Abstract
Strain W712T was isolated from rhizosphere soil of Nicotiana tabacum L. collected from Kunming, south-west China. Cells were Gram-staining negative, aerobic, motile and rod shaped. The isolate grew at 20–45 °C (optimum 30 °C), pH 6.0–8.0 (optimum pH 7.0) and in the presence of up to 3.0% (w/v) NaCl (optimum 1%, w/v). Ubiquinone-10 was the only respiratory quinone type. Polar lipids contained diphosphatidylglycerol, phosphatidylmehtylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified aminolipid. The major fatty acids were detected as summed feature 8 (C18:1 ω7c or C18:1 ω6c), summed feature 3 (C16:1 ω7c or C16:1 ω6c) and C18:1 2OH. The genomic DNA G + C content was 68.7%. The ANI values were 94.3%, 93.3% and 93.6% between Azospirillum baldaniorum Sp245T, Azospirillum brasilense ATCC 49958T, Azospirillum formosense CC-Nfb-7T and strain W712T, respectively, which were lower than the prokaryotic species delineation threshold of 95.0–96.0%. The digital DNA–DNA hybridization values between A. baldaniorum Sp245T, A. brasilense ATCC 49958T, A. formosense CC-Nfb-7T and strain W712T indicated that the candidate represents a novel genomic species. According to the phenotypic and genotypic characteristics, we propose that strain W712T warrants the assignment to a novel species, for which the name Azospirillum tabaci sp. nov. (type strain W712T = CGMCC 1.18567T = KCTC 82186T) is proposed.
Similar content being viewed by others
References
Aziz A, Martin-Tanguy J, Larher F (1997) Plasticity of polyamine metabolism associated with high osmotic stress in rape leaf discs and with ethylene treatment. Plant Growth Regul 21:153–163. https://doi.org/10.1023/A:1005730509433
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206-214. https://doi.org/10.1093/nar/gkt1226
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477. https://doi.org/10.1089/cmb.2012.0021
Bashan Y, Holguin G, de Bashan LE (2004) Azospirillum–plant relationships: physiological, molecular, agricultural, and environmental advances (1997–2003). Can J Microbiol 50:521–577. https://doi.org/10.1139/w04-035
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, Da CM, Rooney AP, Yi H, Xu XW, De MS (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516
Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230. https://doi.org/10.1099/00221287-100-2-221
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–789. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Ferreira NdS, Anna FHS, Reis VM, Ambrosini A, Volpiano CG, Rothballer M, Schwab S, Baura VA, Balsanelli E, Pedrosa FdO, Passaglia LMP, Souza EMd, Hartmann A, Cassan F, Zilli JE (2020) Genome-based reclassification of Azospirillum brasilense Sp245 as the type strain of Azospirillum baldaniorum sp. nov. Int J Syst Evol Microbiol 70:6203–6212. https://doi.org/10.1099/ijsem.0.004517
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416. https://doi.org/10.2307/2412116
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0
Gregersen T (1978) Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5:123–127. https://doi.org/10.1007/BF00498806
Groth I, Schumann P, Weiss N, Martin K, Rainey FA (1996) Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 46:234–239. https://doi.org/10.1099/00207713-46-1-234
Hardy RWF, Burns RC, Holsten RD (1973) Application of the acetylene-ethylene assay for measurement of nitrogen fixation. Soil Biol Biochem 5:47–81. https://doi.org/10.1016/0038-0717(73)90093-X
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/BF01731581
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Lin SY, Shen FT, Yong LS, Zhu ZL, Chen WM, Young CC (2012) Azospirillum formosense sp. nov., a diazotroph from agricultural soil. Int J Syst Evol Microbiol 62:1185–1190. https://doi.org/10.1099/ijs.0.030585-0
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60
Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95. https://doi.org/10.1111/j.1365-2672.1979.tb01172.x
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6
Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J (2018) UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56(4):280–285. https://doi.org/10.1007/s12275-018-8014-6
Okon Y, Vanderleyden J (1997) Root-associated Azospirillum species can stimulate plants. ASM News 63:366–370
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7):1043–1055. https://doi.org/10.1101/gr.186072.114
Reasoner DJ, Geldreich EF (1985) A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microb 49:1–7. https://doi.org/10.1128/aem.49.1.1-7.1985
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131. https://doi.org/10.1073/pnas.0906412106
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic tree. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. MIDI Inc, Newwark
Saxena B, Modi M, Modi V (1986) Isolation and characterization of siderophores from Azospirillum lipoferum D-2. J Gen Microbiol 132:2219–2224. https://doi.org/10.1099/00221287-132-8-2219
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153
Seshadri S, Muthukumarasamy R, Lakshinarasimhan C, Ignacimuthu S (2000) Solubilization of inorganic phosphates by Azospirillum halopraeferans. Curr Sci 79:565–567. https://doi.org/10.1021/pr049965y
Skerman VBD (1967) A guide to the identification of the Genera of Bacteria, 2nd edn. Williams & Wilkins, Baltimore
Steenhoudt O, Vanderleyden J (2000) Azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: genetic, biochemical and ecological aspects. FEMS Microbiol Rev 24:487–506. https://doi.org/10.1111/j.1574-6976.2000.tb00552.x
Tarrand JJ, Krieg NR, Döbereiner J (1978) A taxonomic study of the Spirillum lipoferum group, with descriptions of a new genus, Azospirillum gen. nov. and two species, Azospirillum lipoferum (Beijerinck) comb. nov. and Azospirillum brasilense sp. nov. Can J Microbiol 24:967–980. https://doi.org/10.1139/m78-160
Thuler DS, Floh EI, Handro W, Barbosa HR (2003) Plant growth regulators and amino acids released by Azospirillum sp in chemically defined media. Lett Appl Microbiol 37:174–178. https://doi.org/10.1046/j.1472-765x.2003.01373.x
Wang YN, Cai H, Yu SL, Wang ZY, Liu J, Wu XL (2007) Halomonas gudaonensis sp. nov., isolated from a saline soil contaminated by crude oil. Int J Syst Evol Microbiol 57:911–915. https://doi.org/10.1099/ijs.0.64826-0
Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler OK (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacterio. https://doi.org/10.1099/00207713-37-4-463
Xi L, Zhang Z, Qiao N, Zhang Y, Li J, Jing-Yi Z, Xiao Z (2016) Complete genome sequence of the novel thermophilic polyhydroxyalkanoates producer Aneurinibacillus sp. XH2 isolated from Gudao oilfield in China. J Biotechnol 227:54–55. https://doi.org/10.1016/j.jbiotec.2016.03.056
Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153. https://doi.org/10.1099/ijs.0.63407-0
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017a) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1618. https://doi.org/10.1099/ijsem.0.001755
Yoon SH, Sm Ha, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110(10):1281–6253. https://doi.org/10.1007/s10482-017-0844-4
Acknowledgements
The authors are grateful to Takuji Kudo (JCM, Japan) for providing the reference strains.
Funding
This research was funded by China Tobacco Yunnan Industrial Corp, (Grant No. 2020CL04) and Natural Science Foundation of Guangdong Province, China (No. 2016A030312003).
Author information
Authors and Affiliations
Contributions
GD and WJL designed research and project outline. YQD, XKZ, NH, SQG performed isolation, deposition, and identification. XKZ, LMD, XFL and YMS performed fatty acids analysis. All authors read and approved the final manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that there are no conflicts of interest.
Ethical statement
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
Communicated by Erko Stackebrandt.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Duan, YQ., Zhou, XK., Habib, N. et al. Azospirillum tabaci sp. nov., a bacterium isolated from rhizosphere soil of Nicotiana tabacum L. Arch Microbiol 204, 80 (2022). https://doi.org/10.1007/s00203-021-02688-7
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-021-02688-7