuwenhoek 1957; 23:15–22 [View Article] [PubMed]
    [Google Scholar]
  27. McClung LS, Toabe R. The egg yolk plate reaction for the presumptive diagnosis of Clostridium sporogenes and certain species of the gangrene and botulinum groups. J Bacteriol 1947; 53:139–147 [View Article] [PubMed]
    [Google Scholar]
  28. Alnahdi HS. Isolation and screening of extracellular proteases produced by new isolated Bacillus sp. J App Pharm Sci 2012; 2:071–074 [View Article]
    [Google Scholar]
  29. Gerceker D, Karasartova D, Elyürek E, Barkar S, Kiyan M et al. A new, simple, rapid test for detection of DNase activity of microorganisms: DNase Tube test. J Gen Appl Microbiol 2009; 55:291–294 [View Article] [PubMed]
    [Google Scholar]
  30. 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]
  31. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  32. Tailliez P, Pagès S, Ginibre N, Boemare N. New insight into diversity in the genus Xenorhabdus, including the description of ten novel species. Int J Syst Evol Microbiol 2006; 56:2805–2818 [View Article] [PubMed]
    [Google Scholar]
  33. Kuwata R, Qiu L-H, Wang W, Harada Y, Yoshida M et al. Xenorhabdus ishibashii sp. nov., isolated from the entomopathogenic nematode Steinernema aciari. Int J Syst Evol Microbiol 2013; 63:1690–1695 [View Article] [PubMed]
    [Google Scholar]
  34. Ferreira T, van Reenen CA, Endo A, Spröer C, Malan AP et al. Description of Xenorhabdus khoisanae sp. nov., the symbiont of the entomopathogenic nematode Steinernema khoisanae. Int J Syst Evol Microbiol 2013; 63:3220–3224 [View Article] [PubMed]
    [Google Scholar]
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