Journal of Biotechnology 211 (2015) 1–2
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Complete genome sequence of the petroleum-emulsifying bacterium Pseudomonas stutzeri SLG510A3-8 Bing Hu a , Yong Nie a , Shuang Geng a , Xiao-Lei Wu a,b,∗ a b
College of Engineering, Peking University, Beijing 100871, PR China Institute of Engineering (Baotou), College of Engineering, Peking University, Baotou 014030, PR China
a r t i c l e
i n f o
Article history: Received 26 June 2015 Accepted 26 June 2015 Available online 2 July 2015 Keywords: Pseudomonas stutzeri SLG510A3-8 Complete genome sequencing Microbial enhanced oil recovery
a b s t r a c t Pseudomonas stutzeri SLG510A3-8, isolated from oil-contaminated soil in Shengli Oilfield, China, has the potential to be applied for microbial enhanced oil recovery. Here, we reported the complete genome sequence of this bacterium. It has a 4,650,155 bp circular chromosome encoding 4450 genes, and the genome consists of genes that are involved in denitrification, chemotaxis, benzoate degradation, molecule transportation, and other functions. The genome contains a complete set of genes for type I secretion system in comparison with sequences of other P. stutzeri strains. © 2015 Elsevier B.V. All rights reserved.
Pseudomonas stutzeri is a Gram-negative, rod-shaped, flagellated bacterium. Members of the species were isolated from various terrestrial and marine environments. Some of them have received particular attention because of their great metabolic properties, such as nitrogen fixation, denitrification, and environmental pollutant degradation (Lalucat et al., 2006; Méndez et al., 2010). Until now, complete genome sequencing has been established for eight P. stutzeri strains, none of which is from oil-contaminated environment (http://www.ncbi.nlm.nih. gov/genome/genomes/1432). P. stutzeri strain SLG510A3-8 was originally isolated from petroleum-contaminated soil in Shengli Oilfield, Shandong, China. It displayed effective emulsifying properties of petroleum in mineral medium, and is promising for microbial enhanced oil recovery (MEOR) in the future. Here, we report the complete genome sequence of the strain, which would be valuable for understanding its metabolic properties and for genetic engineering. The genome of strain SLG510A3-8 was sequenced by integrating Illumina Hiseq2000 and Pacific Biosciences (PacBio) RSII sequencing technology, of which Illumina pair-end sequencing library was prepared using TruSeq DNA sample prep kit and the PacBio RSII Single Molecule Real Time (SMRT) sequencing platform was prepared from sheared genomic DNA using a 10-kb template library preparation workflow (Gravina et al., 2013; Eid et al.,
∗ Corresponding author at: College of Engineering, Peking University, Beijing 100871, PR China. Fax: +86 10 62759047. E-mail address: xiaolei
[email protected] (X.-L. Wu). http://dx.doi.org/10.1016/j.jbiotec.2015.06.421 0168-1656/© 2015 Elsevier B.V. All rights reserved.
2009). In total, 10,325,800 paired-end reads (1,042,905,800 bp) corresponding to 224 folds of genomic coverage were generated on an Illumina Hiseq 2000 platform, and 37,392 long read (525,160,828 bp) was obtained on a PacBio sequencing platform. Subsequently, the sequenced data after error correction was assembled into a single contig via the hierarchical genome assembly process (HGAP) de novo workflow as available in SMRT Analysis v2.1 (Chin et al., 2013). Open reading frames (ORFs) were predicted using Glimmer software program (Delcher et al., 2007), of which tRNA and rRNA genes were predicted with tRNAscan-SE and RNAmmer, respectively (Schattner et al., 2005; Lagesen et al., 2007). Function annotation was based on a BLASTP search against GenBank’s nonredundant protein database (NR; http://www.ncbi. nlm.nih.gov/), Kyoto Encyclopedia of Genes and Genomes database (KEGG; http://www.genome.jp/kegg/), the Pfam protein family database (http://pfam.xfam.org/), and database of the Clusters of Orthologous Groups of proteins (COG; http://www.ncbi.nlm.nih. gov/COG/). The metabolic pathways were predicted using KEGG automatic annotation server (KAAS; http://www.genome.jp/tools/ kaas/). The complete genome of P. stutzeri SLG510A3-8 is composed of a single circular chromosome of 4,650,155 bp with an average GC content of 63.99%, which is similar with those of the previously reported P. stutzeri strains. In total, the genome contains 4, 379 protein-coding sequences (CDS), 59 tRNA genes and four rRNA operons. (Table 1). Genome analysis revealed that genes for complete glycolysis, pentose phosphate pathways, citrate cycle, and oxidative phosphorylation were present, as expected for aerobically heterotrophic
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Table 1 Pseudomonas stutzeri SLG510A3-8 genome features.
Acknowledgements
Feature
Chromosome
Genome size (bp) GC content (%) rRNA operons tRNAs Total number of genes Protein coding genes (cds) Genes with predicted functions
4,650,155 63.99 4 59 4,450 4,379 3,317
bacteria. Furthermore, as in other P. stutzeri strains, the genome of strain SLG510A3-8 has complete sets of genes for denitrification, flagellum synthesis, and bacterial chemotaxis. Similar with P. stutzeri strain CCUG29243, all genes needed for benzoate degradation were detected in strain SLG510A3-8. More than 200 genes were annotated as being involved in the transport systems of type II, IV, and VI secretion systems, sec-SRP pathway, twin-arginine translocation (Tat) pathway, ABC transporter, and two-component systems. In addition, unlike all other reported P. stutzeri strains, the genome contains the complete set of genes for type I secretion (tolC, hlyD and hlyB), which could transport ions, drugs and proteins with the sizes between 20 and 900 kDa (Delepelaire, 2004). Necleotide sequence accession number The complete genome sequence of P. stutzeri strain SL510A38 has been deposited at Genbank under the accession number CP011854.1. The strain is accessible in China General Microbiological Culture Collection Center (CGMCC) with the identifier of 1.15316.
Tianjin Research Center of Functional Genomics and Biochip was gratefully acknowledged. The authors also thank the financial support from National Natural Science Foundation of China (31400112). References Chin, C.S., Alexander, D.H., Marks, P., Kalmmer, A.A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E.E., Turner, S.W., Korlach, J., 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10 (6), 563–569. 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. Delepelaire, P., 2004. Type I secretion in gram-negative bacteria. Biochem. Biophys. Acta 1694, 149–161. Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., Bibillo, A., Bjornson, K., Chaudhuri, B., Christians, F., Cicero, R., Clark, S., Dalal, R., deWiner, A., Dixon, J., Foquet, M., Gaertner, A., Hardenbol, P., Heiner, C., Hester, K., Holden, D., Kearns, G., Kong, X., Kuse, R., Lacroix, Y., Lin, S., Lundquist, P., Ma, C., Marks, P., Maxham, M., Murphy, D., Park, I., Pham, T., Phillips, M., Roy, J., Sebra, R., Sheng, G., Sorenson, J., Tomaney, A., Travers, K., Trulson, M., Vieceli, J., Wegener, J., Wu, D., Yang, A., Zaccarin, D., Zhao, P., Zhong, F., Korlach, J., Turner, S., 2009. Real-time DNA sequencing from single polymerase molecules. Science 323 (5910), 133–138. Gravina, M.T., Lin, J.H., Levine, S.S., 2013. Lane-by-lane sequencing using Illuminas genome analyzer II. Biotechniques 54 (5), 265–269. 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. Lalucat, J., Bennasar, A., Bosch, R., García-Valdés, E., Palleroni, N.J., 2006. Biology of Pseudomonas stutzeri. Microbiol. Mol. Biol. Rev. 70 (2), 510–547. Méndez, V., Fuentes, S., Hernández, M., Morgante, V., González, M., Seeger, M., 2010. Isolation of hydrocarbon-degrading heavy-metal-resistant bacteria from crude oil-contaminated soil in central chile. J. Biotechnol. 150, 287. Schattner, P., Brooks, A.N., Lowe, T.M., 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33, W686–689.
