Abstract
The Bacillus velezensis YYC strain was isolated from the tomato rhizosphere. In a previous experiment, it increased tomato growth and induced systemic resistance against Ralstonia solanacearum. However, information on its genomic content is lacking. The complete genome sequence of the bacterium was described in this study. The genome size was 3,973,236 bp and consisted of 4034 genes in total, with a mean G + C content of 46.52%. In addition, 86 tRNAs and 27 ribosomal RNAs were identified. Fourteen clusters of secondary metabolites were identified. The KEGG database analysis showed that 69 genes were related to quorum sensing, which were important for microbe-plant interaction. In addition, genes involved in promoting plant growth and triggering plant immunity were identified from the genome. Based on digital DNA–DNA hybridizations (dDDH), B. velezensis YYC was most closely related with B. velezensis FZB42. The complete genome data of B. velezensis YYC will provide a basis for explanation of its growth-promoting mechanism and biocontrol mechanism.
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References
Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29. https://doi.org/10.1038/75556
Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33:W451–W454. https://doi.org/10.1093/nar/gki487
Bezzate S, Aymerich S, Chambert R et al (2000) Disruption of the Paenibacillus polymyxa levansucrase gene impairs its ability to aggregate soil in the wheat rhizosphere. Environ Microbiol 2:333–342. https://doi.org/10.1046/j.1462-2920.2000.00114.x
Bird C, Wyman M (2003) Nitrate/nitrite assimilation system of the marine picoplanktonic cyanobacterium Synechococcus sp. strain WH 8103: effect of nitrogen source and availability on gene expression. Appl Environ Microbiol 69:7009–7018. https://doi.org/10.1128/AEM.69.12.7009-7018.2003
Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, Medema MH, Weber T (2021) antiSMASH 6.0:improving cluster detection and comparison capabilities. Nucleic Acids Res 49:W29–W35. https://doi.org/10.1093/nar/gkab335
Borriss R (2011) Use of plant-Associated Bacillus strains as biofertilizers and biocontrol agents in agriculture. In: Maheshwari DK (ed) Bacteria in agrobiology: plant growth responses. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 41–76
Branda SS, Gonzalez-Pastor JE, Ben-Yehuda S, Losick R, Kolter R (2001) Fruiting body formation by Bacillus subtilis. PNAS 98:11621–11626. https://doi.org/10.1073/pnas.191384198
Canellas LP, Balmori DM, Medici LO et al (2013) A combination of humic substances and Herbaspirillum seropedicae inoculation enhances the growth of maize (Zea mays L.). Plant Soil 366:119–132. https://doi.org/10.1007/s11104-012-1382-5
Chan PP, Lowe TM (2019) tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods Mol Biol 1962:1–14. https://doi.org/10.1007/978-1-4939-9173-0_1
Chen M, Wang J, Liu B et al (2020) Biocontrol of tomato bacterial wilt by the new strain Bacillus velezensis FJAT-46737 and its lipopeptides. BMC Microbiol 20:160. https://doi.org/10.1186/s12866-020-01851-2
Chowdhury SP, Hartmann A, Gao X, Borriss R (2015) Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42-a review. Front Microbiol 6:780. https://doi.org/10.3389/fmicb.2015.00780
Farzand A, Moosa A, Zubair M, Khan AR, Massawe VC, Tahir HAS, Sheikh TMM, Ayaz M, Gao X (2019) Suppression of sclerotinia sclerotiorum by the induction of systemic resistance and regulation of antioxidant pathways in tomato using fengycin produced by Bacillus amyloliquefaciens FZB42. Biomolecules 9:613. https://doi.org/10.3390/biom9100613
Feng H, Fu R, Hou X et al (2021) Chemotaxis of beneficial rhizobacteria to root exudates: the first step towards root-microbe rhizosphere interactions. Int J Mol Sci 22:6655. https://doi.org/10.3390/ijms22136655
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–D269. https://doi.org/10.1093/nar/gku1223
Guo S, Li X, He P, Ho H, Wu Y, He Y (2015) Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants. J Microbiol Biotechn 42:925–937. https://doi.org/10.1007/s10295-015-1612-y
He PF, Hao K, Blom J et al (2013) Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601–Y2 and expression of mersacidin and other secondary metabolites. J Biotechnol 164:281–291. https://doi.org/10.1016/j.jbiotec.2012.12.014
Jayakumar A, Nair IC, Krishnankutty RE (2021) Environmental adaptations of an extremely plant beneficial Bacillus subtilis Dcl1 identified through the genomic and metabolomic analysis. Microb Ecol 81:687–702. https://doi.org/10.1007/s00248-020-01605-7
Jiang C, Liao M, Wang H, Zheng M, Xu J, Guo J (2018) Bacillus velezensis, a potential and efficient biocontrol agent in control of pepper gray mold caused by Botrytis cinerea. Biol Control 126:147–157. https://doi.org/10.1016/j.biocontrol.2018.07.017
Kan J, Fang R, Jia Y (2017) Interkingdom signaling in plant-microbe interactions. Sci China Life Sci 60:785–796. https://doi.org/10.1007/s11427-017-9092-3
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–D462. https://doi.org/10.1093/nar/gkv1070
Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom 3:e000132. https://doi.org/10.1101/160614
Wu L, Wu H, Qiao J, Gao X, Borriss R (2015) Novel routes for improving biocontrol activity of Bacillus based bioinoculants. Front Microbiol 6:1395. https://doi.org/10.3389/fmicb.2015.01395
Ye M, Tang X, Yang R, Zhang H, Li F, Tao F, Li F, Wang Z (2018) Characteristic and application of a novel species of Bacillus: Bacillus velezensis. Acs Chem Biol 13:500–505. https://doi.org/10.1021/acschembio.7b00874
Zeng T, Rodriguez-Moreno L, Mansurkhodzaev A et al (2020) A lysin motif effector subverts chitin-triggered immunity to facilitate arbuscular mycorrhizal symbiosis. New Phytol 225:448–460. https://doi.org/10.1111/nph.16245
Acknowledgements
This work was supported by the National Natural Science Foundation of China (No. 31870493), the Key Reaserch & Development Project of Heilongjiang Province of China (No. GA21B007) and the Basic Research Fees of Universities in Heilongjiang Province of China (No. 135409103).
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Yan, Y., Xu, W., Chen, W. et al. Complete genome sequence of Bacillus velezensis YYC, a bacterium isolated from the tomato rhizosphere. Arch Microbiol 204, 44 (2022). https://doi.org/10.1007/s00203-021-02709-5
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DOI: https://doi.org/10.1007/s00203-021-02709-5