Polyphase taxonomy and genome analysis reveal the adaptability of Luteolibacter rhizosphaerae sp. nov. to the rhizosphere soil of Ulmus pumila L.


Journal

Antonie van Leeuwenhoek
ISSN: 1572-9699
Titre abrégé: Antonie Van Leeuwenhoek
Pays: Netherlands
ID NLM: 0372625

Informations de publication

Date de publication:
Aug 2023
Historique:
received: 16 11 2022
accepted: 15 05 2023
medline: 17 7 2023
pubmed: 24 5 2023
entrez: 24 5 2023
Statut: ppublish

Résumé

A Gram-stain-negative, rod-shaped, non-flagellated, pale-yellow bacterium, designated GHJ8

Identifiants

pubmed: 37222844
doi: 10.1007/s10482-023-01845-w
pii: 10.1007/s10482-023-01845-w
doi:

Substances chimiques

Soil 0
RNA, Ribosomal, 16S 0
Phospholipids 0
Fatty Acids 0
DNA 9007-49-2
DNA, Bacterial 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

763-772

Subventions

Organisme : National Natural Science Foundation of China
ID : 32171869
Organisme : Fundamental Research Funds for the Central Universities at Beijing Forestry University
ID : 2021ZY61
Organisme : University-Industry Collaborative Education Program
ID : 202102083002

Informations de copyright

© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.

Références

Alanjary M, Steinke K, Ziemert N (2019) AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 47:W276-282. https://doi.org/10.1093/nar/gkz28
doi: 10.1093/nar/gkz28 pubmed: 30997504 pmcid: 6602446
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75
doi: 10.1186/1471-2164-9-75 pubmed: 18261238 pmcid: 2265698
Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G, Winsor GL, Brinkman FSL, Simon Fraser University Research Computing Group (2017) IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 45:W30-35. https://doi.org/10.1093/nar/gkx343
doi: 10.1093/nar/gkx343 pubmed: 28472413 pmcid: 5570257
Busse HJ, Kämpfer P, Szostak MP, Spergser J (2021) Luteolibacter ambystomatis sp. nov., isolated from the skin of an Anderson’s salamander (Ambystoma andersoni). Int J Syst Evol Microbiol 71:005043. https://doi.org/10.1099/ijsem.0.005043
doi: 10.1099/ijsem.0.005043
Collins MD, Goodfellow M, Minnikin DE (1980) Fatty acid, isoprenoid quinone and polar lipid composition in the classification of Curtobacterium and related taxa. J Gen Microbiol 118:29–37. https://doi.org/10.1099/00221287-118-1-29
doi: 10.1099/00221287-118-1-29 pubmed: 6775048
Dahal RH, Chaudhary DK, Kim DU, Kim J (2021) Luteolibacter luteus sp. nov., isolated from stream bank soil. Arch Microbiol 203:377–382. https://doi.org/10.1007/s00203-020-02048-x
doi: 10.1007/s00203-020-02048-x pubmed: 32964255
Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. https://doi.org/10.1186/1471-2105-5-113
doi: 10.1186/1471-2105-5-113 pubmed: 15318951 pmcid: 517706
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/bf01734359
doi: 10.1007/bf01734359 pubmed: 7288891
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
doi: 10.1111/j.1558-5646.1985.tb00420.x pubmed: 28561359
Fraser SL, Jorgensen JH (1997) Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 41:2738–2741. https://doi.org/10.1128/aac.41.12.2738
doi: 10.1128/aac.41.12.2738 pubmed: 9420049 pmcid: 164199
Galperin MY, Makarova KS, Wolf YI, Koonin EV (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 43:D261-269. https://doi.org/10.1093/nar/gku1223
doi: 10.1093/nar/gku1223 pubmed: 25428365
Glaeser SP, Galatis H, Martin K, Kämpfer P (2012) Luteolibacter cuticulihirudinis sp. nov., isolated from Hirudo medicinalis. Antonie Van Leeuwenhoek 102:319–324. https://doi.org/10.1007/s10482-012-9741-z
doi: 10.1007/s10482-012-9741-z pubmed: 22552629
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
Jarvis BDW, Sivakumaran S, Tighe SW, Gillis M (1996) Identification of Agrobacterium and Rhizobium species based on cellular fatty acid composition. Plant Soil 184:143–158. https://doi.org/10.1007/BF00029284
doi: 10.1007/BF00029284
Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FS, Wright GD, McArthur AG (2017) CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 45:D566-573. https://doi.org/10.1093/nar/gkw1004
doi: 10.1093/nar/gkw1004 pubmed: 27789705
Jiang F, Li W, Xiao M, Dai J, Kan W, Chen L, Li W, Fang C, Peng F (2012) Luteolibacter luojiensis sp. nov., isolated from Arctic tundra soil, and emended description of the genus Luteolibacter. Int J Syst Evol Microbiol 62:2259–2263. https://doi.org/10.1099/ijs.0.037309-0
doi: 10.1099/ijs.0.037309-0 pubmed: 22081723
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:D457-462. https://doi.org/10.1093/nar/gkv1070
doi: 10.1093/nar/gkv1070 pubmed: 26476454
Kellogg JA, Bankert DA, Withers GS, Sweimler W, Kiehn TE, Pfyffer GE (2001) Application of the Sherlock Mycobacteria Identification System using high-performance liquid chromatography in a clinical laboratory. J Clin Microbiol 39:964–970. https://doi.org/10.1128/jcm.39.3.964-970.2001
doi: 10.1128/jcm.39.3.964-970.2001 pubmed: 11230412 pmcid: 87858
Kim M, Pak S, Rim S, Ren L, Jiang F, Chang X, Liu P, Zhang Y, Fang C, Zheng C, Peng F (2015) Luteolibacter arcticus sp. nov., isolated from high Arctic tundra soil, and emended description of the genus Luteolibacter. Int J Syst Evol Microbiol 65:1922–1928. https://doi.org/10.1099/ijs.0.000202
doi: 10.1099/ijs.0.000202 pubmed: 25795066
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
doi: 10.1007/bf01731581 pubmed: 7463489
Lee I, Chalita M, Ha SM, Na SI, Yoon SH, Chun J (2017) ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 67:2053–2057. https://doi.org/10.1099/ijsem.0.001872
doi: 10.1099/ijsem.0.001872 pubmed: 28639931
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
Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339-346. https://doi.org/10.1093/nar/gkr466
doi: 10.1093/nar/gkr466 pubmed: 21672958 pmcid: 3125804
Meier-Kolthoff JP, Auch AF, Klenk H-P, 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
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 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6
doi: 10.1016/0167-7012(84)90018-6
Park J, Baek GS, Woo SG, Lee J, Yang J, Lee J (2013) Luteolibacter yonseiensis sp. nov., isolated from activated sludge using algal metabolites. Int J Syst Evol Microbiol 63:1891–1895. https://doi.org/10.1099/ijs.0.046664-0
doi: 10.1099/ijs.0.046664-0 pubmed: 23002048
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996–1004. https://doi.org/10.1038/nbt.4229
doi: 10.1038/nbt.4229 pubmed: 30148503
Pascual J, García-López M, González I, Genilloud O (2017) Luteolibacter gellanilyticus sp. nov., a gellan-gum-degrading bacterium of the phylum Verrucomicrobia isolated from miniaturized diffusion chambers. Int J Syst Evol Microbiol 67:3951–3959. https://doi.org/10.1099/ijsem.0.002227
doi: 10.1099/ijsem.0.002227 pubmed: 28905697
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 pmcid: 2776425
Rzhetsky A, Nei M (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10:1073–1095. https://doi.org/10.1093/oxfordjournals.molbev.a040056
doi: 10.1093/oxfordjournals.molbev.a040056 pubmed: 8412650
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/10.1093/oxfordjournals.molbev.a040454
doi: 10.1093/oxfordjournals.molbev.a040454 pubmed: 3447015
Shen L, An MM, Liang RN, Liu PX, He XW, Zhao GZ (2022a) Roseococcus pinisoli sp. nov., lacking pufL and pufM bacteriochlorophyll a: synthesizing genes. Arch Microbiol 204:293. https://doi.org/10.1007/s00203-022-02920-y
doi: 10.1007/s00203-022-02920-y pubmed: 35507236
Shen L, Liu JJ, Liu PX, An MM, He XW, Zhao GZ (2021) A non-symbiotic novel species, Rhizobium populisoli sp. nov., isolated from rhizosphere soil of Populus popularis. Arch Microbiol 204:50. https://doi.org/10.1007/s00203-021-02706-8
doi: 10.1007/s00203-021-02706-8 pubmed: 34935074
Shen L, Liu P, An M, Liang R, He X, Zhao G (2022b) Sphingomonas quercus sp. nov., Isolated from Rhizosphere Soil of Quercus mongolica. Curr Microbiol 79:122. https://doi.org/10.1007/s00284-022-02819-3
doi: 10.1007/s00284-022-02819-3 pubmed: 35239058
Skinnider MA, Johnston CW, Gunabalasingam M, Merwin NJ, Kieliszek AM, MacLellan RJ, Li H, Ranieri MRM, Webster ALH, Cao MPT, Pfeifle A, Spencer N, To QH, Wallace DP, Dejong CA, Magarvey NA (2020) Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences. Nat Commun 11:6058. https://doi.org/10.1038/s41467-020-19986-1
doi: 10.1038/s41467-020-19986-1 pubmed: 33247171 pmcid: 7699628
Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 607–654
Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120
doi: 10.1093/molbev/msab120 pubmed: 33892491 pmcid: 8233496
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569
doi: 10.1093/nar/gkw569 pubmed: 27342282 pmcid: 5001611
Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202. https://doi.org/10.1111/j.1574-6968.1990.tb03996.x
doi: 10.1111/j.1574-6968.1990.tb03996.x
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
doi: 10.1128/jb.173.2.697-703.1991 pubmed: 1987160 pmcid: 207061
Xie F, Zhu S, Guo C, Liu X, He S, Zhang W (2022) Luteolibacter marinus sp, nov,, a novel bacterium in the family Verrucomicrobiaceae, isolated from marine sediment. Int J Syst Evol Microbiol 72:005544. https://doi.org/10.1099/ijsem.0.005544
doi: 10.1099/ijsem.0.005544
Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153. https://doi.org/10.1099/ijs.0.63407-0
doi: 10.1099/ijs.0.63407-0 pubmed: 15879247
Yoon J, Matsuo Y, Adachi K, Nozawa M, Matsuda S, Kasai H, Yokota A (2008) Description of Persicirhabdus sediminis gen. nov., sp. nov., Roseibacillus ishigakijimensis gen. nov., sp. nov., Roseibacillus ponti sp. nov., Roseibacillus persicicus sp. nov., Luteolibacter pohnpeiensis gen. nov., sp. nov. and Luteolibacter algae sp. nov., six marine members of the phylum ‘Verrucomicrobia’, and emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae. Int J Syst Evol Microbiol 58:998–1007. https://doi.org/10.1099/ijs.0.65520-0
doi: 10.1099/ijs.0.65520-0 pubmed: 18398209
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
doi: 10.1099/ijsem.0.001755 pubmed: 28005526 pmcid: 5563544
Zhang C, Dong B, Wang R, Su Y, Han S, Yu X, Zhao Z, Fu G, Sun C, Wu M (2017) Luteolibacter flavescens sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 67:729–735. https://doi.org/10.1099/ijsem.0.001713
doi: 10.1099/ijsem.0.001713 pubmed: 27911253
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk PK, Xu Y, Yin Y (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46:W95–W101. https://doi.org/10.1093/nar/gky418
doi: 10.1093/nar/gky418 pubmed: 29771380 pmcid: 6031026

Auteurs

Lei Shen (L)

College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China.
College of Life Sciences, Langfang Normal University, Langfang, 065000, China.

Miaomiao An (M)

College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China.

Ruina Liang (R)

College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China.

Ying Li (Y)

College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China.

Xiangwei He (X)

College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China.

Guozhu Zhao (G)

College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China. zhaogz@bjfu.edu.cn.

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Classifications MeSH