Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics

Abstract

Background: The presence of Bacillus in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus evolutionary relationships. By distinguishing between core and pan-genome, we determined the evolutionary and functional relationships of known Bacillus.

Results: Our analysis is based upon twenty complete and draft Bacillus genomes, including a newly sequenced Bacillus isolate from an aquatic environment that we report for the first time here. Using a core genome, we were able to determine the phylogeny of known Bacilli, including aquatic strains whose position in the phylogenetic tree could not be unambiguously determined in the past. Using the pan-genome from the sequenced Bacillus, we identified functional differences, such as carbohydrate utilization and genes involved in signal transduction, which distinguished the taxonomic groups. We also assessed the genetic architecture of the defining traits of Bacillus, such as sporulation and competence, and showed that less than one third of the B. subtilis genes are conserved across other Bacilli. Most variation was shown to occur in genes that are needed to respond to environmental cues, suggesting that Bacilli have genetically specialized to allow for the occupation of diverse habitats and niches.

Conclusions: The aquatic Bacilli are defined here for the first time as a group through the phylogenetic analysis of 814 genes that comprise the core genome. Our data distinguished between genomic components, especially core vs. pan-genome to provide insight into phylogeny and function that would otherwise be difficult to achieve. A phylogeny may mask the diversity of functions, which we tried to uncover in our approach. The diversity of sporulation and competence genes across the Bacilli was unexpected based on previous studies of the B. subtilis model alone. The challenge of uncovering the novelties and variations among genes of the non-subtilis groups still remains. This task will be best accomplished by directing efforts toward understanding phylogenetic groups with similar ecological niches.

Figure 1

Overview of this work.

Figure 2

Phylogenetic reconstruction for Bacillus. A. Concatenated 814 translated genes of the core genome maximum likelihood (ML) phylogeny. Bootstrap values are shown. B. Genome Similarity Score (GSS) distance matrix plotted as a Neighbor-Joining tree. C. ML phylogeny using 16S rRNA. C. Concatenated 20 Conserved Universal Cogs (uCOGs) ML phylogeny. Note how inner groups are well defined and supported only in the core genome phylogeny (A) and how the GSS distance (B) resembles the inner groups described in the core's genome phylogeny.

Figure 3

Heat map comparison of the core genome, pan-genome, and Bacillus groups conservancy of COGs. Normalized Cluster of Orthologous Groups (COGs) frequencies within each group are shown as a two way clustering; interestingly the clustering supports the groups formed in the core genome phylogeny (horizontal axis). In vertical axis COGs are grouped according to their abundance showing moderate conserved COGs in the top, low frequency conserved COGs in the central clusters and highly abundant COGs cluster in the lower clusters. In the bottom total numbers of proteins families mapped to COG within each row are shown.

Figure 4

Bacillus selected sporulation and competence genes conservancy. In this heat map shows the presence/absence of the set of 185 sporulation and competence related genes according to KEGG's BRITE hierarchies http://www.genome.jp/kegg/brite.html. Each column stands for a Bacillus strain and each row represents a gene and here are shown present (in gray) or absent genes (in black). Is possible to distinguish between 4 major clusters according to the conservancy level of the genes, (A) the first upper cluster stands for the sporulation core genes; (B) second is a group of sporulation genes diminished mostly in the extremophile and aquatic species of Bacillus; (C) cluster is defined as genes present in almost all the strains of B. subtilis' related group but depleted in the B. cereus' group; and (D) are B. subtilis' specialized sporulation genes. A comprensive list of each cluster of genes is available in Additional file 2: Table S3. Figure Abbreviations: B. subtilis (bsu), B. pumilus(bpu), B. licheniformis ATCC 14580 (bli), B. licheniformis DSM13 (bld), B. halodurans (bha), O. iheyensis (oih), B. coahuilensis (bcoa), B. clausii (bcl), Bacillus sp. m3-13 (M3.13), G. kaustophilus (gka), Bacillus sp.NRRLB-14911 (b14911), B. cereusATCC 14579 (bce), B. weihenstephanensis (bwe), B. thuringiensis Al Hakam (btl), B. thuringiensis97-27 (btk), B. cereus ZK (bcz), B. cereus ATCC 10987 (bca), B. anthracis Sterne (bat), B. anthracis Ames (ban), B. anthracis Ames 0581 (bar).