Alkalihalobacillus deserti sp. nov., Isolated from the Saline–Alkaline Soil
Tóm tắt
A bacterial strain, designated TRPH29T, was isolated from saline-alkaline soil, collected from the southern edge of the Gurbantunggut desert, Xinjiang, People’s Republic of China. The isolate was Gram-staining positive, facultatively anaerobic, straight rods. Growth occurred at 15–40 °C (optimum, 28 °C), pH 8.0–13.0 (optimum, 10.0), and in the presence of 0–15% (w/v) NaCl (optimum, 2%). Phylogenetic analysis using 16S rRNA gene sequence indicated that strain TRPH29T showed the highest sequence similarities to Alkalihalobacillus krulwichiae (98.31%), Alkalihalobacillus wakoensis (98.04%), and Alkalihalobacillus akibai (97.69%). Average nucleotide identity (ANI) and digital DNA-DNA hybridization values between strain TRPH29T and Alkalihalobacillus krulwichiae, Alkalihalobacillus wakoensis, Alkalihalobacillus akibai were in the range of 73.62–75.52% and 15.0–21.20%, respectively. Results of genome analyses indicated that the genome size of strain TRPH29T was 5.05 Mb, with a genomic DNA G + C content of 37.30%. Analysis of the cellular component of strain TRPH29T revealed that the primary fatty acids were anteiso-C15:0 and iso-C15:0, and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid, and an unidentified phospholipid. The predominant respiratory quinone was MK-7. Based on the genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain TRPH29T represents a novel species of the genus Alkalihalobacillus, for which the name Alkalihalobacillus deserti sp. nov. is proposed. The type strain is TRPH29T (= CGMCC 1.19067T = NBRC 115475T).
Tài liệu tham khảo
Cohn F (1872) Untersuchungen über Bakterien. Beitr Biol Pflanz 1:127–224
Joshi A, Thite S, Karodi P, Joseph N, Lodha T (2021) Alkalihalobacterium elongatum gen. nov. sp. nov.: an antibiotic-producing bacterium isolated from Lonar Lake and reclassification of the genus Alkalihalobacillus into seven novel genera. Front Microbiol 12:722369. https://doi.org/10.3389/fmicb.2021.722369
Patel S, Gupta RS (2020) A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 70:406–438. https://doi.org/10.1099/ijsem.0.003775
Priest FG, Goodfellow MO, Todd C (1988) A numerical classification of the genus Bacillus. Microbiology 134(7):1847–1882. https://doi.org/10.1099/00221287-134-7-1847
Kämpfer P (1994) Limits and possibilities of total fatty acid analysis for classification and identification of Bacillus species. Syst Appl Microbiol 17(1):86–98. https://doi.org/10.1016/S0723-2020(11)80035-4
Shin B, Park C, Lee BH, Lee KE, Park W (2020) Bacillus miscanthi sp. nov., a alkaliphilic bacterium from the rhizosphere of Miscanthus sacchariflorus. Int J Syst Evol Microbiol 70:1843–1849. https://doi.org/10.1099/ijsem.0.003982
Horikoshi K (1999) Alkaliphiles: some applications of their products for biotechnology. Microbiol Mol Biol R 63(4):735. https://doi.org/10.1128/MMBR.63.4.735-750.1999
Sarethy IP et al (2011) Alkaliphilic bacteria: applications in industrial biotechnology. J Ind Microbiol Biotechnol 38(7):769–790. https://doi.org/10.1007/s10295-011-0968-x
Lee GH, Rhee MS, Chang DH, Kwon KK, Bae KS (2014) Bacillus solimangrovi sp. nov., isolated from mangrove soil. Int J Syst Evol Microbiol 64(Pt 5):1622–1628. https://doi.org/10.1099/ijs.0.058230-0
Li X et al (2018) Actinocorallia populi sp. nov., an endophytic actinomycete isolated from a root of Populus adenopoda (Maxim.). Int J Syst Evol Microbiol 68:2325–2330. https://doi.org/10.1099/ijsem.0.002840
Yoon SH et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67(5):1613–1617. https://doi.org/10.1099/ijsem.0.001755
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Larkin MA et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.0000/PMID3447015
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416. https://doi.org/10.1093/sysbio/20.4.406
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Ewels P, Magnusson M, Lundin S, Käller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048. https://doi.org/10.1093/bioinformatics/btw354
Bankevich A et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
Lagesen K et al (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. https://doi.org/10.1093/nar/gkm160
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955–964. https://doi.org/10.1093/nar/25.5.955
Aziz RK et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75
Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2015) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32(6):929–931. https://doi.org/10.1093/bioinformatics/btv681
Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9(3):111–118. https://doi.org/10.1128/microbe.9.111.1
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinfo 14:60. https://doi.org/10.1186/1471-2105-14-60
Jiao JY et al (2022) Comparative genomic analysis of Thermus provides insights into the evolutionary history of an incomplete denitrification pathway. mLife 1(2):12. https://doi.org/10.1002/mlf2.12009
Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P (ed) Methods for general and molecular bacteriology. American Society for Microbiology, pp 607–654
Kämpfer P et al (2017) Psychromonas aquatilis sp. nov. isolated from seawater samples obtained in the Chilean Antarctica. Int J Syst Evol Microbiol 67:1306–1311. https://doi.org/10.1099/ijsem.0.001801
Gonzalez C, Gutierrez C, Ramirez C (1978) Halobacterium vallismortis sp. nov., An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 24(6):710–715. https://doi.org/10.1139/m78-119
Yumoto I et al (2003) Bacillus krulwichiae sp. nov., a halotolerant obligate alkaliphile that utilizes benzoate and m-hydroxybenzoate. Int J Syst Evol Microbiol 53:1531–1536. https://doi.org/10.1099/ijs.0.02596-0
Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703–704. https://doi.org/10.1038/178703a0
Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5(12):2359–2367. https://doi.org/10.1080/01483918208067640
Hasegawa T, Takizawa M, Tanida S (1983) A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29(4):319–322. https://doi.org/10.2323/jgam.29.319
Lechevalier MP, Lechevalier H (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443. https://doi.org/10.1099/00207713-20-4-435
Minnikin DE et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2(5):233–241. https://doi.org/10.1016/0167-7012(84)90018-6
Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 48:459–470. https://doi.org/10.1111/j.1365-2672.1980.tb01036.x
Mason JR, Cammack R (1992) The electron-transport proteins of hydroxylating bacterial dioxygenases. Annu Rev Microbiol 46:277–305. https://doi.org/10.1146/annurev.mi.46.100192.001425
Borsodi AK et al (2011) Bacillus alkalisediminis sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from sediment of extremely shallow soda ponds. IJSEM 61(8):1880–1886. https://doi.org/10.1099/ijs.0.019489-0
Nogi Y, Takami H, Horikoshi K (2005) Characterization of alkaliphilic bacillus strains used in industry: proposal of five novel species. Int J Syst Evol Microbiol 55(Pt 6):2309–2315. https://doi.org/10.1099/ijs.0.63649-0
Rundlöf AK, Arnér ESJ (2004) Regulation of the mammalian selenoprotein thioredoxin reductase 1 in relation to cellular phenotype, growth, and signaling events. Antioxid Redox Sign 6(1):41–52. https://doi.org/10.1089/152308604771978336
Gibson DT, Yeh WK (1984) Microbial degradation of aromatic hydrocarbons. Microb Degrad Org Compd. https://doi.org/10.1002/jobm.19650050409
Manivasagan P, Venkatesan J, Sivakumar K, Kim SK (2013) Marine actinobacterial metabolites: current status and future perspectives. Microbiol Res. https://doi.org/10.1016/j.micres.2013.02.002
Horikoshi K (1971) Production of alkaline enzymes by alkalophilic microorganisms. Part I. Alkaline protease produced by Bacillus no. 221. Agric Biol Chem 35(9):1407–1414. https://doi.org/10.1080/00021369.1971.10860094
Ito S et al (1989) Alkaline cellulase for laundry detergents-production by Bacillus sp. KSM-635 and enzymatic-properties. Agric Biol Chem 53(5):1275–1281. https://doi.org/10.1080/00021369.1989.10869489
Loiseau C et al (2015) Surfactin from Bacillus subtilis displays an unexpected anti-legionella activity. Appl Microbiol Biotechnol 99(12):5083–5093. https://doi.org/10.1007/s00253-014-6317-z
Qi G et al (2010) Lipopeptide induces apoptosis in fungal cells by a mitochondria-dependent pathway. Peptides 31(11):1978–1986. https://doi.org/10.1016/j.peptides.2010.08.003
Furuya S, Mochizuki M, Aoki Y, Kobayashi H, Takayanagi T, Shimizu M, Suzuki S (2011) Isolation and characterization of Bacillus subtilis KS1 for the biocontrol of grapevine fungal diseases. Biocontrol Sci Technol 21(6):705–720. https://doi.org/10.1080/09583157.2011.574208
Cheng W, Feng YQ, Ren J, Jing D, Wang C (2016) Anti-tumor role of Bacillus subtilis fmbJ-derived fengycin on human colon cancer HT29 cell line. Neoplasma 63(2):215–222. https://doi.org/10.4149/206_150518N270
Tran PN et al (2015) Whole-Genome sequence and classification of 11 endophytic bacteria from poison ivy (Toxicodendron radicans). Genome Announc. https://doi.org/10.1128/genomeA.01319-15
Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 19:161–207. https://doi.org/10.1016/S0580-9517(08)70410-0
Liu B et al (2019) Bacillus urbisdiaboli sp. nov., isolated from soil sampled in Xinjiang. Int J Syst Evol Microbiol 69(6):1591–1596. https://doi.org/10.1099/ijsem.0.003363