Abstract
Bacteria closely related to Bacillus pumilus cannot be distinguished from such other species as B. safensis, B. stratosphericus, B. altitudinis and B. aerophilus simply by 16S rRNA gene sequence. In this report, 76 marine strains were subjected to phylogenetic analysis based on 7 housekeeping genes to understand the phylogeny and biogeography in comparison with other origins. A phylogenetic tree based on the 7 housekeeping genes concatenated in the order of gyrB-rpoB-pycA-pyrE-mutL-aroE-trpB was constructed and compared with trees based on the single genes. All these trees exhibited a similar topology structure with small variations. Our 79 strains were divided into 6 groups from A to F; Group A was the largest and contained 49 strains close to B. altitudinis. Additional two large groups were presented by B. safensis and B. pumilus respectively. Among the housekeeping genes, gyrB and pyrE showed comparatively better resolution power and may serve as molecular markers to distinguish these closely related strains. Furthermore, a recombinant phylogenetic tree based on the gyrB gene and containing 73 terrestrial and our isolates was constructed to detect the relationship between marine and other sources. The tree clearly showed that the bacteria of marine origin were clustered together in all the large groups. In contrast, the cluster belonging to B. safensis was mainly composed of bacteria of terrestrial origin. Interestingly, nearly all the marine isolates were at the top of the tree, indicating the possibility of the recent divergence of this bacterial group in marine environments. We conclude that B. altitudinis bacteria are the most widely spread of the B. pumilus group in marine environments. In summary, this report provides the first evidence regarding the systematic evolution of this bacterial group, and knowledge of their phylogenetic diversity will help in the understanding of their ecological role and distribution in marine environments.
Highlights
Bacillus is an important bacterial genus that consists of a heterogeneous group of aerobic or facultative anaerobic, endospore-forming, Gram-positive, rod-shaped organisms
Many Bacillus strains have recently been isolated from marine environments, with bacteria of B. pumilus being frequently reported, in addition to B. subtilis, B. licheniformis and B. cereus [17,30,31,32,33,34,35,36]
The B. altitudinis, B. pumilus and B. safensis bacteria of the B. pumilus group cannot be differentiated by their 16S rRNA gene sequences, according to the data retrieved from PubMed, the bacteria from marine environments are generally placed in the B. pumilus group
Summary
Bacillus is an important bacterial genus that consists of a heterogeneous group of aerobic or facultative anaerobic, endospore-forming, Gram-positive, rod-shaped organisms. Owing to their metabolic diversity and spore dispersal, Bacillus is ubiquitous in the environment. Phylogenetic analyses based on single or multilocus sequence typing (MLST) of housekeeping genes, such as rpoB (RNA polymerase β subunit), gyrB (gyrase B subunit), 23S rRNA, gyrA and pycA, have been used frequently for this genus [10,11] These genes can effectively differentiate the strains of the B. cereus group and the B. subtilis group [12,13,14,15]
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