1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 9

sp. nov., sp. nov., sp. nov. and sp. nov., isolated from subtropical streams, and phylogenomic analyses of the genera , , , and No Access

Abstract

Six Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT81W, FT82W, FT107W, FT3S, LX20W and LX47W) sharing high 16S rRNA gene sequence similarities with species of the genera (97.0–98.3 %), (96.3–98.8 %), (97.8–98.6 %), (96.8–97.5 %) and (94.5–98.6 %) were isolated from subtropical streams in PR China. The phylogenetic trees reconstructed using the 16S rRNA gene sequences indicated that the species of above five genera often mix together, indicating that the taxonomic statuses of some species were questionable. Phylogenomic reconstruction based on 369 single-copy orthologous clusters indicated that the species of the genus form a distinct cluster, strains FT81W, FT82W and FT107W form a tight cluster with the species of the genus , and strains FT3S, LX20W and LX47W form a tight cluster with the species of genus , and the species of genus form a tight cluster with , , , , sensu Lu , , , , , , , , , and . It should be noted that Lu 2020 non Holochová 2020 is a later homonym and an illegitimate name. The GTDB Release 202 also supported the proposal that , , , , sensu Lu , , , , , , , , , and should be transferred into the genus . The calculated pairwise orthologous average nucleotide identity by (OrthoANIu) values were between 95.0 % and 95.6 % among strains FT81W, FT82W and FT107W, but were less than 91.5 % among strains FT3S, LX20W, LX47W and other related strains. Combining the results of phylogenomic analyses, phenotypic, biochemical and genotypic characteristics, strains FT81W, FT82W and FT107W should represent a novel species of the genus , and strains FT3S, LX20W and LX47W should represent three novel species of the genus , for which the names sp. nov. (type strain FT81W=GDMCC 1.1679 =KACC 21471), sp. nov. (type strain FT3S=GDMCC 1.1907 =KACC 21952), sp. nov. (type strain LX20W=GDMCC 1.1911 =KACC 21956) and sp. nov. (type strain LX47W=GDMCC 1.1914 =KACC 21959) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Duganella , Janthinobacterium , Massilia , Pseudoduganella and Rugamonas
Funding
This study was supported by the:
  • gdas’ special project of science and technology development (Award 2020GDASYL-20200103016; 2020GDASYL-20200402001)
    • Principle Award Recipient: MeiyingXu
  • the Key-Area Research and Development Program of Guangdong Province (Award 2019B110205004)
    • Principle Award Recipient: MeiyingXu
  • National Natural Science Foundation of China (Award 91851202; 51678163)
    • Principle Award Recipient: MeiyingXu
  • guangdong technological innovation strategy of special funds (Award Key Areas of Research and Development Program (2018B020205003))
    • Principle Award Recipient: MeiyingXu
© 2022 The Authors
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2022-09-05
2024-05-02
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References

  1. Lu HB, Song D, Deng TC, Mei CF, Xu MY. Duganella vulcania sp. nov., Rugamonas fusca sp. nov., Rugamonas brunnea sp. nov. and Rugamonas apoptosis sp. nov., isolated from subtropical streams in china and phylogenomic analyses of genera Janthinobacterium, Duganella, Rugamonas, Pseudoduganella and Massilia. Figshare 2022 [View Article]
     [Google Scholar]
  2. Baldani JI, Rouws L, Cruz LM, Olivares FL, Schmid M et al. The Family Oxalobacteraceae. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. eds The Prokaryotes: Alphaproteobacteria and Betaproteobacteria Berlin, Heidelberg: Springer; 2014 pp 919–974
     [Google Scholar]
  3. De Ley J, Segers P, Gillis M. Intra- and intergeneric similarities of Chromobacterium and Janthinobacterium ribosomal ribonucleic acid cistrons. Int J Syst Bacteriol 1978; 28:154–168 [View Article]
     [Google Scholar]
  4. Lincoln SP, Fermor TR, Tindall BJ. Janthinobacterium agaricidamnosum sp. nov., a soft rot pathogen of Agaricus bisporus. Int J Syst Bacteriol 1999; 49 Pt 4:1577–1589 [View Article] [PubMed]
     [Google Scholar]
  5. Lu H, Deng T, Cai Z, Liu F, Yang X et al. Janthinobacterium violaceinigrum sp. nov., Janthinobacterium aquaticum sp. nov. and Janthinobacterium rivuli sp. nov., isolated from a subtropical stream in China. Int J Syst Evol Microbiol 2020; 70:2719–2725 [View Article]
     [Google Scholar]
  6. Ambrožič Avguštin J, Žgur Bertok D, Kostanjšek R, Avguštin G. Isolation and characterization of a novel violacein-like pigment producing psychrotrophic bacterial species Janthinobacterium svalbardensis sp. nov. Antonie Van Leeuwenhoek 2013; 103:763–769 [View Article] [PubMed]
     [Google Scholar]
  7. Jung WJ, Kim SW, Giri SS, Kim HJ, Kim SG et al. Janthinobacterium tructae sp. nov., isolated from kidney of rainbow trout (Oncorhynchus mykiss). Pathogens 2021; 10:229 [View Article]
     [Google Scholar]
  8. Hiraishi A, Shin YK, Sugiyama J. Proposal to reclassify Zoogloea ramigera IAM 12670 (P. R. Dugan 115) as Duganella zoogloeoides gen. nov., sp. nov. Int J Syst Bacteriol 1997; 47:1249–1252 [View Article]
     [Google Scholar]
  9. Kämpfer P, Wellner S, Lohse K, Martin K, Lodders N. Duganella phyllosphaerae sp. nov., isolated from the leaf surface of Trifolium repens and proposal to reclassify Duganella violaceinigra into a novel genus as Pseudoduganella violceinigra gen. nov., comb. nov. Syst Appl Microbiol 2012; 35:19–23 [View Article] [PubMed]
     [Google Scholar]
  10. Zhang J, Kim Y-J, Hoang V-A, Lan Nguyen N, Wang C et al. Duganella ginsengisoli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 2016; 66:56–61 [View Article] [PubMed]
     [Google Scholar]
  11. Madhaiyan M, Poonguzhali S, Saravanan VS, Hari K, Lee K-C et al. Duganella sacchari sp. nov. and Duganella radicis sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane. Int J Syst Evol Microbiol 2013; 63:1126–1131 [View Article] [PubMed]
     [Google Scholar]
  12. Lu H, Deng T, Liu F, Wang Y, Yang X et al. Duganella albus sp. nov., Duganella aquatilis sp. nov., Duganella pernnla sp. nov. and Duganella levis sp. nov., isolated from subtropical streams in China. Int J Syst Evol Microbiol 2020; 70:3801–3808 [View Article]
     [Google Scholar]
  13. Lu HB, Cai ZP, Yang YG, Xu MY. Duganella rivus sp. nov., Duganella fentianensis sp. nov., Duganella qianjiadongensis sp. nov. and Massilia guangdongensis sp. nov., isolated from subtropical streams in China and reclassification of all species within genus Pseudoduganella. Antonie Van Leeuwenhoek 2020; 113:1155–1165 [View Article]
     [Google Scholar]
  14. Lu H, Deng T, Liu F, Wang Y, Yang X et al. Duganella lactea sp. nov., Duganella guangzhouensis sp. nov., Duganella flavida sp. nov. and Massilia rivuli sp. nov., isolated from a subtropical stream in PR China and proposal to reclassify Duganella ginsengisoli as Massilia ginsengisoli comb. nov. Int J Syst Evol Microbiol 2020; 70:4822–4830 [View Article]
     [Google Scholar]
  15. Jeon D, Kim IS, Choe H, Kim JS, Lee SD. Duganella aceris sp. nov., isolated from tree sap and proposal to transfer of Rugamonas aquatica and Rugamonas rivuli to the genus Duganella as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas. Arch Microbiol 2021; 203:2843–2852 [View Article] [PubMed]
     [Google Scholar]
  16. Raths R, Peta V, Bücking H. Duganella callida sp. nov., a novel addition to the Duganella genus, isolated from the soil of a cultivated maize field. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  17. Kämpfer P, Irgang R, Busse H-J, Poblete-Morales M, Kleinhagauer T et al. Pseudoduganella danionis sp. nov., isolated from zebrafish (Danio rerio). Int J Syst Evol Microbiol 2016; 66:4671–4675 [View Article] [PubMed]
     [Google Scholar]
  18. Jin DH, Subhash Y, Lee SS. Psedoduganella eburnea sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2017; 67:5268–5272 [View Article] [PubMed]
     [Google Scholar]
  19. Austin DA, Moss MO. Numerical taxonomy of red-pigmented bacteria isolated from a lowland river, with the description of a new taxon, Rugamonas rubra gen. nov., sp. nov. Microbiology 1986; 132:1899–1909 [View Article]
     [Google Scholar]
  20. Lu HB, Deng TC, Liu FF, Wang YH, Xu MY. Rugamonas aquatica sp. nov. and Rugamonas rivuli sp. nov., isolated from a subtropical stream in PR China. Int J Syst Evol Microbiol 2020; 70:3328–3334 [View Article]
     [Google Scholar]
  21. Sedláček I, Holochová P, Sobotka R, Busse H-J, Švec P et al. Classification of a violacein-producing psychrophilic group of Isolates associated with freshwater in Antarctica and description of Rugamonas violacea sp. nov. Microbiol Spectr 2021; 9:e0045221 [View Article] [PubMed]
     [Google Scholar]
  22. La Scola B, Birtles RJ, Mallet MN, Raoult D. Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions. J Clin Microbiol 1998; 36:2847–2852 [View Article]
     [Google Scholar]
  23. Kämpfer P, Lodders N, Martin K, Falsen E. Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov. Int J Syst Evol Microbiol 2011; 61:1528–1533 [View Article]
     [Google Scholar]
  24. Singh H, Du J, Won K, Yang J-E, Yin C et al. Massilia arvi sp. nov., isolated from fallow-land soil previously cultivated with Brassica oleracea, and emended description of the genus Massilia. Int J Syst Evol Microbiol 2015; 65:3690–3696 [View Article] [PubMed]
     [Google Scholar]
  25. Lu HB, Deng TC, Xu MY. Massilia aquatica sp. nov., isolated from a subtropical stream in China. Curr Microbiol 2020; 77:3185–3191 [View Article] [PubMed]
     [Google Scholar]
  26. Holochová P, Mašlaňová I, Sedláček I, Švec P, Králová S et al. Description of Massilia rubra sp. nov., Massilia aquatica sp. nov., Massilia mucilaginosa sp. nov., Massilia frigida sp. nov., and one Massilia genomospecies isolated from Antarctic streams, lakes and regoliths. Syst Appl Microbiol 2020; 43:126112 [View Article]
     [Google Scholar]
  27. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Sequencing Techniques in Bacterial Systematics New York, USA: Wiley; 1991 pp 115–175
     [Google Scholar]
  28. 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]
  29. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  30. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  35. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  36. 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]
  37. Yoon SH, Ha SM, 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]
  38. 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]
  39. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  40. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
     [Google Scholar]
  41. Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 2022; 50:D785–D794 [View Article] [PubMed]
     [Google Scholar]
  42. 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]
  43. Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Front Microbiol 2018; 9:771 [View Article] [PubMed]
     [Google Scholar]
  44. Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M. New approach for understanding genome variations in KEGG. Nucleic Acids Res 2019; 47:D590–D595 [View Article] [PubMed]
     [Google Scholar]
  45. Zhu XF. Modern experimental technique of microbiology Hangzhou, China: Zhejiang University Press; 2011
     [Google Scholar]
  46. Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Numerical taxonomy of moderately halophilic Gram-negative rods. Microbiology 1982; 128:1959–1968 [View Article]
     [Google Scholar]
  47. Zhong Z-P, Liu Y, Wang F, Zhou Y-G, Liu H-C et al. Lacimicrobium alkaliphilum gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:422–429 [View Article]
     [Google Scholar]
  48. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  49. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. eds Methods in Phytobacteriology Budapest, Hungary: Akademiai Kaido; 1990 pp 199–204
     [Google Scholar]
  50. 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]
  51. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  52. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  53. 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 Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  54. Zhang Y-Q, Li W-J, Zhang K-Y, Tian X-P, Jiang Y et al. Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China. Int J Syst Evol Microbiol 2006; 56:459–463 [View Article] [PubMed]
     [Google Scholar]
  55. Wang J, Zhang J, Pang H, Zhang Y, Li Y et al. Massilia flava sp. nov., isolated from soil. Int J Syst Evol Microbiol 2012; 62:580–585 [View Article] [PubMed]
     [Google Scholar]
  56. Luo X, Xie Q, Wang J, Pang H, Fan J et al. Massilia lurida sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013; 63:2118–2123 [View Article] [PubMed]
     [Google Scholar]
  57. Rodríguez-Díaz M, Cerrone F, Sánchez-Peinado M, SantaCruz-Calvo L, Pozo C et al. Massilia umbonata sp. nov., able to accumulate poly-β-hydroxybutyrate, isolated from a sewage sludge compost–soil microcosm. Int J Syst Evol Microbiol 2014; 64:131–137 [View Article] [PubMed]
     [Google Scholar]
  58. Sun L-N, Yang E-D, Cui D-X, Ni Y-W, Wang Y-B et al. Massilia buxea sp. nov., isolated from a rock surface. Int J Syst Evol Microbiol 2017; 67:4390–4396 [View Article] [PubMed]
     [Google Scholar]
  59. Ren M, Li X, Zhang Y, Jin Y, Li S et al. Massilia armeniaca sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2018; 68:2319–2324 [View Article] [PubMed]
     [Google Scholar]
  60. Kong BH, Li YH, Liu M, Liu Y, Li CL et al. Massilia namucuonensis sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 2013; 63:352–357 [View Article] [PubMed]
     [Google Scholar]
  61. Embarcadero-Jiménez S, Peix Á, Igual JM, Rivera-Orduña FN, Tao Wang E. Massilia violacea sp. nov., isolated from riverbank soil. Int J Syst Evol Microbiol 2016; 66:707–711 [View Article] [PubMed]
     [Google Scholar]
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Duganella vulcania sp. nov., Rugamonas fusca sp. nov., Rugamonas brunnea sp. nov. and Rugamonas apoptosis sp. nov., isolated from subtropical streams, and phylogenomic analyses of the genera Janthinobacterium, Duganella, Rugamonas, Pseudoduganella and Massilia
Int J Syst Evol Microbiol 72, 005407 (2022); https://doi.org/10.1099/ijsem.0.005407
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