- Email: [email protected]
Draft genome of Bacillus sp. A053 isolated from the Arctic seawater with antimicrobial activity
Marine Genomics 22 (2015) 19–21
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/technical resources
Draft genome of Bacillus sp. A053 isolated from the Arctic seawater with antimicrobial activity Wenbin Guo, Zhiteng Chen, Pengfei Cui, Xinhua Chen ⁎ Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, China
a r t i c l e
i n f o
Article history: Received 20 January 2015 Received in revised form 22 February 2015 Accepted 16 March 2015 Available online 24 March 2015 Keywords: Arctic seawater Bacillus Genome Antimicrobial activity
a b s t r a c t Bacillus sp. A053, isolated from the Arctic seawater, shows strong antifungal activity against plant pathogenic fungi. Here, we report the draft sequence of the approximately 4.1-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Bacillus strain isolated from the Arctic seawater with antifungal activity. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of antimicrobial compound in this strain. © 2015 Elsevier B.V. All rights reserved.
1. Introduction Bacillus is a genus of Gram-positive, rod-shaped bacteria and a member of the phylum Firmicutes. Many species of Bacillus can produce copious amounts of antimicrobial chemical compounds which may be used in developing drugs. Bacillus cereus (Kumar et al., 2014), endophytic Bacillus vallismortis ZZ185 (Zhao et al., 2010) and Bacillus amyloliquefaciens SQR9 (Li et al., 2014) are reported to exhibit strong antimicrobial activity. However, most of the strains with antimicrobial activity are from the land. In recent years, the antimicrobial substances from marine microorganisms are becoming an important part in discovering new antimicrobial antibiotics and developing marine drugs. In this study, Bacillus sp. A053 was isolated from the Arctic seawater (N78°57′09.2″, E12°00′02.3″) and has been deposited in the China Center for Type Culture Collection (CCTCC) with accession number CCTCC M 2010269. Analysis of the 16S rRNA gene sequence (locus tag of SC22_00035 in the genome) showed that it shared 100% identity with Bacillus sp. JS. This indicated that this strain belongs to Bacillus genus. Bacillus sp. A053 exhibits strong antifungal activity against plant pathogenic fungi including Paecilomyces variotii (CGMCC 3.776, China General Microbiological Culture Collection Center), Colletotrichum gloeosporioides (ACCC 31200, Agricultural Cultural Collection of China), Fusarium oxysporum (ACCC 31352), Trichoderma viride (ACCC 30902), Rhizoctonia solani Kühn (ACCC 36316), Alternaria longipes (ACCC 30002) and Sclerotinia sclerrotioru (ACCC 36081). The Bacillus sp. A053 genome ⁎ Corresponding author at: Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China. Tel.: +86 592 2195297; fax: +86 592 2085376. E-mail address: [email protected] (X. Chen).
http://dx.doi.org/10.1016/j.margen.2015.03.008 1874-7787/© 2015 Elsevier B.V. All rights reserved.
sequence may provide fundamental molecular information on elucidating the metabolic pathway of antimicrobial compound in this strain. 2. Data description Bacillus sp. A053 was cultured in LB medium and incubated at 28 °C, 180 rpm for 48 h. The genome DNA was obtained using DNA extraction kit provided by TIANGEN Biotech (Beijing) Co., Ltd., China. The genome sequence of Bacillus sp. A053 was obtained by paired-end sequencing on Illumina HiSeq 2000 instrument at the BGI, Shenzhen. Reads were assembled using SOAPdenovo software version 2.04 (Li et al., 2008, 2010). Protein-coding sequences were predicted by Glimmer software version 3.02 (Delcher et al., 2007) and annotated using BLAST searches of nonredundant protein sequences from the NCBI, Swiss-Prot and TrEMBL, COG (Tatusov et al., 2003), Gene Ontology (GO) (Ashburner et al., 2000) and KEGG (Kanehisa et al., 2004) databases. Ribosomal RNA genes were detected using RNAmmer software version 1.2 Table 1 General features of Bacillus sp. A053 genome. Attribute
Bacillus sp. A053
Assembly size (bp) Contigs Contig N50 GC content % Predicted ORFs Tandem repeat sequence tRNA rRNA sRNA
4,139,313 5 1,694,278 43.87% 4221 61 81 25 8
20
W. Guo et al. / Marine Genomics 22 (2015) 19–21
(Lagesen et al., 2007), and transfer RNA genes were detected using tRNAscan-SE (Lowe & Eddy, 1997). Additionally, small ncRNA (sRNA) genes were detected using Rfam software version 10.1 (Gardner et al., 2009). Genes possibly involved in metabolic pathway of antimicrobial compound were manually evaluated. The draft genome of Bacillus sp. A053 comprises 5 contigs, with an N50 value of 1,694,278 bp (Table 1). The draft genome is made up of a circular chromosome of approximately 4.1-Mbp with 43.87% GC content and no plasmid (Table 1). It is smaller than the 4.2-Mbp
genome of Bacillus subtilis subsp. spizizenii strain gtP20b which was reported to be the first genome sequence of B. subtilis from the marine environment (Fan et al., 2011). The graphical map of the chromosome of Bacillus sp. A053 was illustrated in Fig. 1. The genome of Bacillus sp. A053 encodes 4221 proteins, and the total length of genes was 3,668,205 bp, which makes up 88.46% of the genome (Table 1). The number of tandem repeat sequence was 61 with total length of 10,190 bp, which makes up 0.2457% of the genome (Table 1). The genome also encodes 81 tRNAs, 25 rRNAs and 8 sRNAs, which make up
Fig. 1. Graphical map of the chromosome of Bacillus sp. A053.
W. Guo et al. / Marine Genomics 22 (2015) 19–21
1.0628% of the genome (Table 1). To the best of our knowledge, this is the first genome sequence of Bacillus strain isolated from the Arctic seawater with antifungal activity. 3. Nucleotide sequence accession number This Whole Genome Shotgun project has been deposited at DDBJ/ EMBL/GenBank under the accession JXAJ00000000. The version described in this paper is version JXAJ01000000. Acknowledgments The study was financially supported by grants from the Scientific Research Project of the Marine Public Welfare Industry of China (201205020), National key Basic Research Program of China (2015CB755903), Natural Science Foundation of China (41306166), China Polar Environment Comprehensive investigation and Assessment Program (CHINARE2015-04-03), and the Xiamen South Ocean Research Center (13GZP002NF08). References Kumar, S., Nambisan, B., Sundaresan, A., Mohandas, C., Anto, R., 2014. Isolation and identification of antimicrobial secondary metabolites from Bacillus cereus associated with a rhabditid entomopathogenic nematode. Ann. Microbiol. 64, 209–218. Zhao, Z., Wang, Q., Wang, K., Brian, K., Liu, C., Gu, Y., 2010. Study of the antifungal activity of Bacillus vallismortis ZZ185 in vitro and identification of its antifungal components. Bioresour. Technol. 101, 292–297.
21
Li, B., Li, Q., Xu, Z., Zhang, N., Shen, Q., Zhang, R., 2014. Responses of beneficial Bacillus amyloliquefaciens SQR9 to different soilborne fungal pathogens through the alteration of antifungal compounds production. Front. Microbiol. 5, 636. Li, R., Li, Y., Kristiansen, K., Wang, J., 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714 (Oxford, England). Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., Li, S., Yang, H., Wang, J., Wang, J., 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272. Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679 (Oxford, England). Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., Rao, B.S., Smirnov, S., Sverdlov, A.V., Vasudevan, S., Wolf, Y.I., Yin, J.J., Natale, D.A., 2003. The COG database: an updated version includes eukaryotes. BMC Bioinforma. 4, 41. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G., 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M., 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–D280. Lagesen, K., Hallin, P., Rodland, E.A., Staerfeldt, H.H., Rognes, T., Ussery, D.W., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964. Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R., Bateman, A., 2009. Rfam: updates to the RNA families database. Nucleic Acids Res. 37, D136–D140. Fan, L., Bo, S., Chen, H., Ye, W., Kleinschmidt, K., Baumann, H.I., Imhoff, J.F., Kleine, M., Cai, D., 2011. Genome sequence of Bacillus subtilis subsp. spizizenii gtP20b, isolated from the Indian Ocean. J. Bacteriol. 193, 1276–1277.
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/technical resources
Draft genome of Bacillus sp. A053 isolated from the Arctic seawater with antimicrobial activity Wenbin Guo, Zhiteng Chen, Pengfei Cui, Xinhua Chen ⁎ Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, China
a r t i c l e
i n f o
Article history: Received 20 January 2015 Received in revised form 22 February 2015 Accepted 16 March 2015 Available online 24 March 2015 Keywords: Arctic seawater Bacillus Genome Antimicrobial activity
a b s t r a c t Bacillus sp. A053, isolated from the Arctic seawater, shows strong antifungal activity against plant pathogenic fungi. Here, we report the draft sequence of the approximately 4.1-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Bacillus strain isolated from the Arctic seawater with antifungal activity. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of antimicrobial compound in this strain. © 2015 Elsevier B.V. All rights reserved.
1. Introduction Bacillus is a genus of Gram-positive, rod-shaped bacteria and a member of the phylum Firmicutes. Many species of Bacillus can produce copious amounts of antimicrobial chemical compounds which may be used in developing drugs. Bacillus cereus (Kumar et al., 2014), endophytic Bacillus vallismortis ZZ185 (Zhao et al., 2010) and Bacillus amyloliquefaciens SQR9 (Li et al., 2014) are reported to exhibit strong antimicrobial activity. However, most of the strains with antimicrobial activity are from the land. In recent years, the antimicrobial substances from marine microorganisms are becoming an important part in discovering new antimicrobial antibiotics and developing marine drugs. In this study, Bacillus sp. A053 was isolated from the Arctic seawater (N78°57′09.2″, E12°00′02.3″) and has been deposited in the China Center for Type Culture Collection (CCTCC) with accession number CCTCC M 2010269. Analysis of the 16S rRNA gene sequence (locus tag of SC22_00035 in the genome) showed that it shared 100% identity with Bacillus sp. JS. This indicated that this strain belongs to Bacillus genus. Bacillus sp. A053 exhibits strong antifungal activity against plant pathogenic fungi including Paecilomyces variotii (CGMCC 3.776, China General Microbiological Culture Collection Center), Colletotrichum gloeosporioides (ACCC 31200, Agricultural Cultural Collection of China), Fusarium oxysporum (ACCC 31352), Trichoderma viride (ACCC 30902), Rhizoctonia solani Kühn (ACCC 36316), Alternaria longipes (ACCC 30002) and Sclerotinia sclerrotioru (ACCC 36081). The Bacillus sp. A053 genome ⁎ Corresponding author at: Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China. Tel.: +86 592 2195297; fax: +86 592 2085376. E-mail address: [email protected] (X. Chen).
http://dx.doi.org/10.1016/j.margen.2015.03.008 1874-7787/© 2015 Elsevier B.V. All rights reserved.
sequence may provide fundamental molecular information on elucidating the metabolic pathway of antimicrobial compound in this strain. 2. Data description Bacillus sp. A053 was cultured in LB medium and incubated at 28 °C, 180 rpm for 48 h. The genome DNA was obtained using DNA extraction kit provided by TIANGEN Biotech (Beijing) Co., Ltd., China. The genome sequence of Bacillus sp. A053 was obtained by paired-end sequencing on Illumina HiSeq 2000 instrument at the BGI, Shenzhen. Reads were assembled using SOAPdenovo software version 2.04 (Li et al., 2008, 2010). Protein-coding sequences were predicted by Glimmer software version 3.02 (Delcher et al., 2007) and annotated using BLAST searches of nonredundant protein sequences from the NCBI, Swiss-Prot and TrEMBL, COG (Tatusov et al., 2003), Gene Ontology (GO) (Ashburner et al., 2000) and KEGG (Kanehisa et al., 2004) databases. Ribosomal RNA genes were detected using RNAmmer software version 1.2 Table 1 General features of Bacillus sp. A053 genome. Attribute
Bacillus sp. A053
Assembly size (bp) Contigs Contig N50 GC content % Predicted ORFs Tandem repeat sequence tRNA rRNA sRNA
4,139,313 5 1,694,278 43.87% 4221 61 81 25 8
20
W. Guo et al. / Marine Genomics 22 (2015) 19–21
(Lagesen et al., 2007), and transfer RNA genes were detected using tRNAscan-SE (Lowe & Eddy, 1997). Additionally, small ncRNA (sRNA) genes were detected using Rfam software version 10.1 (Gardner et al., 2009). Genes possibly involved in metabolic pathway of antimicrobial compound were manually evaluated. The draft genome of Bacillus sp. A053 comprises 5 contigs, with an N50 value of 1,694,278 bp (Table 1). The draft genome is made up of a circular chromosome of approximately 4.1-Mbp with 43.87% GC content and no plasmid (Table 1). It is smaller than the 4.2-Mbp
genome of Bacillus subtilis subsp. spizizenii strain gtP20b which was reported to be the first genome sequence of B. subtilis from the marine environment (Fan et al., 2011). The graphical map of the chromosome of Bacillus sp. A053 was illustrated in Fig. 1. The genome of Bacillus sp. A053 encodes 4221 proteins, and the total length of genes was 3,668,205 bp, which makes up 88.46% of the genome (Table 1). The number of tandem repeat sequence was 61 with total length of 10,190 bp, which makes up 0.2457% of the genome (Table 1). The genome also encodes 81 tRNAs, 25 rRNAs and 8 sRNAs, which make up
Fig. 1. Graphical map of the chromosome of Bacillus sp. A053.
W. Guo et al. / Marine Genomics 22 (2015) 19–21
1.0628% of the genome (Table 1). To the best of our knowledge, this is the first genome sequence of Bacillus strain isolated from the Arctic seawater with antifungal activity. 3. Nucleotide sequence accession number This Whole Genome Shotgun project has been deposited at DDBJ/ EMBL/GenBank under the accession JXAJ00000000. The version described in this paper is version JXAJ01000000. Acknowledgments The study was financially supported by grants from the Scientific Research Project of the Marine Public Welfare Industry of China (201205020), National key Basic Research Program of China (2015CB755903), Natural Science Foundation of China (41306166), China Polar Environment Comprehensive investigation and Assessment Program (CHINARE2015-04-03), and the Xiamen South Ocean Research Center (13GZP002NF08). References Kumar, S., Nambisan, B., Sundaresan, A., Mohandas, C., Anto, R., 2014. Isolation and identification of antimicrobial secondary metabolites from Bacillus cereus associated with a rhabditid entomopathogenic nematode. Ann. Microbiol. 64, 209–218. Zhao, Z., Wang, Q., Wang, K., Brian, K., Liu, C., Gu, Y., 2010. Study of the antifungal activity of Bacillus vallismortis ZZ185 in vitro and identification of its antifungal components. Bioresour. Technol. 101, 292–297.
21
Li, B., Li, Q., Xu, Z., Zhang, N., Shen, Q., Zhang, R., 2014. Responses of beneficial Bacillus amyloliquefaciens SQR9 to different soilborne fungal pathogens through the alteration of antifungal compounds production. Front. Microbiol. 5, 636. Li, R., Li, Y., Kristiansen, K., Wang, J., 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714 (Oxford, England). Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., Li, S., Yang, H., Wang, J., Wang, J., 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272. Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679 (Oxford, England). Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., Rao, B.S., Smirnov, S., Sverdlov, A.V., Vasudevan, S., Wolf, Y.I., Yin, J.J., Natale, D.A., 2003. The COG database: an updated version includes eukaryotes. BMC Bioinforma. 4, 41. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G., 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M., 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–D280. Lagesen, K., Hallin, P., Rodland, E.A., Staerfeldt, H.H., Rognes, T., Ussery, D.W., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964. Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R., Bateman, A., 2009. Rfam: updates to the RNA families database. Nucleic Acids Res. 37, D136–D140. Fan, L., Bo, S., Chen, H., Ye, W., Kleinschmidt, K., Baumann, H.I., Imhoff, J.F., Kleine, M., Cai, D., 2011. Genome sequence of Bacillus subtilis subsp. spizizenii gtP20b, isolated from the Indian Ocean. J. Bacteriol. 193, 1276–1277.