- Extended genome report
- Open Access
Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5
© Peña-Montenegro et al.; licensee BioMed Central. 2015
- Received: 12 June 2014
- Accepted: 21 November 2014
- Published: 20 January 2015
Lysinibacillus sphaericus CBAM5, was isolated from subsurface soil of oil well explorations in the Easter Planes of Colombia. This strain has potential in bioremediation of heavy-metal polluted environments and biological control of Culex quinquefasciatus. According to the phylogenetic analysis of 16S rRNA gene sequences, the strain CBAM5 was assigned to the Lysinibacillus sphaericus taxonomic group 1 that comprises mosquito pathogenic strains. After a combination assembly-integration, alignment and gap-filling steps, we propose a 4,610,292 bp chromosomal scaffold. The whole genome (consisting of 5,146,656 bp long, 60 contigs and 5,209 predicted-coding sequences) revealed strong functional and syntenial similarities to the L. sphaericus C3-41 genome. Mosquitocidal (Mtx), binary (Bin) toxins, cereolysin O, and heavy metal resistance clusters from nik, ars, czc, mnt, ter, cop, cad, and znu operons were identified.
- Lysinibacillus sphaericus CBAM5
- DNA homology
- Binary toxins
- Mosquitocidal toxins
- S-layer proteins
- Heavy metal tolerance
Lysinibacillus sphaericus is one of the bacteria used as a bio-insecticide as part of vector control programs against tropical diseases, such as malaria, filariasis, yellow fever, dengue fever and West Nile virus . L. sphaericus isolates may be classified according to their larvicidal activity into high and low toxicity strains. High- and low-toxicity strains synthesize mosquitocidal toxins (Mtx) in vegetative growth cells . Highly toxic strains produce a binary toxin coded by binA and binB genes in sporulating stages . In addition, L. sphaericus larvicidal toxicity may be explained due to expression of Cry48/Cry49 toxin  and the S-layer protein . Vegetative and sporulated cells of L. sphaericus CBAM5 are pathogenic towards Culex quinquefasciatus larvae . LC50 (50% lethal concentration) toward C. quinquefasciatus larvae of strain CBAM5 is 1400 cells/mL from sporulated cultures, being this isolate assigned as a high-toxicity strain .
The biotechnological application of L. sphaericus is not limited to biological control. L. sphaericus biomass has been applied in the bioremediation of heavy metals, such as cobalt, copper, chromium and lead  with specific metal binding in the cell surface . Native Colombian isolates L. sphaericus OT4b.31 and IV(4)10 showed heavy metal biosorption in living and dead biomass, both strains expressing the S-layer proteins . L. sphaericus strain CBAM5, along with other 24 native isolates, shown effective growth in arsenate, hexavalent chromium and/or lead [6, 10].
Considering that Lysinibacillus sphaericus CBAM5 is a relevant native strain, not only by its highly toxic larvicidal activity but also by its heavy metal tolerance, we have chosen this strain to analyze its genomic sequence. In this report, we present a summary classification, and set of general features for Lysinibacillus sphaericus strain CBAM5 including previously unreported aspects of its phenotype, together with the description of its genome sequence and annotation.
Lysinibacillus sphaericus is an aerobic, mesophilic, spore-forming and Gram-positive bacterium, commonly isolated from soil and water . Formerly known as Bacillus sphaericus, the species was later reassigned to the genus Lysinibacillus because of its distinctive peptidoglycan membrane composition, and physiological features [12, 13]. Lysinibacillus sphaericus strains have been classified into five DNA homology groups, where mosquito larvicidal strains were placed into DNA subgroup IIA  while the subgroup IIB was reclassified as Lysinibacillus fusiformis . Later, according to 16S rDNA and lipid profile comparisons, Lysinibacillus sphaericus strains were classified into seven similarity subgroups, of which only four retained the previous description by Krych et al. . Groups VI and VII were later reclassified as new species . Because of the phenotypic and genetic diversity summarized above, most of the groups remain designated as Lysinibacillus sphaericus sensu lato.
Classification and general features of Lysinibacillus sphaericus CBAM5 according to the MIGS recommendations 
Evidence code a
Species Lysinibacillus sphaericus
Positive in vegetative cells, variable in sporulating stages
15 – 40°C
Growth in Luria-Bertani broth (5% NaCl)
Pathogenic toward Culex quinquefasciatus larvae
Eastern Planes oil basins, Colombia
Sample collection time
350 m above sea level
Genome sequencing information
Genome project history
Genome sequencing project information
Improved high-quality draft
One paired end tags 90:90 bp with 500 bp insert
Illumina Hi-Seq 2000
CISA version 1.3, SOAPdenovo version 2.04, Velvet version 1.2.10, ABySS version 1.3.7, CLC Assembly Cell version 4.0.10
Gene calling method
Glimmer3, tRNAscan-SE, RNAmmer
Genbank Date of Release
February 1, 2014
Biotechnology, metabolic pathway
Growth conditions and DNA isolation
Lysinibacillus sphaericus strain CBAM5 was grown in nutrient broth for 16 hours at 30°C and 150 rev/min. High molecular weight DNA was isolated using the EasyDNA® Kit (Carlsbad, CA, USA. Invitrogen) as indicated by the manufacturer. DNA purity and concentration were determined in a NanoDrop spectrophotometer (Wilmington, DE, USA. Thermo Scientific).
Genome sequencing and assembly
After DNA extraction, samples were sent to the Beijing Genome Institute (BGI) Americas Laboratory (Tai Po, Hong Kong). Purified DNA sample was first sheared into smaller fragments with a desired size by a Covaris E210 ultrasonicator. Then the overhangs resulting from fragmentation were converted into blunt ends by using T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase. After adding an “A” base to the 3’ end of the blunt phosphorylated DNA fragments, adapters were ligated to the ends of the DNA fragments. The desired fragments were purified though gel-electrophoresis, then selectively enriched and amplified by PCR. The index tag was introduced into the adapter at the PCR stage as appropriate, and a library quality test was performed. Lastly, qualified, short, paired-ends of 90:90 bp length with 500 bp insert libraries were used to cluster preparation and to conduct whole-shotgun sequencing in Illumina Hi-Seq 2000 sequencers.
Using the FASTX-Toolkit version 0.6.1  and clean_reads version 0.2.3 from the ngs_backbone pipeline  reads were trimmed and quality filtered. Four preliminary assemblies were obtained by using: SOAPdenovo version 2.04 , Velvet version 1.2.10 , ABySS version 1.3.7 , and CLC Assembly Cell version 4.0.10 . Those assemblies were integrated in the CISA pipeline resulting in a consensus assembly . SOAPdenovo and CLC Assembly Cell packages included automatic scaffolding and k-mer/overlapping optimization steps. To obtain structural insight of a chromosomal scaffold, we used CONTIGuator.2 , using the Lysinibacillus sphaericus strain C3-41 chromosome (accession number: CP000817.1) as reference. Some gaps were successfully filled by using GapFiller . Gap-filling steps were applied over each one of the preliminary assemblies and over the final consensus assembly. Quality assessment of the assembly was performed with iCORN . The error rate of the final assembly is less than 1 in 1,000,000 bp. We compared the chromosomal assembly of L. sphaericus CBAM5 with the chromosome sequences of L. sphaericus C3-41 and L. sphaericus OT4b.31 by maximal unique matching of translated sequences with PROmer , and a read mapping single nucleotide polymorphism (SNP) effect analysis with SnpEff package .
The Glimmer 3 gene finder was used to identify and extract sequences for potential coding regions. To achieve the functional annotation steps, the RAST server  and Blast2GO pipelines  were used. Blast2GO performed the blasting, GO-mapping and annotation steps; which included a description according to the ProDom, FingerPRINTScan, PIR-PSD, Pfam, TIRGfam, PROSITE, ProDom, SMART, SuperFamily, Pattern, Gene3D, PANTHER, SignalIP and TM-HMM databases. The results were summarized with InterPro . Additionally, a GO-EnzymeCode mapping step was used to retrieve KEGG pathway-maps. tRNA genes were identified by using tRNAscan-SE  and rRNA genes by using RNAmmer . The possible orthologs of the genome were identified based on the COG database and classified accordingly . Prophage region prediction was also conducted by using the PHAST tool .
Summary of genome
Nucleotide content and gene count levels of the genome
% of total a
Genome size (bp)
DNA GC content (bp)
DNA coding region (bp)
Number of replicons
Genes in paralog clusters
Genes assigned to COGs
1 or more conserved domains
2 or more conserved domains
3 or more conserved domains
Genes with function prediction
Genes assigned Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with the 25 general COG functional categories
% age a
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, mitosis and meiosis
Signal transduction mechanisms
Cell wall/membrane biogénesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversión
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
The origin of replication of the chromosome of L. sphaericus CBAM5 was estimated by similarities to several features of the corresponding regions in L. sphaericus C3-41, Bacillus sp. B-14905 and other close related bacteria, including colocalization of the genes: dnaA, dnaN, dnaX, recR and recF; and GC nucleotide skew [(G–C)/(G + C)] analysis. In the contig 19 (EWH31640:EWH31645) we found a typical cluster consisting of dnaA, dnaN, recF, gyrA and gyrB boxes. The predicted genes dnaB, dnaI, dnaG, dnaE, holA, holB, priAB, polA and recA were also found spread in the chromosomal and extrachosmomal sequences. The replication termination site of the chromosomal scaffold is believed to be localized near 2.92 Mbp in the contig 14. According to GC skew analysis, the coding bias for the two strands of the chromosome is for the majority of CDSs to be on the outer strand from 0 to ~2.92 Mbp, and on the inner strand from ~2.92 Mbp to the end of the chromosomal scaffold (contig 19, Figure 2). This was also confirmed by the presence of parC (EWH32537) and parE (EWH32538), which encode the subunits of the chromosome-partitioning enzyme topoisomerase IV. Similar to previous reports [50, 51], we did not find the homolog of rtp (replication terminator protein-encoding gene) in the chromosomal assembly of CBAM5.
Lysinibacillus sphaericus CBAM5 displays 28 CDSs annotated as transposases, including three allocated in the extrachromosomal sequences. The most frequent families are IS1182, IS3 and IS4. In addition, four incomplete prophage regions were identified as follows: Thermus phage φOH2 (contig 12), Burkholderia phage ST79 (contig 14), and two regions comprising the Clostridium phage φSM101 (contigs 14 and 28). Prophage regions φOH2 and ST79 included putative encoding sequences for tail, lysis and baseplate proteins. None of the reported phages has been described in the Colombian strain L. sphaericus OT4b.31 .
The genome of L. sphaericus CBAM5 shows a wide repertoire of potential encoding sequences in terms of mosquitocidal toxins. In the contig 11, we found Mtx1 (EWH35097) and Mtx2 (EWH35034) CDSs located in an identical cluster as Hu et al.  described in the genome of L. sphaericus C3-41. This cluster includes two insertion sequences, one of them consisting of a disrupted transposase between the mtx1 and mtx2, as well. One Mtx3 CDSs (EWH32377) was found in contig 14. Upstream of this sequence, we could identify some IS3 family mobile elements and putative DeoR family transcriptional regulators. In addition, we found one hypothetical toxin from the family Mtx2 (PFam PF03318) in contig 11 (EWH35106) and a putative cereolysin O CDS (EWH31995) being described to be active against the German cockroach Blattela germanica  in contig 15.
Surface (S) layer proteins and toxic metal resistances
L. sphaericus CBAM5 exhibits 21 CDSs described as surface (S) layer proteins or S-layer homologs in its genome. The fragment covered from EWH35069 to EWH35072 includes four CDSs encoding for a variable protein, a putative S-layer associated protein, a P60 invasion-associated protein and a N-acetylmuramoyl-L-alanine amidase. Probably the genes located in this fragment may participate in the larvicidal activity of the strain CBAM5, given that the same genes have been described as differentially expressed in virulent infections of Lysteria monocytogenes . A total of 14 CDSs show three SLHs motifs near to the N terminal region, similarly to the slpC gene previously described in native strains . In addition, we found two S-layer surface array proteins in the chromosomal scaffold and another in extracromosomal sequences.
A total of 64 CDSs corresponded to encoding sequences involved in responses against toxic metal(oid)s. Among those coding sequences, we found the following operons: arsRBCDA, arsRBC, cadCA, mntABCD, nikABCDE, terD-terD-terD, zurR-znuBC, and czrA-czcD-csoR-copZA. We could identify various genes probably involved in metal(loid) resistances spread across the genome (Additional file 4: Table S2). The chrA gene seems to be the only representative of the chr operon in the genome of L. sphaericus CBAM5. Previous reports have shown that microorganisms bearing chrA homologues display highly variable resistance levels against Cr(VI) . However, two superoxide dismutase putative proteins (EWH33050, EWH30224) and several CDS ascribed as flavin reductases (EC 126.96.36.199), nitroreductases (EC 188.8.131.52) and quinone reductases (EC 184.108.40.206) could cooperate in the Cr(VI) resistance, in agreement with previous reports [55, 56].
Given the heavy metal resistance of L. sphaericus CBAM5 in polluted environments, and supported by the identification of genes in Additional file 4: Table S2, we could expect the assistance of efflux pump systems and heavy-metal resistance proteins specific to As, Sb, Ni, Zn, Cu, Cd, Te, Cr, Mn and Co. By the evaluation of coalescent models, Villegas-Torres et al.  proposed that L. sphaericus CBAM5 may have acquired the arsC gene through recent events of horizontal gene transfer as a possible adaptation to polluted environments. However, we found highly similar homologues of heavy metal resistance proteins of the CBAM5 strain in microorganisms isolated from non-polluted environments (i.e. czrA-czcD-csoR-copZA, cadCA, and arsRBC in L sphaericus OT4B.31 ). Further analysis on plasmids, prophage content, or conjugation factors may clarify the origin of resistance (as well as larvicidal) genes. Finally, based in the KEGG analysis, some predicted proteins might participate in peripheral pathways for the degradation of geraniol, chlorocyclohexane, chlorobenzene, benzoate, bisphenol, fluorobenzoate, toluene, chloroalkane, chloroalkene, naphthalene, aminobenzoate, styrene, atrazine, limonene and pinene.
Lysinibacillus sphaericus CBAM5 was isolated from drilling mineral base oil samples at the subsurface soil level. By comparing the chromosomal sequences between L. sphaericus strains CBAM5 and C3-41, we identified distinctive similarities of the DNA homology group IIA. The evidence of the binary toxins allocated in a conserved cluster delimited by mobile elements, resembles a probable phage invasion in the DNA subgroup IIA of the Lysinibacillus sphaericus species. Along with the biological control potential given by the Mtx, Bin and cerolysin toxins, L. sphaericus CBAM5 displays encoding sequences for S-layer proteins and heavy-metal efflux pumps, which may confer resistance to As, Sb, Ni, Zn, Cu, Cd, Te, Cr, Mn and Co in polluted environments.
This work was performed under the auspices of the Grant 1204-452-21129 from the Instituto Colombiano para el fomento de la Investigación Francisco José de Caldas – Colciencias, the Research Fund from the Faculty of Sciences at Universidad de los Andes, and the Centro de Investigaciones Microbiológicas (CIMIC).
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