- Email: [email protected]
Complete genome sequence of Bacillus amyloliquefaciens L-S60, a plant growth-promoting and antifungal bacterium
Journal of Biotechnology 212 (2015) 67–68
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome announcement
Complete genome sequence of Bacillus amyloliquefaciens L-S60, a plant growth-promoting and antifungal bacterium Yuxuan Qin a , Yuzhu Han a , Yaqiong Yu b , Qingmao Shang b , Bao Zhang a , Pinglan Li a,∗ a
College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China b
a r t i c l e
i n f o
Article history: Received 7 August 2015 Received in revised form 12 August 2015 Accepted 13 August 2015 Available online 20 August 2015 Keywords: Bacillus amyloliquefaciens L-S60 Genome sequence Plant growth promotion Antifungal Biofilm
a b s t r a c t Bacillus amyloliquefaciens L-S60, a gram-positive plant-associated bacterium, which could stimulate plant growth and shows strong antifungal function, was isolated from the turfy soil in Beijing, China. The genome of B. amyloliquefaciens L-S60 comprises a 3903,017 bp long circular chromosome that consists of 3909 protein-coding genes and 117 RNA genes. Based on genomic analysis, we identified gene clusters responsible for the biosynthesis of numerous bioactive metabolites with well-established in-vitro activity such as surfactin, iturin and fengycins. Additionally, we also found functionally related genes in the genome of L-S60, which play key roles in the process of plant growth promotion hormone secretion, biofilm formation and volatile compounds production. © 2015 Elsevier B.V. All rights reserved.
Bacteria that are associated with plant roots and exert beneficial effects on plant development are referred to as plant growth-promoting rhizobacteria (PGPR) (Chen et al., 2007). Bacillus amyloliquefaciens species (Priest et al., 1987), which belong to Bacillus spp., are known to produce important enzymes and bioactive compounds, and thus have been used as biological control agents and biofertilizer for agriculture (Compant et al., 2005; Lugtenberg and Kamilova, 2009; Ye et al., 2012). Strain L-S60, a PGPR strain, has been classified as B. amyloliquefaciens subsp. plantarum based on the phylogenetic analysis of 16S rRNA gene and DNA gyrase subunit B gene sequences. B. amyloliquefaciens L-S60 was isolated from the turfy soil in Beijing, China. This strain showed strong inhibition capacity against several vegetable fungal pathogens, including Rhizoctonia solani, Fusarium oxysporum and Phytophthora capsici, and it also showed capability for phosphorus and potassium dissolving (data not shown). According to comparative experiments, which were performed in the tomato seedling stage, this strain dramatically increased plant height, stem diameter, leaf area and total dry weight as compared to the control group, and therefore makes itself a good candidate of biological control and biofertilizer agent (data not shown). In this study, the genome sequence and its annotation
∗ Corresponding author. Fax: +86 10 62737604. E-mail address: [email protected] (P. Li). http://dx.doi.org/10.1016/j.jbiotec.2015.08.008 0168-1656/© 2015 Elsevier B.V. All rights reserved.
of B. amyloliquefaciens L-S60 are presented together with the biological features to shed light on the molecular mechanism of the plant growth promotion and antifungal action, and to provide the basis for good utilization of this strain in the future. The genome sequencing of B. amyloliquefaciens L-S60 was performed on Illumina Hiseq 2000 platform. After quality filtering, 5242,236 high-quality paired-end reads (2 × 100 bp) were assembled using SOAPdenovo v.2.04 (http://soap.genomics.org.cn) (Li et al., 2008). The total reads coverage was 300-fold. After gap closing by SOAP GapCloser, a draft genome with 15 scaffolds was obtained. Gaps between scaffolds were closed by PCR and Sanger sequencing. The genome annotation was accomplished by RAST (Aziz et al., 2008). The genome of B. amyloliquefaciens L-S60 consists of a circular chromosome of 3903,017 bp with no plasmid (46.67% GC content). Out of the total 4019 predicted genes, 3909 (97.26%) are proteincoding genes (CDSs), and 3399 (86.95%) of the CDSs were assigned to a putative function while the others were annotated as hypothetical proteins. Meanwhile, 117 RNA genes were also identified in the genome of strain L-S60. The properties and the statistics of the genome are summarized in Table 1. After annotation we identified genes or gene clusters related with the biosynthesis of some antifungal secondary metabolites like surfactin, iturin and fengycins. In comparison with the genome of a well-studied PGPR strain B. amyloliquefaciens FZB42 (accession no. CP000560), we found that the key genes involved in
68
Y. Qin et al. / Journal of Biotechnology 212 (2015) 67–68
Table 1 Features of B. amyloliquefaciens L-S60 genome.
Acknowledgments
Attributes
Value
Genome size (bp) GC content (%) Plasmid rRNA operons tRNA operons Total predicted CDSs
3,903,017 46.67% 0 26 91 3909
plant growth promotion, hormone secretion, biofilm formation and volatile compounds production were also present in this genome. Additionally, the L-S60 genome also contains 30 nitrogen metabolism genes, 28 phosphorus metabolism genes and 10 potassium metabolism genes. The genome sequencing and analysis of strain L-S60 in this study provides valuable information to reveal the molecular mechanism of plant growth promotion and antifungal action and to build the foundation for the utilization of this stain as biological control agent and biofertilizer in the future. Nucleotide sequence accession number The complete genome sequence of B. amyloliquefaciens L-S60 has been deposited in GenBank under the accession number CP011278. This strain has been deposited at China General Microbiological Culture Collection Center under the accession number CGMCC No. 10044.
This work was supported by the Special Fund for Agro-scientific Research in the Public Interest of China (201303014) and the National Natural Science Foundation of China (31172001). References Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., Kubal, M., Meyer, F., Olsen, G.J., Olson, R., Osterman, A.L., Overbeek, R.A., McNeil, L.K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G.D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., Zagnitko, O., 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9. Chen, X.H., Koumoutsi, A., Scholz, R., Eisenreich, A., Schneider, K., Heinemeyer, I., Morgenstern, B., Voss, B., Hess, W.R., Reva, O., Junge, H., Voigt, B., Jungblut, P.R., Vater, J., Sussmuth, 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. Compant, S., Duffy, B., Nowak, J., Clement, C., Barka, E.A., 2005. Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl. Environ. Microbiol. 71, 4951–4959. Li, R.Q., Li, Y.R., Kristiansen, K., Wang, J., 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714. Lugtenberg, B., Kamilova, F., 2009. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63, 541–556. Priest, F.G., Goodfellow, M., Shute, L.A., Berkeley, R.C.W., 1987. Bacillus-amyloliquefaciens Sp.-Nov., Nom. Rev. Int. J. Syst. Bacteriol. 37, 69–71. Ye, Y.F., Li, Q.Q., Fu, G., Yuan, G.Q., Miao, W., Lin, J.H., 2012. Identification of antifungal substance (Iturin A(2)) produced by Bacillus subtilis B47 and its effect on Southern Corn Leaf Blight. J. Integr. Agric. 11, 90–99.
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome announcement
Complete genome sequence of Bacillus amyloliquefaciens L-S60, a plant growth-promoting and antifungal bacterium Yuxuan Qin a , Yuzhu Han a , Yaqiong Yu b , Qingmao Shang b , Bao Zhang a , Pinglan Li a,∗ a
College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China b
a r t i c l e
i n f o
Article history: Received 7 August 2015 Received in revised form 12 August 2015 Accepted 13 August 2015 Available online 20 August 2015 Keywords: Bacillus amyloliquefaciens L-S60 Genome sequence Plant growth promotion Antifungal Biofilm
a b s t r a c t Bacillus amyloliquefaciens L-S60, a gram-positive plant-associated bacterium, which could stimulate plant growth and shows strong antifungal function, was isolated from the turfy soil in Beijing, China. The genome of B. amyloliquefaciens L-S60 comprises a 3903,017 bp long circular chromosome that consists of 3909 protein-coding genes and 117 RNA genes. Based on genomic analysis, we identified gene clusters responsible for the biosynthesis of numerous bioactive metabolites with well-established in-vitro activity such as surfactin, iturin and fengycins. Additionally, we also found functionally related genes in the genome of L-S60, which play key roles in the process of plant growth promotion hormone secretion, biofilm formation and volatile compounds production. © 2015 Elsevier B.V. All rights reserved.
Bacteria that are associated with plant roots and exert beneficial effects on plant development are referred to as plant growth-promoting rhizobacteria (PGPR) (Chen et al., 2007). Bacillus amyloliquefaciens species (Priest et al., 1987), which belong to Bacillus spp., are known to produce important enzymes and bioactive compounds, and thus have been used as biological control agents and biofertilizer for agriculture (Compant et al., 2005; Lugtenberg and Kamilova, 2009; Ye et al., 2012). Strain L-S60, a PGPR strain, has been classified as B. amyloliquefaciens subsp. plantarum based on the phylogenetic analysis of 16S rRNA gene and DNA gyrase subunit B gene sequences. B. amyloliquefaciens L-S60 was isolated from the turfy soil in Beijing, China. This strain showed strong inhibition capacity against several vegetable fungal pathogens, including Rhizoctonia solani, Fusarium oxysporum and Phytophthora capsici, and it also showed capability for phosphorus and potassium dissolving (data not shown). According to comparative experiments, which were performed in the tomato seedling stage, this strain dramatically increased plant height, stem diameter, leaf area and total dry weight as compared to the control group, and therefore makes itself a good candidate of biological control and biofertilizer agent (data not shown). In this study, the genome sequence and its annotation
∗ Corresponding author. Fax: +86 10 62737604. E-mail address: [email protected] (P. Li). http://dx.doi.org/10.1016/j.jbiotec.2015.08.008 0168-1656/© 2015 Elsevier B.V. All rights reserved.
of B. amyloliquefaciens L-S60 are presented together with the biological features to shed light on the molecular mechanism of the plant growth promotion and antifungal action, and to provide the basis for good utilization of this strain in the future. The genome sequencing of B. amyloliquefaciens L-S60 was performed on Illumina Hiseq 2000 platform. After quality filtering, 5242,236 high-quality paired-end reads (2 × 100 bp) were assembled using SOAPdenovo v.2.04 (http://soap.genomics.org.cn) (Li et al., 2008). The total reads coverage was 300-fold. After gap closing by SOAP GapCloser, a draft genome with 15 scaffolds was obtained. Gaps between scaffolds were closed by PCR and Sanger sequencing. The genome annotation was accomplished by RAST (Aziz et al., 2008). The genome of B. amyloliquefaciens L-S60 consists of a circular chromosome of 3903,017 bp with no plasmid (46.67% GC content). Out of the total 4019 predicted genes, 3909 (97.26%) are proteincoding genes (CDSs), and 3399 (86.95%) of the CDSs were assigned to a putative function while the others were annotated as hypothetical proteins. Meanwhile, 117 RNA genes were also identified in the genome of strain L-S60. The properties and the statistics of the genome are summarized in Table 1. After annotation we identified genes or gene clusters related with the biosynthesis of some antifungal secondary metabolites like surfactin, iturin and fengycins. In comparison with the genome of a well-studied PGPR strain B. amyloliquefaciens FZB42 (accession no. CP000560), we found that the key genes involved in
68
Y. Qin et al. / Journal of Biotechnology 212 (2015) 67–68
Table 1 Features of B. amyloliquefaciens L-S60 genome.
Acknowledgments
Attributes
Value
Genome size (bp) GC content (%) Plasmid rRNA operons tRNA operons Total predicted CDSs
3,903,017 46.67% 0 26 91 3909
plant growth promotion, hormone secretion, biofilm formation and volatile compounds production were also present in this genome. Additionally, the L-S60 genome also contains 30 nitrogen metabolism genes, 28 phosphorus metabolism genes and 10 potassium metabolism genes. The genome sequencing and analysis of strain L-S60 in this study provides valuable information to reveal the molecular mechanism of plant growth promotion and antifungal action and to build the foundation for the utilization of this stain as biological control agent and biofertilizer in the future. Nucleotide sequence accession number The complete genome sequence of B. amyloliquefaciens L-S60 has been deposited in GenBank under the accession number CP011278. This strain has been deposited at China General Microbiological Culture Collection Center under the accession number CGMCC No. 10044.
This work was supported by the Special Fund for Agro-scientific Research in the Public Interest of China (201303014) and the National Natural Science Foundation of China (31172001). References Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., Kubal, M., Meyer, F., Olsen, G.J., Olson, R., Osterman, A.L., Overbeek, R.A., McNeil, L.K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G.D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., Zagnitko, O., 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9. Chen, X.H., Koumoutsi, A., Scholz, R., Eisenreich, A., Schneider, K., Heinemeyer, I., Morgenstern, B., Voss, B., Hess, W.R., Reva, O., Junge, H., Voigt, B., Jungblut, P.R., Vater, J., Sussmuth, 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. Compant, S., Duffy, B., Nowak, J., Clement, C., Barka, E.A., 2005. Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl. Environ. Microbiol. 71, 4951–4959. Li, R.Q., Li, Y.R., Kristiansen, K., Wang, J., 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714. Lugtenberg, B., Kamilova, F., 2009. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63, 541–556. Priest, F.G., Goodfellow, M., Shute, L.A., Berkeley, R.C.W., 1987. Bacillus-amyloliquefaciens Sp.-Nov., Nom. Rev. Int. J. Syst. Bacteriol. 37, 69–71. Ye, Y.F., Li, Q.Q., Fu, G., Yuan, G.Q., Miao, W., Lin, J.H., 2012. Identification of antifungal substance (Iturin A(2)) produced by Bacillus subtilis B47 and its effect on Southern Corn Leaf Blight. J. Integr. Agric. 11, 90–99.