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Volume 72, Issue 1

sp. nov., a 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from camel faeces No Access

Abstract

An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel bacterial strain designated C459-1. It was Gram-stain-negative, short-rod-shaped and non-motile. Strain C459-1 was observed to grow optimally at 35 °C, at pH 7.0 and in the presence of 0 % NaCl on Luria–Bertani agar medium. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as iso-C, summed feature 3 (C 6 and/or C 7) and iso-C 3-OH. The predominant menaquinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, one sphingophospholipid, two unknown aminophospholipids, three unknown glycolipids and five unknown lipids. The genomic DNA G+C content was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C459-1 was affiliated with the genus and had the highest sequence similarity to h337 (97.0 %) and HER1398 (95.6 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain C459-1 and h337 were 83.8 and 33.8 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilization differentiated strain C459-1 from other species. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain C459-1 represents a novel species of the genus , for which the name sp. nov. is proposed, with strain is C459-1 (CGMCC 1.18716=KCTC 82381) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , camel faeces , polyphasic taxonomic and Sphingobacterium faecale sp. nov.
Funding
This study was supported by the:
  • Recruitment Program of Global Experts (Award YNWR-CYJS-2019-042)
    • Principle Award Recipient: MingHe Mo
  • China Tobacco Guizhou Industrial (Award 2021XM12)
    • Principle Award Recipient: MingHe Mo
  • China Tobacco Yunnan Industrial Corp (Award 2021530000241006)
    • Principle Award Recipient: MingHe Mo
  • Applied Basic Research Key Project of Yunnan (Award 202001BB050072,2019ZG0090)
    • Principle Award Recipient: LiMa
  • Major Research Plan (Award 31960022, 32170131, 31870091)
    • Principle Award Recipient: MingHe Mo
© 2022 The Authors
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References

  1. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N. Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting Gram-negative rods in CDC groups IIK-2 and IIb. Int J Syst Bacteriol 1983; 33:580–598 [View Article]
     [Google Scholar]
  2. Wauters G, Janssens M, De Baere T, Vaneechoutte M, Deschaght P. Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium . Int J Syst Evol Microbiol 2012; 62:2598–2601 [View Article] [PubMed]
     [Google Scholar]
  3. Zhou X-K, Huang Y, Li M, Zhang X-F, Wei Y-Q et al. Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave. Int J Syst Evol Microbiol 2020; 70:2348–2354 [View Article] [PubMed]
     [Google Scholar]
  4. Chaudhary DK, Kim J. Sphingobacterium terrae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:609–615 [View Article] [PubMed]
     [Google Scholar]
  5. Fu Y-S, Hussain F, Habib N, Khan IU, Chu X et al. Sphingobacteriumsoli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:2284–2288 [View Article] [PubMed]
     [Google Scholar]
  6. Lee Y, Jin HM, Jung HS, Jeon CO. Sphingobacterium humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:4632–4638 [View Article] [PubMed]
     [Google Scholar]
  7. Xu L, Sun J-Q, Wang L-J, Gao Z-W, Sun L-Z et al. Sphingobacterium alkalisoli sp. nov., isolated from a saline-alkaline soil. Int J Syst Evol Microbiol 2017; 67:1943–1948 [View Article]
     [Google Scholar]
  8. Du J, Singh H, Won K, Yang J-E, Jin F-X et al. Sphingobacterium mucilaginosum sp. nov., isolated from rhizosphere soil of a rose. Int J Syst Evol Microbiol 2015; 65:2949–2954 [View Article] [PubMed]
     [Google Scholar]
  9. Liu H, Zhang J, Chen D, Cao L, Lu P et al. Sphingobacterium changzhouense sp. nov., a bacterium isolated from a rice field. Int J Syst Evol Microbiol 2013; 63:4515–4518 [View Article] [PubMed]
     [Google Scholar]
  10. Son H-M, Yang J-E, Kook M-C, Shin H-S, Park S-Y et al. Sphingobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from the soil of a ginseng field. J Gen Appl Microbiol 2013; 59:345–352 [View Article] [PubMed]
     [Google Scholar]
  11. Zhou X-K, Li Q-Q, Mo M-H, Zhang Y-G, Dong L-M et al. Sphingobacterium tabacisoli sp. nov., isolated from a tobacco field soil sample. Int J Syst Evol Microbiol 2017; 67:4808–4813 [View Article] [PubMed]
     [Google Scholar]
  12. Schmidt VSJ, Wenning M, Scherer S. Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment. Int J Syst Evol Microbiol 2012; 62:1506–1511 [View Article] [PubMed]
     [Google Scholar]
  13. Kaur M, Singh H, Sharma S, Mishra S, Tanuku NRS et al. Sphingobacterium bovisgrunnientis sp. nov., isolated from yak milk. Int J Syst Evol Microbiol 2018; 68:636–642 [View Article] [PubMed]
     [Google Scholar]
  14. Li G-D, Chen X, Li Q-Y, Xu F-J, Qiu S-M et al. Sphingobacterium rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis . Antonie van Leeuwenhoek 2015; 108:1099–1105 [View Article] [PubMed]
     [Google Scholar]
  15. Song J, Joung Y, Li SH, Hwang J, Cho JC. Sphingobacterium chungjuense sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2020; 70:6126–6132 [View Article] [PubMed]
     [Google Scholar]
  16. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im W-T, Aslam Z. Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost. Int J Syst Evol Microbiol 2016; 66:4433–4439 [View Article] [PubMed]
     [Google Scholar]
  17. Li Y, Guo L-M, Chang J-P, Yang X-Q, Xie S-J et al. Sphingobacterium corticibacter sp. nov., isolated from bark of Populus × euramericana . Int J Syst Evol Microbiol 2019; 69:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  18. Liu J, Yang L-L, Xu C-K, Xi J-Q, Yang F-X et al. Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. Int J Syst Evol Microbiol 2012; 62:1809–1813 [View Article] [PubMed]
     [Google Scholar]
  19. Huys G, Purohit P, Tan CH, Snauwaert C, Vos PD et al. Sphingobacterium cellulitidis sp. nov., isolated from clinical and environmental sources. Int J Syst Evol Microbiol 2017; 67:1415–1421 [View Article] [PubMed]
     [Google Scholar]
  20. Dubois M, Van den Broeck L, Inzé D. The pivotal role of ethylene in plant growth. Trends Plant Sci 2018; 23:311–323 [View Article] [PubMed]
     [Google Scholar]
  21. Potuschak T, Lechner E, Parmentier Y, Yanagisawa S, Grava S et al. EIN3-dependent regulation of plant ethylene hormone signaling by two arabidopsis F box proteins: EBF1 and EBF2. Cell 2003; 115:679–689 [View Article] [PubMed]
     [Google Scholar]
  22. Gupta S, Pandey S. Unravelling the biochemistry and genetics of ACC deaminase-An enzyme alleviating the biotic and abiotic stress in plants. Plant Gene 2019; 18:100175 [View Article]
     [Google Scholar]
  23. Singh RP, Shelke GM, Kumar A, Jha PN. Biochemistry and genetics of ACC deaminase: a weapon to “stress ethylene” produced in plants. Front Microbiol 2015; 6:937 [View Article] [PubMed]
     [Google Scholar]
  24. Honma M, Shimomura T. Metabolism of 1-aminocyclopropane-1-carboxylic acid. Agri Biol Chem 2014; 42:1825–1831 [View Article]
     [Google Scholar]
  25. Etesami H, Maheshwari DK. Use of plant growth promoting rhizobacteria (PGPRs) with multiple plant growth promoting traits in stress agriculture: Action mechanisms and future prospects. Ecotoxicol Environ Saf 2018; 156:225–246 [View Article] [PubMed]
     [Google Scholar]
  26. Qin S, Zhang Y-J, Yuan B, Xu P-Y, Xing K et al. Isolation of ACC deaminase-producing habitat-adapted symbiotic bacteria associated with halophyte Limonium sinense (Girard) Kuntze and evaluating their plant growth-promoting activity under salt stress. Plant Soil 2013; 374:753–766 [View Article]
     [Google Scholar]
  27. Gupta S, Pandey S. ACC deaminase producing bacteria with multifarious plant growth promoting traits alleviates salinity stress in French bean (Phaseolus vulgaris) plants. Front Microbiol 2019; 10:1506 [View Article] [PubMed]
     [Google Scholar]
  28. Gamalero E, Glick BR. Bacterial modulation of plant ethylene levels. Plant Physiol 2015; 169:13–22 [View Article] [PubMed]
     [Google Scholar]
  29. Ravanbakhsh M, Sasidharan R, Voesenek LACJ, Kowalchuk GA, Jousset A et al. ACC deaminase‐producing rhizosphere bacteria modulate plant responses to flooding. J Ecol 2017; 105:979–986 [View Article]
     [Google Scholar]
  30. Maheshwari R, Bhutani N, Suneja P. Isolation and characterization of acc deaminase producing endophytic bbacillus mojavensis prnprn2 from pisum sativum. Int J Biotechnol 2020; 18:2308
     [Google Scholar]
  31. Pandey S, Gupta S. Diversity analysis of ACC deaminase producing bacteria associated with rhizosphere of coconut tree (Cocos nucifera L.) grown in Lakshadweep islands of India and their ability to promote plant growth under saline conditions. J Biotechnol 2020; 324:183–197 [View Article] [PubMed]
     [Google Scholar]
  32. Sarkar A, Pramanik K, Mitra S, Soren T, Maiti TK. Enhancement of growth and salt tolerance of rice seedlings by ACC deaminase-producing Burkholderia sp. MTCC 12259. J Plant Physiol 2018; 231:434–442 [View Article] [PubMed]
     [Google Scholar]
  33. Gupta A, Singh SK, Singh MK, Singh VK, Modi A et al. Plant growth–promoting rhizobacteria and their functional role in salinity stress management. J Abate Envir Pollut 2020151–160
     [Google Scholar]
  34. Islam MT, Rahman MM, Pandey P, Boehme MH, Haesaert G et al. Bacilli and Agrobiotechnology: Phytostimulation and Biocontrol. In Agrobiotechnology: Phytostimulation and Biocontrol. Bacilli in Climate Resilient Agriculture and Bioprospecting. Cham: Springer; 2019 pp 81–95 [View Article]
     [Google Scholar]
  35. Glick BR. Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 2014; 169:30–39 [View Article] [PubMed]
     [Google Scholar]
  36. Penrose DM, Glick BR. Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria. Physiol Plant 2003; 118:10–15 [View Article] [PubMed]
     [Google Scholar]
  37. Li Z, Chang S, Ye S, Chen M, Lin L et al. Differentiation of 1-aminocyclopropane-1-carboxylate (ACC) deaminase from its homologs is the key for identifying bacteria containing ACC deaminase. FEMS Microbiol Ecol 2015; 91:10 [View Article] [PubMed]
     [Google Scholar]
  38. 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]
  39. 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]
  40. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  41. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biology 1971; 20:406–416 [View Article]
     [Google Scholar]
  42. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  43. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  44. 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]
  45. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  46. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015; 16:157 [View Article] [PubMed]
     [Google Scholar]
  47. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 2011; 7:539 [View Article] [PubMed]
     [Google Scholar]
  48. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
     [Google Scholar]
  49. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  50. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994; 44:846–849 [View Article]
     [Google Scholar]
  51. Xi L, Zhang Z, Qiao N, Zhang Y, Li J et al. Complete genome sequence of the novel thermophilic polyhydroxyalkanoates producer Aneurinibacillus sp. XH2 isolated from Gudao oilfield in China. J Biotechnol 2016; 227:54–55 [View Article] [PubMed]
     [Google Scholar]
  52. 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]
  53. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  54. 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]
  55. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  56. 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]
  57. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–W185 [View Article]
     [Google Scholar]
  58. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article] [PubMed]
     [Google Scholar]
  59. Skerman VBD. A guide to the identification of the genera of bacteria, with methods and digests of generic characteristics based on data given in the seventh edition. In Bergey’s Manual of Determinative Bacteriology and on Original Papers, 7th edn. Williams & Wilkins; 1967
     [Google Scholar]
  60. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article]
     [Google Scholar]
  61. Fraser SL, Jorgensen JH. Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 1997; 41:2738–2741 [View Article] [PubMed]
     [Google Scholar]
  62. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  63. 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 1984; 2:233–241 [View Article]
     [Google Scholar]
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Sphingobacterium faecale sp. nov., a 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from camel faeces
Int J Syst Evol Microbiol 72, 005215 (2022); https://doi.org/10.1099/ijsem.0.005215
/content/journal/ijsem/10.1099/ijsem.0.005215
/content/journal/ijsem/10.1099/ijsem.0.005215
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