Abstract
A plant growth hormone indoleacetic acid-producing strain LX3-4T was isolated from a carrot rhizosphere soil sample collected in Shandong Province, China. It is Gram-stain-positive, non-motile, and has irregular short rod-shaped cells. LX3-4T shared high 16S rRNA gene sequence identity with Microbacterium oleivorans DSM 16091T (99.4%), M. testaceum NBRC 12675T (98.6%), M. marinum DSM 24947T (98.5%), M. resistens NBRC 103078T (98.4%), and M. paraoxydans NBRC 103076T (98.3%). Phylogenetic analysis based on the concatenated gene sequences of 16S rRNA gene, housekeeping genes gryB and rpoB also showed the distinction between strain LX3-4T and other Microbacterium species. Furthermore, analysis of the average nucleotide identities (ANI), the average amino acid identity (AAI), and the digital DNA-DNA hybridization (dDDH) values between strain LX3-4T and its relatives revealed that strain LX3-4T represents a distinct species. The genomic DNA G + C content of the strain is 69.5%. It can grow at 25–37 °C (optimum 37 °C), pH 5.0–10.0 (optimum pH 6.0–8.0), and the range of NaCl concentration is 0–7% (w/v) (optimum 1–5%). The colonies on agar plates are smooth, translucent, and pale yellow. The main cellular fatty acids of strain LX3-4T are anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The predominant respiratory quinones are MK-12 and MK-11. Diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, and an unidentified phosphoglycolipid are major polar lipids. The cell-wall sugar of strain LX3-4T is glucose. The cell-wall peptidoglycan contains glycine, alanine, lysine, and glutamic acid. In addition, this strain carries nitrogen fixation genes and can grow in nitrogen-free medium. Based on the polyphasic data, strain LX3-4T represents a novel species of the genus Microbacterium, for which the name Microbacterium dauci sp. nov. is proposed with strain LX3-4T (= CCTCC AB 2023103T = LMG 33159T) designated as the type strain.
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Strain LX3-4T = CCTCC AB 2023103T = LMG 33159T. The GenBank accession number for the whole genome sequences of strain LX3-4T is JASJND000000000.
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References
Blin K, Shaw S, Augustijn HE et al (2023) antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 51:W46–W50. https://doi.org/10.1093/nar/gkad344
Brisman K, Engel MH, Macko SA (2001) Distribution, stereochemistry, and stable isotope composition of amino acids in K/T boundary sediments. Precambrian Res 106:59–77. https://doi.org/10.1016/S0301-9268(00)00125-X
Chen Y, Xie M, Wang Y et al (2009) Analysis of the monosaccharide composition of purified polysaccharides in Ganoderma atrum by capillary gas chromatography. Phytochem Anal 20:503–510. https://doi.org/10.1002/pca.1153
Chen Y, Li Y, Shen J et al (2022) Bacillus arachidis sp. nov., isolated from peanut rhizosphere soil. Curr Microbiol 79:231. https://doi.org/10.1007/s00284-022-02925-2
Dong X, Cai Y (2001) Common bacteria system identification manual. Science press, Beijing, pp 373–384 (in Chinese)
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Funke G, Lawson PA, Nolte FS et al (1998) Aureobacterium resistens sp. nov., exhibiting vancomycin resistance and teicoplanin susceptibility. FEMS Microbiol Lett 158:89–93. https://doi.org/10.1111/j.1574-6968.1998.tb12805.x
Glickmann E, Dessaux Y (1995) A critical examination of the specificity of the salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol 61:793–796. https://doi.org/10.1128/aem.61.2.793-796.1995
Goris J, Konstantinidis KT, Klappenbach JA et al (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
Hwang YJ, Lee SY, Son JS et al (2023) Microbacterium elymi sp. nov., isolated from the rhizospheric soil of Elymus tsukushiensis, a plant native to the Dokdo islands, Republic of Korea. J Microbiol Biotechnol 33:188–194. https://doi.org/10.4014/jmb.2211.11024
Jensen MP, Ardö Y, Vogensen FK (2009) Isolation of cultivable thermophilic lactic acid bacteria from cheeses made with mesophilic starter and molecular comparison with dairy-related Lactobacillus helveticus strains. Lett Appl Microbiol 49:396–402. https://doi.org/10.1111/j.1472-765X.2009.02673.x
Kageyama A, Takahashi Y, Matsuo Y et al (2007a) Microbacterium flavum sp. nov. and Microbacterium lacus sp. nov., isolated from marine environments. Actinomycetologica 21:53–58. https://doi.org/10.3209/saj.SAJ210201
Kageyama A, Takahashi Y, Omura S (2007b) Microbacterium terricolae sp. nov., isolated from soil in Japan. J Gen Appl Microbiol 53:1–5. https://doi.org/10.2323/jgam.53.1
Kim YJ, Roh SW, Jung MJ et al (2011) Microbacterium mitrae sp. nov., isolated from salted turban shell. Int J Syst Evol Microbiol 61:399–403. https://doi.org/10.1099/ijs.0.021519-0
Komagata K, Iizuka H (1964) New species of Brevibacterium isolated from rice (studies on the microorganisms of cereal grains: part VII). Nippon Nogeikagaku Kaishi 38:496–502. https://doi.org/10.1271/nogeikagaku1924.38.496
Kook M, Son HM, Yi TH (2014) Microbacterium kyungheense sp. nov. and Microbacterium jejuense sp. nov., isolated from salty soil. Int J Syst Evol Microbiol 64:2267–2273. https://doi.org/10.1099/ijs.0.054973-0
Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Laffineur K, Avesani V, Cornu G et al (2003) Bacteremia due to a novel Microbacterium species in a patient with leukemia and description of Microbacterium paraoxydans sp. nov. J Clin Microbiol 41:2242–2246. https://doi.org/10.1128/JCM.41.5.2242-2246.2003
Ma Q, Kong D, Zhang Q et al (2022) Microbacterium sulfonylureivorans sp. nov., isolated from sulfonylurea herbicides degrading consortium. Arch Microbiol 204:136. https://doi.org/10.1007/s00203-021-02750-4
Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M (2022) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 50:D801–D807. https://doi.org/10.1093/nar/gkab902
Minnikin DE, Abdolrahimzadeh H (1971) Thin-layer chromatography of bacterial lipids on sodium acetate-impregnated silica gel. J Chromatogr 63:452–454. https://doi.org/10.1016/S0021-9673(01)85672-7
Minnikin DE, Patel PV, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of nocardia and related bacteria. Int J Syst Bacteriol 27:104–117. https://doi.org/10.1099/00207713-27-2-104
Minnikin DE, O’Donnell AG, Goodfellow M et al (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
Orla-Jensen S (1919) The lactic acid bacteria. Host and Son, Copenhagen
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131. https://doi.org/10.1073/pnas.0906412106
Shao J, Li S, Zhang N et al (2015) Analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefaciens SQR9. Microb Cell Fact 14:130. https://doi.org/10.1186/s12934-015-0323-4
Takeuchi M, Hatano K (1998) Proposal of six new species in the genus Microbacterium and transfer of Flavobacterium marinotypicum ZoBell and Upham to the genus Microbacterium as Microbacterium maritypicum comb. nov. Int J Syst Evol Microbiol 48:973–982. https://doi.org/10.1099/00207713-48-3-973
Xie F, Niu S, Lin X et al (2021) Description of Microbacterium luteum sp. nov., Microbacterium cremeum sp. nov., and Microbacterium atlanticum sp. nov., three novel C50 carotenoid producing bacteria. J Microbiol 59:886–897. https://doi.org/10.1007/s12275-021-1186-5
Zhang L, Xi L, Ruan J, Huang Y (2012) Microbacterium marinum sp. nov., isolated from deep-sea water. Syst Appl Microbiol 35:81–85. https://doi.org/10.1016/j.syapm.2011.11.004
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This research was funded by the National Natural Science Foundation of China (grant No. 31771946).
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Conceived and designed the experiments: ZX. Performed the experiments: JZ, YL, YL, DL, YS. Analyzed the data: JZ, ZX. Contributed reagents/materials/analysis tools: ZX. Wrote the paper: JZ, ZX.
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Zheng, J., Liao, Y., Li, Y. et al. Description of Microbacterium dauci sp. nov., a plant growth hormone indoleacetic acid-producing and nitrogen-fixing bacterium isolated from carrot rhizosphere soil. Arch Microbiol 206, 102 (2024). https://doi.org/10.1007/s00203-023-03810-7
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DOI: https://doi.org/10.1007/s00203-023-03810-7