1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 9

Five novel species isolated from air: sp. nov., sp. nov., sp. nov., sp. nov. and sp. nov. No Access

Abstract

Five strains isolated from air samples collected from the Suwon and Jeju regions of the Republic of Korea were studied using polyphasic taxonomic methods. Using 16S rRNA gene sequences and the resulting phylogenetic tree, the strains were primarily identified as members of the genus . Digital DNA–DNA hybridization values and average nucleotide identities values for species delineation (70 and 95–96 %, respectively) between the five strains and their nearest type strains indicated that each strain represented a novel species. All strains were aerobic, Gram-stain-negative, mesophilic, rod-shaped and catalase- and oxidase-positive, with red to pink coloured colonies. The genome sizes of the five strains varied from 4.8 to 7.1 Mb and their G+C contents were between 54.1 and 59.4 mol%. Based on their phenotypic, chemotaxonomic and genotypic characteristics, we propose to classify these isolates into five novel species within the genus for which we propose the names, sp. nov., sp. nov., sp. nov., sp. nov. and sp. nov., with strains 5116 S-3 (=KACC 21925=JCM 35216), 5116 S-27 (=KACC 21926=JCM 35217), 5413 J-13 (=KACC 21928=JCM 35219), 5516 S-25 (=KACC 21931=JCM 35222) and 5420 S-77 (=KACC 21932=JCM 35223) as the type strains, respectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): air , genome , Hymenobacter , polyphasic taxonomy and species
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006026
2023-09-19
2024-05-08
Loading full text...

Full text loading...

References

  1. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B et al. Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 1998; 21:374–383 [View Article] [PubMed]
     [Google Scholar]
  2. Han L, Wu S-J, Qin C-Y, Zhu Y-H, Lu Z-Q et al. Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter. Antonie van Leeuwenhoek 2014; 105:971–978 [View Article] [PubMed]
     [Google Scholar]
  3. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
     [Google Scholar]
  4. Buczolits S, Denner EBM, Vybiral D, Wieser M, Kämpfer P et al. Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov. Int J Syst Evol Microbiol 2002; 52:445–456 [View Article] [PubMed]
     [Google Scholar]
  5. Roldán DM, Kyrpides N, Woyke T, Shapiro N, Whitman WB et al. Hymenobacter artigasi sp. nov., isolated from air sampling in maritime Antarctica. Int J Syst Evol Microbiol 2020; 70:4935–4941 [View Article] [PubMed]
     [Google Scholar]
  6. Roldán DM, Kyrpides N, Woyke T, Shapiro N, Whitman WB et al. Hymenobacter caeli sp. nov., an airborne bacterium isolated from King George Island, Antarctica. Int J Syst Evol Microbiol 2021; 71:004838 [View Article] [PubMed]
     [Google Scholar]
  7. Lee J-J, Park S-J, Lee Y-H, Lee S-Y, Ten LN et al. Hymenobacter aquaticus sp. nov., a radiation-resistant bacterium isolated from a river. Int J Syst Evol Microbiol 2017; 67:1206–1211 [View Article] [PubMed]
     [Google Scholar]
  8. Gu Z, Liu Y, Xu B, Wang N, Jiao N et al. Hymenobacter frigidus sp. nov., isolated from a glacier ice core. Int J Syst Evol Microbiol 2017; 67:4121–4125 [View Article]
     [Google Scholar]
  9. Chhetri G, Kim J, Kim I, Kim H, Seo T. Hymenobacter setariae sp. nov., isolated from the ubiquitous weedy grass Setaria viridis. Int J Syst Evol Microbiol 2020; 70:3724–3730 [View Article]
     [Google Scholar]
  10. Subhash Y, Sasikala C, Ramana CV. Hymenobacter roseus sp. nov., isolated from sand. Int J Syst Evol Microbiol 2014; 64:4129–4133 [View Article] [PubMed]
     [Google Scholar]
  11. Zhang D-C, Busse H-J, Liu H-C, Zhou Y-G, Schinner F et al. Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2011; 61:859–863 [View Article] [PubMed]
     [Google Scholar]
  12. Srinivasan S, Joo ES, Lee J-J, Kim MK. Hymenobacter humi sp. nov., a bacterium isolated from soil. Antonie van Leeuwenhoek 2015; 107:1411–1419 [View Article] [PubMed]
     [Google Scholar]
  13. Sun J, Xing M, Wang W, Dai F, Liu J et al. Hymenobacter profundi sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2018; 68:947–950 [View Article]
     [Google Scholar]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  20. 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]
     [Google Scholar]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  22. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
     [Google Scholar]
  23. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  26. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  27. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
  29. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  30. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acid Res 2018; 46:W95–W101 [View Article] [PubMed]
     [Google Scholar]
  33. Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 2010; 11:431 [View Article]
     [Google Scholar]
  34. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acid Res 2011; 39:W339–46 [View Article] [PubMed]
     [Google Scholar]
  35. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acid Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  36. Albrecht M, Takaichi S, Steiger S, Wang ZY, Sandmann G. Novel hydroxycarotenoids with improved antioxidative properties produced by gene combination in Escherichia coli. Nat Biotechnol 2000; 18:843–846 [View Article] [PubMed]
     [Google Scholar]
  37. Shindo K, Kikuta K, Suzuki A, Katsuta A, Kasai H et al. Rare carotenoids, (3R)-saproxanthin and (3R,2’S)-myxol, isolated from novel marine bacteria (Flavobacteriaceae) and their antioxidative activities. Appl Microbiol Biotechnol 2007; 74:1350–1357 [View Article] [PubMed]
     [Google Scholar]
  38. Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 2023; 51:D690–D699 [View Article] [PubMed]
     [Google Scholar]
  39. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article] [PubMed]
     [Google Scholar]
  40. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  41. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE, USA: Microbial ID Inc; 1990
     [Google Scholar]
  42. 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]
  43. Buczolits S, Denner EBM, Kämpfer P, Busse H-J. Proposal of Hymenobacter norwichensis sp. nov., classification of “Taxeobacter ocellatus”, “Taxeobacter gelupurpurascens” and “Taxeobacter chitinovorans” as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999. Int J Syst Evol Microbiol 2006; 56:2071–2078 [View Article] [PubMed]
     [Google Scholar]
  44. Feng GD, Zhang J, Chen W, Wang SN, Zhu H. Isolated from abandoned lead-zinc mine. Int J Syst Evol Microbiol 2020; 70:4867–4873 [View Article] [PubMed]
     [Google Scholar]
  45. Kang JW, Choi S, Choe HN, Seong CN. Hymenobacter defluvii sp. nov., isolated from wastewater of an acidic water neutralization facility. Int J Syst Evol Microbiol 2018; 68:277–282 [View Article]
     [Google Scholar]
  46. Liu K, Liu Y, Wang N, Gu Z, Shen L et al. Hymenobacter glacieicola sp. nov., isolated from glacier ice. Int J Syst Evol Microbiol 2016; 66:3793–3798 [View Article] [PubMed]
     [Google Scholar]
  47. Dai J, Wang Y, Zhang L, Tang Y, Luo X et al. Hymenobacter tibetensis sp. nov., a UV-resistant bacterium isolated from Qinghai-Tibet plateau. Syst Appl Microbiol 2009; 32:543–548 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006026
Loading
Five novel Hymenobacter species isolated from air: Hymenobacter cellulosilyticus sp. nov., Hymenobacter cellulosivorans sp. nov., Hymenobacter aerilatus sp. nov., Hymenobacter sublimis sp. nov. and Hymenobacter volaticus sp. nov.
Int J Syst Evol Microbiol 73, 006026 (2023); https://doi.org/10.1099/ijsem.0.006026
/content/journal/ijsem/10.1099/ijsem.0.006026
/content/journal/ijsem/10.1099/ijsem.0.006026
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