1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 1

sp. nov., a novel indole acetic acid producing endophyte isolated from bamboo in China No Access

Abstract

Two novel indole acetic acid-producing strains, 5MLIR and D4N7, were isolated from in Yongzhou, Hunan province, and in Hangzhou, Zhejiang province, respectively. Based on their sequences, strains 5MLIR and D4N7 were closely related to 16-35-5 (98.4 % sequence similarity), and the results of 92-core gene phylogenetic trees showed that strains 5MLIR and D4N7 formed a phylogenetic lineage within the clade comprising species. The complete genome size of strain 5MLIR was 4.49 Mb including two plasmids, and the DNA G+C content was 66.5 mol%. The draft genome of strain D4N7 was 4.26 Mb with 66.7 mol% G+C content. The average nucleotide identity and digital DNA–DNA hybridization values among strain 5MLIR and species in the genus were all below the species delineation threshold. The colonies of strain 5MLIR and D4N7 were circular with regular margins, convex, pale yellow and 1.0–2.0 mm in diameter when incubated at 30 °C for 3 days. Strains 5MLIR and D4N7 grew optimally at 30 °C, pH 7.0 and 1.0 % NaCl. The respiratory isoprenoid quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Polyphasic analyses indicated that strains 5MLIR and D4N7 could be distinguished from related validly named species and represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 5MLIR (=ACCC 62069=GDMCC 1.2958=JCM 35331).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Comamonas , Indosasa shibataeoides , Phyllostachys edulis , phylogeny and polyphasic approach
Funding
This study was supported by the:
  • Fundamental Research Funds for the Central Non-profit Research Institution of Chinese Academy of Forestry (Award CAFYBB2022XE001)
© 2024 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006217
2024-01-08
2024-05-21
Loading full text...

Full text loading...

References

  1. De Vos P, Kersters K, Falsen E, Pot B, Gillis M et al. Comamonas Davis and Park 1962 gen. nov., nom. rev. emend., and Comamonas terrigena Hugh 1962 sp. nov., nom. rev. Int J Syst Bacteriol 1985; 35:443–453 [View Article]
     [Google Scholar]
  2. Tamaoka J, Ha DM, Komagata K. Reclassification of Pseudomonas acidovorans den Dooren de Jong 1926 and Pseudomonas testosteroni Marcus and Talalay 1956 as Comamonas acidovorans comb. nov. and Comamonas testosteroni comb. nov., with an emended description of the genus Comamonas. Int J Syst Bacteriol 1987; 37:52–59 [View Article]
     [Google Scholar]
  3. Willems A, Pot B, Falsen E, Vandamme P, Gillis M et al. Polyphasic taxonomic study of the emended genus Comamonas: relationship to Aquaspirillum aquaticum, E. Falsen group 10, and other clinical isolates. Int J Syst Bacteriol 1991; 41:427–444 [View Article]
     [Google Scholar]
  4. Zhang J, Wang Y, Zhou S, Wu C, He J et al. Comamonas guangdongensis sp. nov., isolated from subterranean forest sediment, and emended description of the genus Comamonas. Int J Syst Evol Microbiol 2013; 63:809–814 [View Article] [PubMed]
     [Google Scholar]
  5. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  6. Xu Q, Peng X, Wang Y, Lu L, Zhang Y et al. Acidovorax antarcticus sp. nov., isolated from a soil sample of Collins Glacier front, Antarctica. Int J Syst Evol Microbiol 2019; 71: [View Article] [PubMed]
     [Google Scholar]
  7. Hatayama K. Comamonas humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:3976–3982 [View Article] [PubMed]
     [Google Scholar]
  8. Sun L-N, Zhang J, Chen Q, He J, Li Q-F et al. Comamonas jiangduensis sp. nov., a biosurfactant-producing bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 2013; 63:2168–2173 [View Article] [PubMed]
     [Google Scholar]
  9. Chipirom K, Tanasupawat S, Akaracharanya A, Leepepatpiboon N, Prange A et al. Comamonas terrae sp. nov., an arsenite-oxidizing bacterium isolated from agricultural soil in Thailand. J Gen Appl Microbiol 2012; 58:245–251 [View Article] [PubMed]
     [Google Scholar]
  10. Yu X-Y, Li Y-F, Zheng J-W, Li Y, Li L et al. Comamonas zonglianii sp. nov., isolated from phenol-contaminated soil. Int J Syst Evol Microbiol 2011; 61:255–258 [View Article] [PubMed]
     [Google Scholar]
  11. Tago Y, Yokota A. Comamonas badia sp. nov., a floc-forming bacterium isolated from activated sludge. J Gen Appl Microbiol 2004; 50:243–248 [View Article] [PubMed]
     [Google Scholar]
  12. Gumaelius L, Magnusson G, Pettersson B, Dalhammar G. Comamonas denitrificans sp. nov., an efficient denitrifying bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2001; 51:999–1006 [View Article] [PubMed]
     [Google Scholar]
  13. Chou J-H, Sheu S-Y, Lin K-Y, Chen W-M, Arun AB et al. Comamonas odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus. Int J Syst Evol Microbiol 2007; 57:887–891 [View Article] [PubMed]
     [Google Scholar]
  14. Kang W, Soo Kim P, Hyun D-W, Lee J-Y, Sik Kim H et al. Comamonas piscis sp. nov., isolated from the intestine of a Korean rockfish, Sebastes schlegelii. Int J Syst Evol Microbiol 2016; 66:780–785 [View Article] [PubMed]
     [Google Scholar]
  15. Wauters G, Baere T, Willems A, Falsen E, Vaneechoutte M. Description of Comamonas aquatica comb. nov. and Comamonas kerstersii sp. nov. for two subgroups of Comamonas terrigena and emended description of Comamonas terrigena. Int J Syst Evol Microbiol 2003; 53:859–862 [View Article] [PubMed]
     [Google Scholar]
  16. Kämpfer P, Busse H-J, Baars S, Wilharm G, Glaeser SP. Comamonas aquatilis sp. nov., isolated from a garden pond. Int J Syst Evol Microbiol 2018; 68:1210–1214 [View Article] [PubMed]
     [Google Scholar]
  17. Park EH, Kim YS, Cha CJ. Comamonas fluminis sp. nov., isolated from the Han River, Republic of Korea. Int J Syst Evol Microbiol 2022; 72:5287 [View Article] [PubMed]
     [Google Scholar]
  18. Kim KH, Ten LN, Liu QM, Im WT, Lee ST. Comamonas granuli sp. nov., isolated from granules used in a wastewater treatment plant. J Microbiol 2008; 46:390–395 [View Article] [PubMed]
     [Google Scholar]
  19. Park KH, Yu Z, Dong K, Lee SS. Comamonas suwonensis sp. nov., isolated from stream water in the Republic of Korea. Int J Syst Evol Microbiol 2021; 71:4681 [View Article] [PubMed]
     [Google Scholar]
  20. Etchebehere C, Errazquin MI, Dabert P, Moletta R, Muxí L. Comamonas nitrativorans sp. nov., a novel denitrifier isolated from a denitrifying reactor treating landfill leachate. Int J Syst Evol Microbiol 2001; 51:977–983 [View Article] [PubMed]
     [Google Scholar]
  21. Xie F, Ma H, Quan S, Liu D, Chen G. Comamonas phosphati sp. nov., isolated from a phosphate mine. Int J Syst Evol Microbiol 2016; 66:456–461 [View Article] [PubMed]
     [Google Scholar]
  22. Subhash Y, Bang JJ, You TH, Lee SS. Description of Comamonas sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:2735–2739 [View Article] [PubMed]
     [Google Scholar]
  23. Narayan KD, Pandey SK, Das SK. Characterization of Comamonas thiooxidans sp. nov., and comparison of thiosulfate oxidation with Comamonas testosteroni and Comamonas composti. Curr Microbiol 2010; 61:248–253 [View Article] [PubMed]
     [Google Scholar]
  24. Xing Y, Shi W, Zhu Y, Wang F, Wu H et al. Screening and activity assessing of phosphorus availability improving microorganisms associated with bamboo rhizosphere in subtropical China. Environ Microbiol 2021; 23:6074–6088 [View Article] [PubMed]
     [Google Scholar]
  25. Liu L, Liang L, Xu L, Chi M, Zhang X et al. Rhizobium deserti sp. nov isolated from biological soil crusts collected at Mu Us sandy land, China. Curr Microbiol 2020; 77:327–333 [View Article] [PubMed]
     [Google Scholar]
  26. Lane D-J. 16S/23S rRNA Sequencing New York: Wiley Interscience; 1991
     [Google Scholar]
  27. 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]
  28. 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]
  29. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  30. 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]
  31. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
     [Google Scholar]
  32. Li B, Yang X, Tan H, Ke B, He D et al. Vibrio parahaemolyticus O4:K8 forms a potential predominant clone in southern China as detected by whole-genome sequence analysis. Int J Food Microbiol 2017; 244:90–95 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
     [Google Scholar]
  35. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
     [Google Scholar]
  36. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  37. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
     [Google Scholar]
  38. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525 [View Article] [PubMed]
     [Google Scholar]
  39. Chen H, Boutros PC. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 2011; 12:35 [View Article] [PubMed]
     [Google Scholar]
  40. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  41. 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]
  42. 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]
  43. Jeong J, Weerawongwiwat V, Kim J-H, Suh MK, Kim HS et al. Arenibacterium arenosum sp. nov., isolated from sea sand. Arch Microbiol 2022; 204:147 [View Article] [PubMed]
     [Google Scholar]
  44. 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; 59:609–615 [View Article] [PubMed]
     [Google Scholar]
  45. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article] [PubMed]
     [Google Scholar]
  46. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article] [PubMed]
     [Google Scholar]
  47. 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]
  48. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  49. Chen C, Chen H, Zhang Y, Thomas HR, Frank MH et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant 2020; 13:1194–1202 [View Article] [PubMed]
     [Google Scholar]
  50. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. US Fed Cult Collection Newsletter 1990; 20:1–6
     [Google Scholar]
  51. 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]
  52. Glickmann E, Dessaux Y. A critical examination of the specificity of the salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol 1995; 61:793–796 [View Article] [PubMed]
     [Google Scholar]
  53. Teitzel GM, Geddie A, De Long SK, Kirisits MJ, Whiteley M et al. Survival and growth in the presence of elevated copper: transcriptional profiling of copper-stressed Pseudomonas aeruginosa. J Bacteriol 2006; 188:7242–7256 [View Article] [PubMed]
     [Google Scholar]
  54. Trias J, Nikaido H. Protein D2 channel of the Pseudomonas aeruginosa outer membrane has a binding site for basic amino acids and peptides. J Biol Chem 1990; 265:15680–15684 [PubMed]
     [Google Scholar]
  55. Caille O, Rossier C, Perron K. A copper-activated two-component system interacts with zinc and imipenem resistance in Pseudomonas aeruginosa. J Bacteriol 2007; 189:4561–4568 [View Article] [PubMed]
     [Google Scholar]
  56. Kumar A, Mayo M, Trunck LA, Cheng AC, Currie BJ et al. Expression of resistance-nodulation-cell-division efflux pumps in commonly used Burkholderia pseudomallei strains and clinical isolates from northern Australia. Trans R Soc Trop Med Hyg 2008; 102:S145–S151 [View Article] [PubMed]
     [Google Scholar]
  57. Oku S, Komatsu A, Tajima T, Nakashimada Y, Kato J. Identification of chemotaxis sensory proteins for amino acids in Pseudomonas fluorescens Pf0-1 and their involvement in chemotaxis to tomato root exudate and root colonization. Microbes Environ 2012; 27:462–469 [View Article] [PubMed]
     [Google Scholar]
  58. Benini S. Carbohydrate-active enzymes: structure, activity, and reaction products. Int J Mol Sci 2020; 21:2727 [View Article] [PubMed]
     [Google Scholar]
  59. Siani R, Stabl G, Gutjahr C, Schloter M, Radl V. Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations. Microb Genom 2021; 7:000666 [View Article] [PubMed]
     [Google Scholar]
  60. Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S et al. Genomic features of bacterial adaptation to plants. Nat Genet 2017; 50:138–150 [View Article] [PubMed]
     [Google Scholar]
  61. Lebrazi S, Niehaus K, Bednarz H, Fadil M, Chraibi M et al. Screening and optimization of indole-3-acetic acid production and phosphate solubilization by rhizobacterial strains isolated from Acacia cyanophylla root nodules and their effects on its plant growth. J Genet Eng Biotechnol 2020; 18:71 [View Article] [PubMed]
     [Google Scholar]
  62. Bishnu Maya KC, Dhurva Prasad G, Sanjay Nath K, Sharmila C, Janardan L. Extraction of indole-3-acetic acid from plant growth promoting rhizobacteria of bamboo rhizosphere and its effect on biosynthesis of chlorophyll in bamboo seedlings. Indian J Agric Sci 2020; 54:781–786 [View Article]
     [Google Scholar]
  63. Du XC, He XB, Zhao YP, Zhang JD, Guo CY. Changes of endogenous hormones in Bashania fargesii in the process of blooming. J Yunnan Univ Nat Sci Ed 2022; 44:612–618 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006217
Loading
Comamonas endophytica sp. nov., a novel indole acetic acid producing endophyte isolated from bamboo in China
Int J Syst Evol Microbiol 74, 006217 (2024); https://doi.org/10.1099/ijsem.0.006217
/content/journal/ijsem/10.1099/ijsem.0.006217
/content/journal/ijsem/10.1099/ijsem.0.006217
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