دورية أكاديمية

Pelagibacterium flavum sp. nov., Isolated from Soil Sample.

التفاصيل البيبلوغرافية
العنوان: Pelagibacterium flavum sp. nov., Isolated from Soil Sample.
المؤلفون: Chen XM; School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China., Yang ZZ; School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China., He SR; School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China., Xiong LS; School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China., Yuan Q; School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China., Zuo SY; School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China., Jiang CL; School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China., Jiang Y; School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China. jiangyi@ynu.edu.cn.
المصدر: Current microbiology [Curr Microbiol] 2024 Jan 23; Vol. 81 (3), pp. 72. Date of Electronic Publication: 2024 Jan 23.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Springer International Country of Publication: United States NLM ID: 7808448 Publication Model: Electronic Cited Medium: Internet ISSN: 1432-0991 (Electronic) Linking ISSN: 03438651 NLM ISO Abbreviation: Curr Microbiol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: New York, Springer International.
مواضيع طبية MeSH: Sodium Chloride* , Alphaproteobacteria*, China ; DNA ; Soil
مستخلص: A Gram-stain-negative, yellow, moist and circular, aerobic, motile, and rod-shaped bacterium, designated YIM 151497 T , was isolated from soil sample collected from Blue-Bridge, Weizhou Island, Guangxi province, China. Classification using a polyphasic approach suggested that strain YIM 151497 T belonged to the genus Pelagibacterium, and was closely relevant to Pelagibacterium nitratireducens JLT2005 T (98.8%), Pelagibacterium halotolerans CGMCC 1.7692 T (98.7%), Pelagibacterium lixinzhangensis H64 T (98.1%), and Pelagibacterium luteolum CGMCC 1.10267 T (97.1%). The growth ranges of temperature, pH, and NaCl were 4-40 ℃, pH 4.0-10.0, and 0-7% NaCl, respectively. It was positive for catalase and oxidase. The primary respiratory quinone was Q-10. The elemental fatty acids were Summed Feature 8 (constituting C 18:1 ω7c and/or C 18:1 ω6c), C 19:0 cyclo ω8c, C 16:0 , and C 18:1 ω7c 11-methyl. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and three unidentified glycolipids. The DNA G+C content based on the complete genome sequence was 60.7 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between strain YIM 151497 T and species of Pelagibacterium were in the ranges of 73.9-86.3% and 19.7-31.3%, respectively. The Average Amino Acid Identity (AAI) between strain YIM 151497 T and species of Pelagibacterium were in the ranges of 68.8-88.8%. On the basis of these data, strain YIM 151497 T is considered to represent a novel species of the genus Pelagibacterium with the name of Pelagibacterium flavum sp. nov. Type strain is strain YIM 151497 T (= KCTC 49826 T  = CGMCC 1.61521 T  = MCCC 1K08053 T ).
(© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
References: Xu X-W, Huo Y-Y, Wang C-S, Oren A, Cui H-L, Vedler E, Wu M (2011) Pelagibacterium halotolerans gen. nov., sp. Nov. and Pelagibacterium luteolum sp. Nov., novel members of the family Hyphomicrobiaceae. Int J Syst Evol Microbiol 61(8):1817–1822. https://doi.org/10.1099/ijs.0.023325-0. (PMID: 10.1099/ijs.0.023325-020817840)
Li Q, Xu Y, Liu K, Cai L, Fu Y, Sun J, Zhang R (2013) Pelagibacterium nitratireducens sp. nov., a marine Alphaproteobacterium isolated from the east China Sea. Curr Microbiol 66(5):450–455. https://doi.org/10.1007/s00284-012-0299-9. (PMID: 10.1007/s00284-012-0299-923299946)
Yang N, Sun C (2016) Pelagibacterium lixinzhangensis sp. nov., a novel member of the genus Pelagibacterium. Curr Microbiol 72(5):551–556. https://doi.org/10.1007/s00284-016-0989-9. (PMID: 10.1007/s00284-016-0989-926787545)
He Y, Lyu L, Dong C, Wang W, Yu Z, Shao Z (2022) Pelagibacterium xiamenense sp. nov., isolated from intertidal sediment. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.005462. (PMID: 10.1099/ijsem.0.00546236748585)
Liu B-T, Wang C, Wang X-M, Chen G-J, Du Z-J (2019) Pelagibacterium lacus sp. nov., isolated from lake water. Int J Syst Evol Microbiol 69(6):1807–1813. https://doi.org/10.1099/ijsem.0.003398. (PMID: 10.1099/ijsem.0.00339830994429)
Jang H-J, Song J, Joung Y, Cho J-C (2019) Pelagibacterium sediminicola sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 69(9):2651–2657. https://doi.org/10.1099/ijsem.0.003499. (PMID: 10.1099/ijsem.0.00349931157611)
Chen X-M, An D-F, He S-R, Yang S-J, Yang Z-Z, Xiong L-S, Li G-D, Jiang M-G, Jiang C-L, Jiang Y (2022) Acinetobacter faecalis sp. nov., isolated from elephant faeces. Curr Microbiol 80(1):21. https://doi.org/10.1007/s00284-022-03097-9. (PMID: 10.1007/s00284-022-03097-936460940)
Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R, Xu L-H, Stackebrandt E, Jiang C-L (2007) Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57(7):1424–1428. https://doi.org/10.1099/ijs.0.64749-0. (PMID: 10.1099/ijs.0.64749-017625169)
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A 82(20):6955–6959. https://doi.org/10.1073/pnas.82.20.6955. (PMID: 10.1073/pnas.82.20.69552413450391288)
Chun J, Lee J-H, Jung Y, Kim M, Kim S, Kim BK, Lim Y-W (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57(10):2259–2261. https://doi.org/10.1099/ijs.0.64915-0. (PMID: 10.1099/ijs.0.64915-017911292)
Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis, version 11. Mol Biol Evol 38(7):3022–3027. https://doi.org/10.1093/molbev/msab120. (PMID: 10.1093/molbev/msab120338924918233496)
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x. (PMID: 10.1111/j.1558-5646.1985.tb00420.x28561359)
Sergey K, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27(5):722–736. https://doi.org/10.1101/gr.215087.116. (PMID: 10.1101/gr.215087.116)
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 25:1043–1055. https://doi.org/10.1101/gr.186072.114. (PMID: 10.1101/gr.186072.114259774774484387)
Yoon S-H, Ha S-m, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110(10):1281–1286. https://doi.org/10.1007/s10482-017-0844-4. (PMID: 10.1007/s10482-017-0844-428204908)
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(W1):W81–W87. https://doi.org/10.1093/nar/gkz310. (PMID: 10.1093/nar/gkz310310325196602434)
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14(1):60. https://doi.org/10.1186/1471-2105-14-60. (PMID: 10.1186/1471-2105-14-60234329623665452)
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068–2069. https://doi.org/10.1093/bioinformatics/btu153. (PMID: 10.1093/bioinformatics/btu15324642063)
Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9(3):111–118.
Danquah MK, Forde GM (2007) Growth Medium selection and its economic impact on plasmid DNA production. J Biosci Bioeng 104(6):490–497. https://doi.org/10.1263/jbb.104.490. (PMID: 10.1263/jbb.104.49018215636)
Gregersen T (1978) Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5(2):123–127. https://doi.org/10.1007/BF00498806. (PMID: 10.1007/BF00498806)
Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z, Chen H-H, Xu L-H, Jiang C-L (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55(3):1149–1153. https://doi.org/10.1099/ijs.0.63407-0. (PMID: 10.1099/ijs.0.63407-015879247)
Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178(4535):703–703. https://doi.org/10.1038/178703a0. (PMID: 10.1038/178703a013369512)
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, Snyder LR (eds) Methods for general and molecular microbiology. American Society for Microbiology, Washington, pp 330–393.
Kämpfer RP (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005. https://doi.org/10.1139/m96-128. (PMID: 10.1139/m96-128)
Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207. (PMID: 10.1016/S0580-9517(08)70410-0)
Collins MD (1985) 11 Analysis of isoprenoid quinones. Methods Microbiol 18(08):329–366. https://doi.org/10.1016/S0580-9517(08)70480-X. (PMID: 10.1016/S0580-9517(08)70480-X)
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. (PMID: 10.1080/01483918208067640)
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(5):233–241. https://doi.org/10.1016/0167-7012(84)90018-6. (PMID: 10.1016/0167-7012(84)90018-6)
Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64(Pt 2):346–351. https://doi.org/10.1099/ijs.0.059774-0. (PMID: 10.1099/ijs.0.059774-024505072)
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(1):461. https://doi.org/10.1099/ijsem.0.002516. (PMID: 10.1099/ijsem.0.00251629292687)
Meier-Kolthoff JP, Klenk HP, Goker M (2014) Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64(Pt 2):352. https://doi.org/10.1099/ijs.0.056994-0. (PMID: 10.1099/ijs.0.056994-024505073)
Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60(1):249–266. https://doi.org/10.1099/ijs.0.016949-0. (PMID: 10.1099/ijs.0.016949-019700448)
Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187(18):6258–6264. https://doi.org/10.1128/JB.187.18.6258-6264.2005. (PMID: 10.1128/JB.187.18.6258-6264.2005161597571236649)
معلومات مُعتمدة: AA18242026 Guangxi for science and technology; 32060001 National Natural Science Foundation of China; YNWR-QNBJ-2018-085 The Government Project of Yunnan Province
المشرفين على المادة: 451W47IQ8X (Sodium Chloride)
9007-49-2 (DNA)
0 (Soil)
تواريخ الأحداث: Date Created: 20240122 Date Completed: 20240124 Latest Revision: 20240212
رمز التحديث: 20240213
DOI: 10.1007/s00284-023-03583-8
PMID: 38253909
قاعدة البيانات: MEDLINE
الوصف
تدمد:1432-0991
DOI:10.1007/s00284-023-03583-8