Bacillus safensisFO-36b andBacillus pumilusSAFR-032: A Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates

Abstract

BackgroundBacillus 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 spore resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, as well as draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. In addition, comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis.ResultsThe FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains [1]. 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 either MERTA or ATCC7061T. The FO-36b genome was found to have ten unique reading frames and two phage-like regions, which have homology with the Bacillus bacteriophage SPP1 (NC_004166) and Brevibacillus phage Jimmer1 (NC_029104). Differing remnants of the Jimmer1 phage are found in essentially all safensis/pumilus strains. Seven unique genes are part of these phage elements. Comparison of gyrA sequences from FO-36b, SAFR-032, ATCC7061T, and 61 other draft genomes separate the various strains into three distinct clusters. Two of these are subgroups of B. pumilus while the other houses all the B. safensis strains.ConclusionsIt 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 change the level of expression 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. The larger comparison of multiple strains indicates that many strains named as B. pumilus actually belong to the B. safensis group.