Abstract
A Gram-stain-negative, motile (by single polar flagellum) and rod-shaped bacterium, designated W1-6T, was isolated from a sediment of drainage ditch in winery in Guiyang, south-western China. Strain W1-6T showed the highest 16S rRNA gene sequence similarities with the type strain of Acidovorax wautersii (98.1%) and Simplicispira lacusdiani (97.9%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W1-6T was placed adjacent to the members of the genus Simplicispira and formed a separat subclade. Cells showed oxidase and catalase negative reactions. The only respiratory quinone detected was ubiquinone-8 (Q-8). Summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) were predominant cellular fatty acids (> 10%) of strain W1-6T. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and five unidentified phospholipids were found in the polar lipid extraction. The genomic DNA G + C content was 65.6%. Strain W1-6T shared the highest digital DNA-DNA hybridization [dDDH, (27.6%)] and average nucleotide identity [ANI (84.3%)] values with the type strain of S. lacusdiani. The dDDH and ANI values were below the cutoff level (dDDH 70%; ANI 95–96%) for species delineation. The polyphasic characteristics indicated that the strain W1-6T represents a novel species of the genus Simplicispira, for which the name Simplicispira sedimenti sp. nov. is proposed. The type strain is W1-6T (= CGMCC 1.16274T = NBRC 115624T).
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References
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
Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87. https://doi.org/10.1093/nar/gkz310
Chaudhary DK, Kim J (2018) Acidovorax monticola sp. nov., isolated from soil. Antonie van Leeuwenhock 111:1925–1934. https://doi.org/10.1007/s10482-018-1083-z
Cho HY, Heo J, Hong SB, Kim JS, Kwon SW, Kim SJ (2018) Simplicispira suum sp. nov., isolated from a dust collector at a pig farm. Int J Syst Evol Microbiol 68:2557–2561. https://doi.org/10.1099/ijsem.0.00287
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
Dahal RH, Kim J (2018) Simplicispira soli sp. nov., a betaproteobacterium isolated from stream bank soil. Int J Syst Evol Microbiol 68:951–956. https://doi.org/10.1099/ijsem.0.002618
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
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
Grabovich M, Gavrish E, Kuever J, Lysenko AM, Podkopaeva D, Galina D (2006) Proposal of Giesbergeria voronezhensis gen. nov., sp. nov. and G. kuznetsovii sp. nov. and reclassification of [Aquaspirillum] anulus, [A.] sinuosum and [A.] giesbergeri as Giesbergeria annulus comb. nov., G. sinuosa comb. nov. and G. giesbergeri comb. nov., and [Aquaspirillum] metamorphum and [A.] psychrophilum as Simplicispira metamorpha gen. nov., comb. nov. and S. psychrophila comb. nov. Int J Syst Evol Microbiol 56:569–576
Hyun DW, Oh SJ, Kim MS, Whon TW, Jung MJ, Shin NR, Kim PS, Kim HS, Lee JY, Kang W, Bae JW (2015) Simplicispira piscis sp. nov., isolated from the gut of a Korean rockfish, Sebastes schlegelii. Int J Syst Evol Microbiol 65:4689–4694. https://doi.org/10.1099/ijsem.0.000635
Kim MK, Park S, Kim TS, Joung Y, Han JH, Kim SB (2019) Mucibacter soli gen. nov., sp. nov., a new member of the family Chitinophagaceae producing mucin. J Microbiol 57(5):356–361. https://doi.org/10.1007/s12275-019-8512-1
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
Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge, Cambridgeshire
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
Lee JS, Shin YK, Yoon JH, Takeuchi M, Pyun YR, Park YH (2001) Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int J Syst Evol Microbiol 51:1491–1498
Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24(5):713–714. https://doi.org/10.1093/bioinformatics/btn025
Lu S, Ryu SH, Chung BS, Chung YR, Park W, Jeon CO (2007) Simplicispira limi sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 57:31–34. https://doi.org/10.1099/ijs.0.64566-0
Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3(2):208–218. https://doi.org/10.1016/S0022-2836(61)80047-8
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf 14:60. https://doi.org/10.1186/1471-2105-14-60
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
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, DE
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153
Shi YL, Jiang ZM, Ruan ZY, Su J, Yu LY, Zhang YQ (2019) Simplicispira lacusdiani sp. nov., a novel betaproteobacterium isolated from a freshwater reservoir. Int J Syst Evol Microbiol 69:129–133. https://doi.org/10.1099/ijsem.0
Siddiqi MZ, Sok W, Choi G, Kim SY, Wee JH, Im WT (2020) Simplicispira hankyongi sp. nov., a novel denitrifying bacterium isolated from sludge. Antonie Van Leeuwenhoek 113:331–338. https://doi.org/10.1007/s10482-019-01341-0
Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM (eds) Methods for general and molecular microbiology. American Society for Microbiology, Washington, DC, pp 330–393
Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703. https://doi.org/10.1128/jb.173.2.697-703.1991
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
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
Zheng ZH, Lu CY, Lian WH, Han JR, Chen F, Zhou T, Li S, Dong L, Li WJ (2023) Danxiaibacter flavus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from forest soil on Danxia Mountain. Int J Syst Evol Microbiol 73:006082. https://doi.org/10.1099/ijsem.0.006082
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This research was supported by the Foundation of China Tobacco Yunnan Industrial Co., Ltd. (2023XL01).
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WJL and YQD designed research and project outline. XC, XKZ, YQD, NH and LG performed isolation, deposition, and identification. LMD and GD performed fatty acids analysis. All authors read and approved the final manuscript.
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Chen, X., Li, YD., Liu, XM. et al. Simplicispira sedimenti sp. nov., isolated from a sediment of drainage ditch in winery. Antonie van Leeuwenhoek 117, 13 (2024). https://doi.org/10.1007/s10482-023-01899-w
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DOI: https://doi.org/10.1007/s10482-023-01899-w