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Announcement
10 March 2016

Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium

ABSTRACT

The complete genome of Bacillus methylotrophicus strain B25, isolated in Switzerland, was sequenced. Its size is 3.85 Mb, and several genes that may contribute to plant growth-promoting activities were identified in silico.

GENOME ANNOUNCEMENT

Bacillus methylotrophicus strain B25 (formerly Bacillus amyloliquefaciens subsp. plantarum) (1) is a Gram-positive bacterium isolated in Switzerland from the inner wood tissues of a decaying Platanus x acerifolia tree. Bacterial strains belonging to this clade are plant-associated microorganisms known to have beneficial effects on their hosts, such as growth promotion and health enhancement (24). The complete genome sequence of B. methylotrophicus strain B25 is reported here and will provide genomic information on the specific properties of this strain.
DNA was extracted with the GenElute bacterial genomic DNA kit (Sigma-Aldrich), according to the manufacturer's instructions. Two libraries were constructed for sequencing at Genoscope. First, genomic DNA was fragmented, and inserts between 300 and 600 nucleotides (nt) were selected to construct a paired-end indexed library. Second, genomic DNA was fragmented, and inserts of around 8 kb were selected to construct a mate-paired indexed library. These libraries were loaded on an Illumina MiSeq sequencing device flowcell and sequenced on paired-ends, at 300 nt in length.
The reads from the paired-end library were merged with a homemade program and were assembled with mate-paired data using Newbler (overlap layout consensus [OLC]) (Roche). To reduce the number of undetermined bases, GapCloser was used (http://soap.genomics.org.cn/soapdenovo.html).
The remaining gaps were then covered using PCRs and specific primers for gap edges. The PCR fragments were sequenced by primer walking. The whole-assembly data were integrated into the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) for automatic annotation (5).
The complete genome of B. methylotrophicus strain B25 contains a 3,854,619-bp circular chromosome and an 8,138-bp plasmid. The genome contains 3,679 coding sequences (CDSs), with an average length of 934 bp, 21 rRNAs, and 68 tRNAs, and has a G+C content of 46.7%. The annotation predicted gene clusters coding for nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS). Among all predicted protein-coding genes, the strain B25 genome includes interesting genes involved in bacterium-plant interactions and plant growth promotion activities, i.e., the bacillibactin siderophore, an operon required for biofilm formation (epsA-0), and a phytate-degrading enzyme (phytase) (6). Gene resistance analysis was conducted with the CARD system (http://arpcard.mcmaster.ca/) (7). The B25 genome contains only natural resistance genes conserved at the species level. Gene content comparisons and synteny conservations indicate that the closest neighbors of B25 are B. methylotrophicus strains FZB42 (6), IT-45 (6), LFB112 (8), and Y2 (9). Further studies and genome comparisons of B. methylotrophicus strain B25 will enable the elucidation of the mechanisms supporting its plant-benefiting properties.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers LN999829 and LN999830.

ACKNOWLEDGMENTS

The LABGeM (CEA/IG/Genoscope & CNRS UMR8030) and the France Génomique National infrastructure (funded as part of Investissement d'Avenir Program managed by Agence Nationale pour la Recherche, contract ANR-10-INBS-09) are acknowledged for support within the MicroScope annotation platform.

REFERENCES

1.
Dunlap CA, Kim SJ, Kwon SW, Rooney AP. 2015. Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus. Int J Syst Evol Microbiol 65:2104–2109.
2.
Borriss R, Chen XH, Rueckert C, Blom J, Becker A, Baumgarth B, Fan B, Pukall R, Schumann P, Spröer C, Junge H, Vater J, Pühler A, Klenk HP. 2011. Relationship of Bacillus amyloliquefaciens clades associated with strains DSM7 and FZB42: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. Int J Syst Evol Microbiol 61:1786–1801.
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Madhaiyan M, Poonguzhali S, Kwon SW, Sa TM. 2010. Bacillus methylotrophicus sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil. Int J Syst Evol Microbiol 60:2490–2495.
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Niazi A, Manzoor S, Asari S, Bejai S, Meijer J, Bongcam-Rudloff E. 2014. Genome analysis of Bacillus amyloliquefaciens subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management. PLoS One 9:e104651.
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Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fèvre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Médigue C. 2013. MicroScope: an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 41:D636–D647.
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Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J, Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R. 2007. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25:1007–1014.
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McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O'Brien JS, Pawlowski AC, Piddock LJ, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD. 2013. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57:3348–3357.
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Cai J, Liu F, Liao X, Zhang R. 2014. Complete genome sequence of Bacillus amyloliquefaciens LFB112 isolated from Chinese herbs, a strain of a broad inhibitory spectrum against domestic animal pathogens. J Biotechnol 175:63–64.
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Hao K, He P, Blom J, Rueckert C, Mao Z, Wu Y, He Y, Borriss R. 2012. The genome of plant growth-promoting Bacillus amyloliquefaciens subsp. plantarum strain YAU B9601-Y2 contains a gene cluster for mersacidin synthesis. J Bacteriol 194:3264–3265.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 4Number 228 April 2016
eLocator: 10.1128/genomea.00058-16

History

Received: 20 January 2016
Accepted: 28 January 2016
Published online: 10 March 2016

Contributors

Authors

Jonathan Gerbore
BIOVITIS, Saint-Etienne-de-Chomeil, France
Aline Brutel
BIOVITIS, Saint-Etienne-de-Chomeil, France
Arnaud Lemainque
Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, Évry, France
Barbara Mairey
Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, Évry, France
Claudine Médigue
Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, Évry, France
CNRS-UMR8030, Évry, France
Université d'Evry Val d'Essonne, Évry, France
David Vallenet
Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, Évry, France
CNRS-UMR8030, Évry, France
Université d'Evry Val d'Essonne, Évry, France
Francois Lefort
Plants and Pathogens Group, Research Institute Land Nature and Environment, hepia, HES-SO University of Applied Sciences and Arts Western Switzerland, Geneva, Switzerland
Damien Grizard
BIOVITIS, Saint-Etienne-de-Chomeil, France

Notes

Address correspondence to Jonathan Gerbore, [email protected]

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