- Short genome report
- Open Access
High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32T and comparison among Pontibacillus genomes
© Huang et al. 2015
- Received: 14 November 2014
- Accepted: 19 October 2015
- Published: 10 November 2015
Pontibacillus yanchengensis Y32T is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the features of P. yanchengensis strain Y32T together with a comparison with other four Pontibacillus genomes. The 4,281,464 bp high-quality-draft genome of strain Y32T is arranged into 153 contigs containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of strain Y32T possesses many genes related to its halophilic character, flagellar assembly and chemotaxis to support its survival in a salt-rich environment.
- Pontibacillus yanchengensis
- Genomic comparison
- Moderately halophilic
- Flagellar and chemotaxis
Pontibacillus yanchengensis Y32T (= CGMCC 1.10680T = CCTCC AB209311T = NRRL B-59408T ) was isolated from a salt field in Yancheng, China , and affiliated to the family Bacillaceae , order Bacillales , phylum Firmicutes [2, 3]. The genus Pontibacillus means “ Bacillus pertaining to the sea” and was first identified by Lim et al. in 2005 . To date, the genus contains six species, including Pontibacillus yanchengensis , Pontibacillus chungwhensis , Pontibacillus marinus , Pontibacillus halophilus , Pontibacillus litoralis , and Pontibacillus salicampi , which are isolated from a salt field, a solar saltern, a solar saltern, a sea urchin, a sea anemone, and a saltern soil, respectively.
The Pontibacillus members are characterized as moderately halophilic, Gram-positive, aerobic, endospore-forming and rod-shaped bacteria. They are motile by peritrichous flagella and their DNA has a low G + C content. They are able to survive in salt-rich environments and grow optimally at 5-20 % NaCl (w/v) . To adapt to saline environments, halophilic microorganisms have developed various biochemical strategies to maintain cell function, such as induction of Na+/H+ antiporter systems and the production of compatible solutes. The compatible solutes are gaining increasing interest since they can be used as stabilizers, salt antagonists, or stress-protective agents [10–13]. In addition, a Pontibacillus strain could produce biosurfacants which is useful in degradation of paraffinic mixture or saline organic contamination .
In this study, we sequenced five Pontibacillus type strains, including P. yanchengensis Y32T , P. chungwhensis BH030062T, P. marinus BH030004T, P. halophilus JSM076056T and P. litoralis JSM072002T(The GenBank accession summary of the strains is shown in Additional file 2). Here we present the draft genome sequence of P. yanchengensis Y32T and compare it to the genomes of four other type strains. To the best of our knowledge, this is the first description of the Pontibacillus genome.
Classification and features
Seventeen related strains of Bacillaceae  with complete genome sequences were chosen for further phylogenetic analysis, including the four draft-genome sequences of Pontibacillus that were sequenced by us. In total, 602 core protein sequences were extracted using the cluster algorithm tool OrthoMCL [16, 17] with default parameters. The neighbor-joining (NJ) phylogenetic tree showed that the five Pontibacillus species clustered into the same branch (Fig. 1b), which was in accordance with the 16S rRNA gene-based phylogeny (Fig. 1a).
Classification and general features of P. yanchengensis Y32T according to the MIGS recommendations 
Species Pontibacillus yanchengensis
Type strain Y32T
3–20 % (w/v)
6–8 % (w/v)
Sample collection time
When grown on Bacto marine broth 2216 (Difco) agar medium plus 3 % (w/v) NaCl, P. yanchengensis Y32T contained anteiso-C15:0, iso-C15:0, and iso-C14:0 as the major fatty acids and menaquinone (MK-7) as the predominant respiratory quinone. The cell wall peptidoglycan type was meso-diaminopimelic . The classification and general features of P. yanchengensis Y32T are shown in Table 1.
Genome project history
Genome sequencing project information for P. yanchengensis Y32T
Illumina Paired-End library (300 bp insert size)
SOAP denovo v1.05
Gene calling method
GenBank date of release
November 6, 2014
Source material identifier
Growth conditions and DNA isolation
P. yanchengensis Y32T was grown aerobically in 50 mL Bacto marine broth 2216 (Difco) plus 5 % NaCl (w/v) at 37 °C for 2 d with 150 rpm shaking. Cells were harvested by centrifugation and a pellet with an approximate wet weight of 20 mg was obtained. The genomic DNA was extracted using the QIAamp DNA kit according to the manufacturer’s instructions (Qiagen, Germany). The quality and quantity of total DNA was determined using a NanoDrop Spectrophotometer 2000. Five micrograms of genomic DNA was sent to Majorbio (Shanghai, China) for sequencing on a Hiseq2000 (Illumina, CA) sequencer.
Genome sequencing and assembly
The Illumina Hiseq2000 technology of Paired-End (PE) library with an average insert size of 300 bp was used to determine the sequence of P. yanchengensis Y32T. A total of 4,083,912 × 2 high quality reads totaling 824,950,224 bp of data with an average coverage of 186.5 x was generated. Raw reads were filtered using a FastQC toolkit followed by assembly with SOAP denovo v1.05 and optimizing through local gap filling and base correction with Gap Closer.
The draft genome sequence was deposited at NCBI and was annotated through the Prokaryotic Genome Annotation Pipeline, which combined the Best-Placed reference protein set and the gene caller GeneMarkS+. The WebMGA server was used to identify the Clusters of Ortholog Groups . Transmembrane helices and signal peptides were predicted by the online bioinformatic tools TMHMM 2.0 [20, 21] and SignalP 4.1 , respectively.
Genome statistics for P. yanchengensis Y32T
% of Totala
Genome size (bp)
DNA coding region (bp)
DNA G + C content (bp)
Number of contigs
Contig N50 (bp)
Frame shifted genes
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of protein-coding genes associated with the 25 general COG functional categories in the P. yanchengensis Y32T genome
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane/envelope biogenesis
Intracellular trafficking, secretion, and vesicular transport
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Insights from the genome sequence
General features of the five Pontibacillus genome sequences
Genome size (bp)
G + C%
Contigs N50 (bp)
P. yanchengensis Y32T
P. chungwhensis BH030062T
P. marinus BH030004T
P. halophilus JSM076056T
P. litoralis JSM072002T
All the Pontibacillus species were isolated from salty environments. They were characterized as moderately halophilic and cannot grow in the absence of NaCl. As moderate halophiles, effective establishment of ionic and osmotic equilibrium was important for survival in a saline environment. The genome comparison analysis showed that the five Pontibacillus strains possessed genes encoding cation/proton antiporter (e.g., Na+/H+ antiporter, Na+/Ca2+ antiporter), which played a role in tolerance to high concentrations of Na+, K+, Li+ and/or alkali (Additional file 1: Table S2). Numerous studies showed that Na+/H+ antiporters play important roles in the pH and Na+ homeostasis of cells [24, 25]. Meanwhile, the prediction of the membrane helices of the P. yanchengensis Y32T genome suggested that nearly 30% of the genes had transmembrane helix structures (Table 3), which may be involved in ion transport.
This study provided genomic information for P. yanchengensis strain Y32T and the comparison of five Pontibacillus genomes. Strain Y32T has functional genes encoding cation/proton antiporters and proteins for biosynthesis of compatible solutes such as glycine and ectoine. Compatible solutes could be of use in the cosmetic and food industries . The comparative genomic analysis suggested that the five Pontibacillus strains possess different synthetic pathways for compatible solutes which provided diverse applications of the strains.
This work was supported by the China Postdoctoral Science Foundation (2014 M562037) and the National Natural Science Foundation of China (31470227).
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Yang Y, Zou Z, He M, Wang G. Pontibacillus yanchengensis sp. nov., a moderately halophilic bacterium isolated from salt field soil. Int J Syst Evol Microbiol. 2011;61:1906–11. doi:10.1099/ijs.0.023911-0.View ArticlePubMedGoogle Scholar
- Skerman VBD, McGowan V, Sneath PHA. Approved lists of bacterial names. Int J Syst Bacteriol. 1980;30:225–420.View ArticleGoogle Scholar
- Fischer A. Untersuchungen über bakterien. Jahrbüch für Wissenschaftliche Botanik. 1895;27:1–163.Google Scholar
- Lim JM, Jeon CO, Song SM, Kim CJ. Pontibacillus chungwhensis gen. nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern in Korea. Int J Syst Evol Microbiol. 2005;55:165–70. doi:10.1099/ijs.0.63315-0.View ArticlePubMedGoogle Scholar
- Lim JM, Jeon CO, Park DJ, Kim HR, Yoon BJ, Kim CJ. Pontibacillus marinus sp. nov., a moderately halophilic bacterium from a solar saltern, and emended description of the genus Pontibacillus. Int J Syst Evol Microbiol. 2005;55:1027–31. doi:10.1099/ijs.0.63489-0.View ArticlePubMedGoogle Scholar
- Chen YG, Zhang YQ, Xiao HD, Liu ZX, Yi LB, Shi JX, et al. Pontibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from a sea urchin. Int J Syst Evol Microbiol. 2009;59:1635–9. doi:10.1099/ijs.0.002469-0.View ArticlePubMedGoogle Scholar
- Chen YG, Zhang YQ, Yi LB, Li ZY, Wang YX, Xiao HD, et al. Pontibacillus litoralis sp. nov., a facultatively anaerobic bacterium isolated from a sea anemone, and emended description of the genus Pontibacillus. Int J Syst Evol Microbiol. 2010;60:560–5. doi:10.1099/ijs.0.009910-0.View ArticlePubMedGoogle Scholar
- Lee JC, Kim YS, Yun BS, Whang KS. Pontibacillus salicampi sp. nov., a moderate halophilic bacterium isolated from a saltern soil. Int J Syst Evol Microbiol. 2014. Available at: doi:10.1099/ijs.0.066423-0.
- DasSarma S, DasSarma P. Halophiles. In: eLS. John Wiley & Sons, Ltd; 2006. doi:10.1002/9780470015902.a0000394.pub3
- Margesin R, Schinner F. Potential of halotolerant and halophilic microorganisms for biotechnology. Extremophiles. 2001;5:73–83. doi:10.1007/s007920100184.View ArticlePubMedGoogle Scholar
- Kheiralla ZH, Ashour SM, Rushdy AA, Ahmed HA. Characterization of biosurfactants produced by Halobacillus dabanensis and Pontibacillus chungwhensis isolated from oil-contaminated mangrove ecosystem in Egypt. Appl Biochem Microbiol. 2013;49:263–9. doi:10.1134/S0003683813030186.View ArticleGoogle Scholar
- Roberts MF. Organic compatible solutes of halotolerant and halophilic microorganisms. Saline systems. 2005;1:1–30. doi:10.1186/1746-1448-1-5.View ArticleGoogle Scholar
- Sorokin DY, Janssen AJH, Muyzer G. Biodegradation potential of palo(alkali)philic prokaryotes. Crit Rev Env Sci Tec. 2011;42:811–56. doi:10.1080/10643389.2010.534037.View ArticleGoogle Scholar
- Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673–80.PubMed CentralView ArticlePubMedGoogle Scholar
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary geneticsanalysis version 6.0. Mole Biol Evol. 2013;30:2725–9. doi:10.1093/molbev/mst197.View ArticleGoogle Scholar
- Li L, Stoeckert CJ, Roos DS. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178–89. doi:10.1101/gr.1224503.PubMed CentralView ArticlePubMedGoogle Scholar
- Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, et al. Using OrthoMCL toassign proteins to OrthoMCL-DB groups or to clusterproteomes into new orthologgroups: John Wiley & Sons, Inc.; 2011. doi:10.1002/0471250953.bi0612s35
- Iwamoto K, Shiraiwa Y. Salt-Regulated Mannitol Metabolism in Algae. Mar Biotechnol. 2005;7:407–15. doi:10.1007/s10126-005-0029-4.View ArticlePubMedGoogle Scholar
- Wu S, Zhu Z, Fu L, Niu B, Li W. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics. 2011;12:444. doi:10.1186/1471-2164-12-444.PubMed CentralView ArticlePubMedGoogle Scholar
- Sonnhammer EL, Von Heijne G, Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol. 1998;6:175–82.PubMedGoogle Scholar
- Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol. 2001;305:567–80. doi:10.1006/jmbi.2000.4315.View ArticlePubMedGoogle Scholar
- Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Meth. 2011;8:785–6. doi:10.1038/nmeth.1701.View ArticleGoogle Scholar
- Grant J, Arantes A, Stothard P. Comparing thousands of circular genomes using the CGView comparison tool. BMC Genomics. 2012;13:202. doi:10.1186/1471-2164-13-202.PubMed CentralView ArticlePubMedGoogle Scholar
- Padan E, Venturi M, Gerchman Y, Dover N. Na(+)/H(+) antiporters. Biochim Biophys Acta. 2001;1505:144–57. doi:10.1016/S0005-2728(00)00284-X.View ArticlePubMedGoogle Scholar
- Hunte C, Screpanti E, Venturi M, Rimon A, Padan E, Michel H. Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH. Nature. 2005;435:1197–202. doi:10.1038/nature03692.View ArticlePubMedGoogle Scholar
- Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7. doi:10.1038/nbt1360.PubMed CentralView ArticlePubMedGoogle Scholar
- Gibbons NE, Murray RGE. Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol. 1978;28:1–6. doi:10.1099/00207713-28-1-1.View ArticleGoogle Scholar
- Murray R. The higher taxa, or, a place for everything. Bergey’s Manual Syst Bacteriol. 1984;1:31–4.Google Scholar
- Editor L. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol. 2010;60:469–72.View ArticleGoogle Scholar
- Ludwig W, Schleifer KH, Whitman WB. Class I. Bacilli class nov. Bergey’s Manual of Systematic Bacteriology. 2009; 3:19–20Google Scholar
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9. doi:10.1038/75556.PubMed CentralView ArticlePubMedGoogle Scholar