Draft Genome Sequence of Root-Colonizing Bacterium Bacillus sp. Strain PTS-394 Junqing Qiao,a Youzhou Liu,a Xuejie Liang,a Yonghong Hu,b Yan Dua
Here, we report the high-quality draft genome sequence of Bacillus sp. strain PTS-394, isolated from the rhizosphere of tomatoes grown on Putuo Mountain (Xiamen, Fujian province, China), which exhibited excellent colonization ability on plant roots. The 4.0-Mb genome uncovered the mechanism for its potential root colonization ability and may provide novel insights into plantbacterium interactions. Received 12 January 2014 Accepted 15 January 2014 Published 13 February 2014 Citation Qiao J, Liu Y, Liang X, Hu Y, Du Y. 2014. Draft genome sequence of root-colonizing bacterium Bacillus sp. strain PTS-394. Genome Announc. 2(1):e00038-14. doi: 10.1128/genomeA.00038-14. Copyright © 2014 Qiao et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Youzhou Liu, [email protected].
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lant growth-promoting rhizobacteria (PGPR) can colonize on the roots of plants and improve plant growth (1). Several Bacillus species as members of PGPR have been studied extensively, and they possess the ability to suppress microbial plant pathogens and enhance the yields of crop plants (2) by colonizing on plant roots (3), producing antimicrobial secondary metabolites (4) and plant growth-promoting compounds (5, 6). Bacillus sp. strain PTS-394 was isolated from the rhizosphere of tomatoes grown on Putuo Mountain in China and was identified as a strain of Bacillus subtilis by 16S rRNA and gyrB gene sequencing. The strain showed excellent colonization ability on tomato roots and serves as an important biocontrol agent against tomato soil-borne diseases (7). Here, we analyzed its genome sequence to explore its genomic features as a PGPR. Genome sequencing was performed with the Illumina/Solexa HiSeq 2000 at Shanghai Majorbio Bio-pharm Technology Co. Ltd. (Shanghai, China). In total, 1.3 Gb of clean data (12,606,050 paired-end reads with a 100-bp length, 500-bp library, and 314.9⫻ coverage) was obtained for assembly after filtering out the low-quality reads. The total paired reads were de novo assembled with SOAPdenovo (version 2.0) (8). All generated reads were assembled into 40 contigs (N50, 471, 675 bp) and rearranged in order into 29 scaffolds. All the contigs are ⬎500 bp and the largest contig is 400.3 kb. A total of 4,128 coding sequences were predicted by Glimmer and annotated using information from RAST, GenBank, Pfam, and KEGG. Of these, 2,982 protein-coding sequences were assigned to Clusters of Orthologous Groups (COG) families (9, 10). The draft genome of strain PTS-394 consists of 4,006,352 bases, with a 43.7% G⫹C content and 33 tRNAs. The genome includes several genes related to the biosynthesis of antimicrobial products that are similar to those in the genome of B. subtilis 168 (11). There are five gene clusters related to lipopeptide and polyketide synthase in the PTS-394 chromosome, such as surfactin, plipastatin, bacillibactin, bacilysin, and bacillaene. Additionally, extracellular phytase- and 2,3-butanediol synthesis-related
January/February 2014 Volume 2 Issue 1 e00038-14
genes are presented in PTS-394, which are responsible for plant growth promotion (6, 12). PTS-394 has putative biofilm formation-related genes that encode exopolysaccharides and ␥-polyglutamate synthetase, which is a major element in the root colonization of PGPR (13, 14). In conclusion, the genome analysis of strain PTS-394 further demonstrates that it possesses the potential to be used as a biocontrol agent and helps us to study PGPR-plant interactions in the root ecological niche. Nucleotide sequence accession number. The draft genome sequence of B. subtilis PTS-394 has been deposited at DDBJ/EMBL/ GenBank under the accession no. AWXG00000000. The version described in this paper is the first version. ACKNOWLEDGMENTS This work was supported by the National Natural Science Foundation of China (31201556), Jiangsu Academy of Agricultural Innovation funds [CX (13) 5028], and the Jiangsu Province Science and Technology Support Program (BE2013442).
REFERENCES 1. Lugtenberg B, Kamilova F. 2009. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63:541–556. http://dx.doi.org/10.1146/annurev .micro.62.081307.162918. 2. Borriss R. 2011. Use of plant-associated Bacillus strains as biofertilizers and biocontrol agents, p 41–76. In Maheshwari DK (ed), Bacteria in agrobiology: plant growth responses. Springer Verlag-Heidelberg, Heidelberg, Germany. 3. Fan B, Chen XH, Budiharjo A, Bleiss W, Vater J, Borriss R. 2011. Efficient colonization of plant roots by the plant growth promoting bacterium Bacillus amyloliquefaciens FZB42, engineered to express green fluorescent protein. J. Biotechnol. 151:303–311. http://dx.doi.org/10.1016/j .jbiotec.2010.12.022. 4. Ongena M, Jacques P. 2008. Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends Microbiol. 16:115–125. http://dx.doi.org /10.1016/j.tim.2007.12.009. 5. Chen XH, Koumoutsi A, Scholz R, Borriss R. 2009. More than anticipated—production of antibiotics and other secondary metabolites by Bacillus amyloliquefaciens FZB42. J. Mol. Microbiol. Biotechnol. 16:14 –24. http://dx.doi.org/10.1159/000142891. 6. Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, Paré PW, Kloepper
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Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Chinaa; Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, Chinab
Qiao et al.
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Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186 /1471-2164-9-75. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessières P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Danchin A, et al. 1997. The complete genome sequence of the Grampositive bacterium Bacillus subtilis. Nature 390:249 –256. http://dx.doi.org /10.1038/36786. Idriss EE, Makarewicz O, Farouk A, Rosner K, Greiner R, Bochow H, Richter T, Borriss R. 2002. Extracellular phytase activity of Bacillus amyloliquefaciens FZB45 contributes to its plant-growth-promoting effect. Microbiology 148:2097–2109. http://mic.sgmjournals.org/content/148/7 /2097.long. Beauregard PB, Chai Y, Vlamakis H, Losick R, Kolter R. 2013. Bacillus subtilis biofilm induction by plant polysaccharides. Proc. Natl. Acad. Sci. U. S. A. 110:1621–1630. http://dx.doi.org/10.1073/pnas.1218984110. Candela T, Fouet A. 2006. Poly-gamma-glutamate in bacteria. Mol. Microbiol. 60:1091–1098. http://dx.doi.org/10.1111/j.1365-2958.2006.0517 9.x.
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JW. 2003. Bacterial volatiles promote growth in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 100:4927– 4932. http://dx.doi.org/10.1073/pnas.07308 45100. You-zhou L, Zhi-yi C, Xue-jie L, Jian-hua Z. 2012. Screening, evaluation and identification of antagonistic bacteria against Fusarium oxysporum f. sp. lycopersici and Ralstonia solanacearum. Chin. J. Biol. Control 28: 101–108. (Article in Chinese.) Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaogian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 1:18. http: //dx.doi.org/10.1186/2047-217X-1-18. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33–36. http://dx.doi.org/10.1093/nar/28.1.33. 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
Here, we report the high-quality draft genome sequence of Bacillus sp. strain PTS-394, isolated from the rhizosphere of tomatoes grown on Putuo Mountain (Xiamen, Fujian province, China), which exhibited excellent colonization ability on plant roots. The 4.0-Mb genome uncovered the mechanism for its potential root colonization ability and may provide novel insights into plantbacterium interactions. Received 12 January 2014 Accepted 15 January 2014 Published 13 February 2014 Citation Qiao J, Liu Y, Liang X, Hu Y, Du Y. 2014. Draft genome sequence of root-colonizing bacterium Bacillus sp. strain PTS-394. Genome Announc. 2(1):e00038-14. doi: 10.1128/genomeA.00038-14. Copyright © 2014 Qiao et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Youzhou Liu, [email protected].
P
lant growth-promoting rhizobacteria (PGPR) can colonize on the roots of plants and improve plant growth (1). Several Bacillus species as members of PGPR have been studied extensively, and they possess the ability to suppress microbial plant pathogens and enhance the yields of crop plants (2) by colonizing on plant roots (3), producing antimicrobial secondary metabolites (4) and plant growth-promoting compounds (5, 6). Bacillus sp. strain PTS-394 was isolated from the rhizosphere of tomatoes grown on Putuo Mountain in China and was identified as a strain of Bacillus subtilis by 16S rRNA and gyrB gene sequencing. The strain showed excellent colonization ability on tomato roots and serves as an important biocontrol agent against tomato soil-borne diseases (7). Here, we analyzed its genome sequence to explore its genomic features as a PGPR. Genome sequencing was performed with the Illumina/Solexa HiSeq 2000 at Shanghai Majorbio Bio-pharm Technology Co. Ltd. (Shanghai, China). In total, 1.3 Gb of clean data (12,606,050 paired-end reads with a 100-bp length, 500-bp library, and 314.9⫻ coverage) was obtained for assembly after filtering out the low-quality reads. The total paired reads were de novo assembled with SOAPdenovo (version 2.0) (8). All generated reads were assembled into 40 contigs (N50, 471, 675 bp) and rearranged in order into 29 scaffolds. All the contigs are ⬎500 bp and the largest contig is 400.3 kb. A total of 4,128 coding sequences were predicted by Glimmer and annotated using information from RAST, GenBank, Pfam, and KEGG. Of these, 2,982 protein-coding sequences were assigned to Clusters of Orthologous Groups (COG) families (9, 10). The draft genome of strain PTS-394 consists of 4,006,352 bases, with a 43.7% G⫹C content and 33 tRNAs. The genome includes several genes related to the biosynthesis of antimicrobial products that are similar to those in the genome of B. subtilis 168 (11). There are five gene clusters related to lipopeptide and polyketide synthase in the PTS-394 chromosome, such as surfactin, plipastatin, bacillibactin, bacilysin, and bacillaene. Additionally, extracellular phytase- and 2,3-butanediol synthesis-related
January/February 2014 Volume 2 Issue 1 e00038-14
genes are presented in PTS-394, which are responsible for plant growth promotion (6, 12). PTS-394 has putative biofilm formation-related genes that encode exopolysaccharides and ␥-polyglutamate synthetase, which is a major element in the root colonization of PGPR (13, 14). In conclusion, the genome analysis of strain PTS-394 further demonstrates that it possesses the potential to be used as a biocontrol agent and helps us to study PGPR-plant interactions in the root ecological niche. Nucleotide sequence accession number. The draft genome sequence of B. subtilis PTS-394 has been deposited at DDBJ/EMBL/ GenBank under the accession no. AWXG00000000. The version described in this paper is the first version. ACKNOWLEDGMENTS This work was supported by the National Natural Science Foundation of China (31201556), Jiangsu Academy of Agricultural Innovation funds [CX (13) 5028], and the Jiangsu Province Science and Technology Support Program (BE2013442).
REFERENCES 1. Lugtenberg B, Kamilova F. 2009. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63:541–556. http://dx.doi.org/10.1146/annurev .micro.62.081307.162918. 2. Borriss R. 2011. Use of plant-associated Bacillus strains as biofertilizers and biocontrol agents, p 41–76. In Maheshwari DK (ed), Bacteria in agrobiology: plant growth responses. Springer Verlag-Heidelberg, Heidelberg, Germany. 3. Fan B, Chen XH, Budiharjo A, Bleiss W, Vater J, Borriss R. 2011. Efficient colonization of plant roots by the plant growth promoting bacterium Bacillus amyloliquefaciens FZB42, engineered to express green fluorescent protein. J. Biotechnol. 151:303–311. http://dx.doi.org/10.1016/j .jbiotec.2010.12.022. 4. Ongena M, Jacques P. 2008. Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends Microbiol. 16:115–125. http://dx.doi.org /10.1016/j.tim.2007.12.009. 5. Chen XH, Koumoutsi A, Scholz R, Borriss R. 2009. More than anticipated—production of antibiotics and other secondary metabolites by Bacillus amyloliquefaciens FZB42. J. Mol. Microbiol. Biotechnol. 16:14 –24. http://dx.doi.org/10.1159/000142891. 6. Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, Paré PW, Kloepper
Genome Announcements
genomea.asm.org 1
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Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Chinaa; Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, Chinab
Qiao et al.
7.
8.
10.
2 genomea.asm.org
11.
12.
13.
14.
Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186 /1471-2164-9-75. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessières P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Danchin A, et al. 1997. The complete genome sequence of the Grampositive bacterium Bacillus subtilis. Nature 390:249 –256. http://dx.doi.org /10.1038/36786. Idriss EE, Makarewicz O, Farouk A, Rosner K, Greiner R, Bochow H, Richter T, Borriss R. 2002. Extracellular phytase activity of Bacillus amyloliquefaciens FZB45 contributes to its plant-growth-promoting effect. Microbiology 148:2097–2109. http://mic.sgmjournals.org/content/148/7 /2097.long. Beauregard PB, Chai Y, Vlamakis H, Losick R, Kolter R. 2013. Bacillus subtilis biofilm induction by plant polysaccharides. Proc. Natl. Acad. Sci. U. S. A. 110:1621–1630. http://dx.doi.org/10.1073/pnas.1218984110. Candela T, Fouet A. 2006. Poly-gamma-glutamate in bacteria. Mol. Microbiol. 60:1091–1098. http://dx.doi.org/10.1111/j.1365-2958.2006.0517 9.x.
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9.
JW. 2003. Bacterial volatiles promote growth in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 100:4927– 4932. http://dx.doi.org/10.1073/pnas.07308 45100. You-zhou L, Zhi-yi C, Xue-jie L, Jian-hua Z. 2012. Screening, evaluation and identification of antagonistic bacteria against Fusarium oxysporum f. sp. lycopersici and Ralstonia solanacearum. Chin. J. Biol. Control 28: 101–108. (Article in Chinese.) Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaogian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 1:18. http: //dx.doi.org/10.1186/2047-217X-1-18. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33–36. http://dx.doi.org/10.1093/nar/28.1.33. 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
