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Comparative Study
. 2018 Jun 8;18(1):57.
doi: 10.1186/s12866-018-1191-y.

Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates

Madhan R Tirumalai  1 , Victor G Stepanov  1 , Andrea Wünsche  1 , Saied Montazari  1 , Racquel O Gonzalez  1 , Kasturi Venkateswaran  2 , George E Fox  3
Affiliations
Comparative Study

Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates

Madhan R Tirumalai et al. BMC Microbiol. .

Abstract

Background: Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis.

Results: The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results.

Conclusions: It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism's resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group.

Keywords: Bacillus endospores; Extreme radiation resistance; Genome comparison; Peroxide resistance; Phage insertions; Planetary protection.

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Figures

Fig. 1
Fig. 1
The Bacillus bacteriophage SPP1 (NC_004166) homologous region in the B. safensis FO-36b genome, as compared with the equivalent genomic regions of B. pumilus ATCC7061T, B. pumilus SAFR-032 and B .subtilis subsp. subtilis str. 168. The locus tag numbers are given inside the boxes/rectangles. Red diamonds denote absence of a single gene/homolog. Red rectangle denotes absence of a series/cluster of ORFs/genes. Green box encloses the phage insertion region. Green diamond denotes absence of a single gene/homolog within the phage. “hyd” = hydrolase, “chp” = conserved hypothetical protein, “pept” = peptidase, “hp” = hypothetical protein, “TR” = transcriptional regulator, “Ps” = pseudogene, “lp” = lipoprotein, “gsp” = group specific protein, “oxi” = oxidase
Fig. 2
Fig. 2
The Bacillus bacteriophage SPP1 (NC_004166) homologous region in the B. safensis FO-36b genome, as compared with the equivalent genomic region of B. safensis JPL_MERTA8–2. Red diamonds denote absence of a single gene/homolog. Red rectangle denotes absence of a series/cluster of ORFs/genes. Green box encloses the phage insertion region
Fig. 3
Fig. 3
Overall scheme of the Brevibacillus phage Jimmer1 (NC_029104) phage insertion in the B. safensis FO-36b genome. The three blocks A, B and C and the genes they encompass are shown. The first part of Block C is a duplication of Block A
Fig. 4
Fig. 4
The Brevibacillus phage Jimmer1 (NC_029104) phage insertion in the B. safensis FO-36b genome as compared with the equivalent region in the genome of B. pumilus ATCC7061T. Black box encloses the phage insertion region(s). Green (dashed line) box corresponds to block A. Green (dotted line) box corresponds to block B. Blue (dashed line) box corresponds to block C. Red (dashed line) box encloses ‘terminase’ genes. A diamond denotes absence of a single gene/homolog within the phage, while rectangle denotes absence of a cluster of genes/homologs. “hp” = hypothetical protein, “chp” = conserved hypothetical protein, “pp” = phage portal protein, “sp” = structural protein, “sgp” = spore germination protein, “int” = integrase
Fig. 5
Fig. 5
The Brevibacillus phage Jimmer1 (NC_029104) phage insertion in the B. safensis FO-36b genome as compared with the equivalent region in the genome of B. safensis JPL_MERTA8–2. “hp” = hypothetical protein, “chp” = conserved hypothetical protein, “pp” = phage portal protein, “sp” = structural protein, “sgp” = spore germination protein, “int” = integrase
Fig. 6
Fig. 6
The Brevibacillus phage Jimmer1 (NC_029104) phage insertion in the B. safensis FO-36b genome as compared with the equivalent region in the genome of B. pumilus SAFR-032. “hp” = hypothetical protein, “chp” = conserved hypothetical protein, “pp” = phage portal protein, “sp” = structural protein, “sgp” = spore germination protein, “int” = integrase.
Fig. 7
Fig. 7
The Brevibacillus phage Jimmer1 (NC_029104) phage insertion in the B. safensis FO-36b genome as compared with the equivalent region in the genome of B. subtilis. “hp” = hypothetical protein, “chp” = conserved hypothetical protein, “pp” = phage portal protein, “sp” = structural protein,“sgp” = spore germination protein, “int” = integrase
Fig. 8
Fig. 8
Whole genome Phylogenetic Analysis (WGPA) using the latest version of the Genome-BLAST Distance Phylogeny (GBDP). B. safensis FO-36b, B. safensis JPL_MERTA8–2B, B. pumilus SAFR-032, and B. pumilus ATCC7061T are highlighted in red dash-lined rectangles
Fig. 9
Fig. 9
Molecular Phylogenetic analysis by the Maximum Likelihood method. B. safensis FO-36b, B. safensis JPL_MERTA8–2B, B. pumilus SAFR-032, and B. pumilus ATCC7061T are highlighted in red dash-lined rectangles
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