Paenibacillus glycinis sp. nov., an Endophytic Bacterium Isolated from the Nodules of Soybean (Glycine max (L.) Merr).


Journal

Current microbiology
ISSN: 1432-0991
Titre abrégé: Curr Microbiol
Pays: United States
ID NLM: 7808448

Informations de publication

Date de publication:
Apr 2021
Historique:
received: 10 10 2020
accepted: 10 02 2021
pubmed: 6 3 2021
medline: 15 5 2021
entrez: 5 3 2021
Statut: ppublish

Résumé

A Gram-negative-staining, endospore-forming, rod-shaped bacterium, designated T1

Identifiants

pubmed: 33666748
doi: 10.1007/s00284-021-02403-1
pii: 10.1007/s00284-021-02403-1
doi:

Substances chimiques

DNA, Bacterial 0
Fatty Acids 0
Phospholipids 0
RNA, Ribosomal, 16S 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

1678-1685

Subventions

Organisme : National Natural Science Foundation of China
ID : 31700003
Organisme : "Academic Backbone" Project of Northeast Agricultural University
ID : 19XG15
Organisme : Innovation Project of Hebei Academy of Agriculture and Forestry Sciences
ID : 2019-2-5 and 2019-1-4
Organisme : the Heilongjiang Postdoctoral Financial Assistance
ID : LBH-Z14042

Références

Dekaka A, Menasriac T, Benhiziab Y, Chenchouniad H (2020) Endophytic passenger bacteria associated with Genista cinerea nodules growing in North African drylands. Rhizosphere 14:100205. https://doi.org/10.1016/j.rhisph.2020.100205
doi: 10.1016/j.rhisph.2020.100205
Ash C, Priest FG, Collins MD (1993) Molecular identifification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie Van Leeuwenhoek 64:253–260. https://doi.org/10.1007/BF00873085
doi: 10.1007/BF00873085 pubmed: 8085788
Jin HJ, Lv J, Chen SF (2011) Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica. Int J Syst Evol Microbiol 61:767–771. https://doi.org/10.1099/ijs.0.021709-0
doi: 10.1099/ijs.0.021709-0 pubmed: 20435753
Xie JB, Du ZL, Bai LQ, Tian CF, Zhang YZ, Xie JY, Wang TS, Liu XM, Chen X, Cheng Q, Chen SF, Li JL (2014) Comparative genomic analysis of N2 -fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes. PLoS Genet 10:17
doi: 10.1371/journal.pgen.1004231
Lányí B (1987) Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67. https://doi.org/10.1016/S0580-9517(08)70407-0
doi: 10.1016/S0580-9517(08)70407-0
Logan NA, Berge O, Bishop AH, Busse HJ, De Vos P, Fritze D, Heyndrickx M, Kämpfer P, Rabinovitch L, Salkinoja-Salonen MS, Seldin L, Ventosa A (2009) Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 59:2114–2121. https://doi.org/10.1099/ijs.0.013649-0
doi: 10.1099/ijs.0.013649-0 pubmed: 19567583
Krieg NR, Padgett PJ (2011) Phenotypic and physiological characterization methods. Methods Microbiol 38:15–60. https://doi.org/10.1016/B978-0-12-387730-7.00003-6
doi: 10.1016/B978-0-12-387730-7.00003-6
Baker GC, Smith JJ, Cowan DA (2003) Review and reanalysis of domain-specifific 16S primers. J Microbiol Methods 55:541–555. https://doi.org/10.1016/j.mimet.2003.08.009
doi: 10.1016/j.mimet.2003.08.009 pubmed: 14607398
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
doi: 10.1093/molbev/msw054
Coil D, Jospin G, Darling AE (2015) A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31:587–589. https://doi.org/10.1093/bioinformatics/btu661
doi: 10.1093/bioinformatics/btu661 pubmed: 25338718
Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760
doi: 10.1099/ijsem.0.000760 pubmed: 26585518
Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4
doi: 10.1007/s10482-017-0844-4 pubmed: 28204908
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60
doi: 10.1186/1471-2105-14-60
Parrello B, Butler R, Chlenski P, Olson R, Overbeek J, Pusch GD, Vonstein V, Overbeek R (2019) A machine learning-based service for estimating quality of genomes using PATRIC. BMC Bioinform 20:486. https://doi.org/10.1186/s12859-019-3068-y
doi: 10.1186/s12859-019-3068-y
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P (2015) 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
doi: 10.1101/gr.186072.114 pubmed: 25977477 pmcid: 4484387
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033
doi: 10.1093/bioinformatics/btu033 pubmed: 3998144 pmcid: 3998144
Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R, Butler RM, Chlenski P, Conrad N, Dickerman A, Dietrich EM, Gabbard JL, Gerdes S, Guard A, Kenyon RW, Machi D, Mao CH, Murphy-Olson D, Nguyen M, Nordberg EK, Olsen GJ, Olson RD, Overbeek JC, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomas C, VanOeffelen M, Vonstein V, Warren AS, Xia FF, Xie DW, Yoo H, Stevens R (2020) The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res 48:D606–D612. https://doi.org/10.1093/nar/gkz943
doi: 10.1093/nar/gkz943 pubmed: 31667520
Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75
doi: 10.1186/1471-2164-9-75
Sasser M (1990) Identifification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Microbial ID Inc, Newark, DE, USA
Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207. https://doi.org/10.1016/S0580-9517(08)70410-0
doi: 10.1016/S0580-9517(08)70410-0
Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202. https://doi.org/10.1016/0378-1097(90)90282-U
doi: 10.1016/0378-1097(90)90282-U
Hasegawa T, Takizawa M, Tanida S (1983) A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Microbiol 29:319–322. https://doi.org/10.2323/jgam.29.319
doi: 10.2323/jgam.29.319
Tak EJ, Kim HS, Lee JY, Kang W, Hyun DW, Kim PS, Shin NR, Bae JW (2017) Vagococcus martis sp. nov., isolated from the small intestine of a marten, Martes flavigula. Int J Syst Evol Microbiol 67:3398–3402. https://doi.org/10.1099/ijsem.0.002131
doi: 10.1099/ijsem.0.002131 pubmed: 28857031
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 64:346–351. https://doi.org/10.1099/ijs.0.059774-0
doi: 10.1099/ijs.0.059774-0 pubmed: 24505072
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
doi: 10.1099/ijs.0.64483-0 pubmed: 17220447
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
doi: 10.1073/pnas.0906412106 pubmed: 19855009
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (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
doi: 10.1099/ijsem.0.002516 pubmed: 29292687
Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846–849. https://doi.org/10.1099/00207713-44-4-846
doi: 10.1099/00207713-44-4-846
Li Q, Liu XM, Zhang HW, Chen SF (2019) Evolution and functional analysis of orf1 within nif gene cluster from Paenibacillus graminis RSA19. Int J Mol Sci 20:1145. https://doi.org/10.3390/ijms20051145
doi: 10.3390/ijms20051145 pmcid: 6429469
Hanin M, Jabbouri S, Quesada-Vincens D, Freiberg C, Perret X, ProméJ C, Broughton WJ, Fellay R (1997) Sulphation of Rhizobium sp. NGR234 Nod factors is dependent on noeE, a new host-specificity gene. Mol Microbiol 24:1119–1129
doi: 10.1046/j.1365-2958.1997.3981777.x
Delgado M J, Casella S, Bedmar E J (2007) Denitrification in Rhizobia-Legume Symbiosis. In: Bothe H, Ferguson S J, Newton W E (ed) Biology of the Nitrogen Cycle. Elsevier Science, pp 83–91. https://doi.org/ https://doi.org/10.1016/B978-044452857-5.50007-2

Auteurs

Hao Wang (H)

College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China. wanghao80@neau.edu.cn.

Dong Hu (D)

Key Laboratory of Plants Genetic Engineering Center, Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, People's Republic of China.

Ziqi Wang (Z)

College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China.

Chunwei Yang (C)

College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China.

Siyuan Zhu (S)

College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China.

Chuntao Gu (C)

College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China.

En Tao Wang (ET)

Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Cd. México, México.

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Classifications MeSH