Alcaraz et al. BMC Genomics 2010, 11:332 http://www.biomedcentral.com/1471-2164/11/332 the number of genes from COG L when compared with the B. subtilis group (replication, recombination and repair; B. coahuilensis group = 0.06/B. subtilis group = 0.06). We can hypothesize that the latter genes are needed to repair DNA that is damaged by the high radiation exposure. An over-representation of transpo- sons and IS elements may be responsible for acquiring new genes via HGT or pseudogenization and the reduc- tion of the genomes [47]. The B. subtilis-licheniformis-pumilus group has a slightly higher than average number of genes related to carbohydrate transport and metabolism (COG G; B. subtilis group = 0.08/average = 0.07) as expected for a group isolated from the soil and in close contact with plants and their products [2,9]. This group has a reduced number of genes involved in replication, recombination and repair (COG L) that correlates with the scarce repetitive elements such as IS, transposons, and transposases present in B. subtilis, B. pumilus, and other sister species [10]. Therefore, it seems that chro- mosome remodeling and genome reduction [48-50] is not a prevalent feature of B. subtilis. Interestingly, B. pumilus has a reduced number of genes involved in DNA repair and oxidative stress as well as small acid soluble proteins (SASP) that mitigate DNA damage and are involved in the desiccation and UV resistance of spores as compared to B. subtilis and close relatives [36,51]. In contrast, transcription-related genes (COG K; B. subtilis group = 0.1/average = 0.09) are slightly over-represented in the subtilis group. This suggests that the genetic response within this group is finely tuned as previously observed when the large gene families of B. subtilis and B. coahuilensis were com- pared [16]. B. clausii-halodurans form the group of alkalophiles and halotolerant strains. Interestingly, this group has fewer genes involved in the cell wall/membrane/envel- ope category (COG M; B. clausii group = 0.05/average = 0.06) than the average. This could be explained by the loss of 13 genes involved in the synthesis of tei- choic acid and the loss of 6 genes involved in teichuro- nic acid biosynthesis. In addition, there are several known differences in the cell wall composition of B. clausii-halodurans compared to B. subtilis, such as the presence of the major cell wall component teichurono- peptide [14]. The number of genes in B. clausii-halo- durans is similar to other Bacillus for the following categories: coenzyme transport and metabolism (COG H; B. clausii group = 0.03/average = 0.03), nucleotide transport and metabolism (COG F; B. clausii group = 0.03/average = 0.03), and protein turnover and chaper- ones (COG O; B. clausii group = 0.03/average = 0.03). The high number of genes from COG category G (car- bohydrate metabolism; B. clausii group = 0.09/average Page 9 of 17 = 0.07) stand out in this group. There are two possible explanations for this observation. First, Bacillus soil strains are expected to have a vast repertoire of genes for sugar assimilation, as is the case of B. subtilis [9], and B. clausii was isolated from soil [52]. Second, sugars, such as trehalose, function as osmoprotectants and therefore play an important role in halophilic bac- teria [53]. The B. clausii genome has also an unusually high number of ABC transporter permeases (N = 36) that increase the number of genes within the COG G category. A noticeably high number of replication, recombination, and repair genes (COG L; B. clausii group = 0.07/average = 0.06) are present within this group. This may be due to the high number of repeti- tive elements in B. halodurans, which posseses 112 genes similar to transposases or recombinases [14] and numerous IS sequences [10]. Therefore, these repeti- tive elements may be considered as factors important for environment specialization [54-56]. O. iheyensis and G. kaustophilus were isolated from deep sea environments (1,050 and 3,000 m depth, respectively) but have different niche specializations. O. iheyensis, isolated from sediment and adapted to extreme salinity, is a facultative alkaliphilic. In contrast, G. kaustophilus, though also isolated from sediment, is associated with a marine trench and has an optimal growth temperature of 60°C. An important shared func- tional feature of this group is the resistance to osmotic pressure of up to 30 MPa, a unique characteristic when compared to normal atmospheric pressures of 0.1 MPa [10,14]. These two genomes are small in size (~3.6 Mb; see Table 1) and have less genes for several COG including nucleotide metabolism (COG F; O. iheyensis group = 0.03/average = 0.03). The essential genes of B. subtilis, such as ymaA and ydiO, are absent in G. kaus- tophilus[10]. There are only 12 genes in category Q for each of these genomes (secondary metabolism; O. iheyensis group = 0.01/average = 0.02), which is low when compared to an average of 14-21 genes per gen- ome seen in category Q from other groups such as B. cereus. The number of genes categorized for transcrip- tion (COG K; O. iheyensis group = 0.08/average = 0.09) is also lower within this group and resembles the history of the B. coahuilensis group. The small genomes of this group and B. coahuilensis seem to be a result of genome reduction and adaptation to specific niches, such as oli- gotrophic environment, high salinity, high osmotic pres- sure, and thermal environments [47,54,56]. Conservation of genes for competence and sporulation among members of Bacillus Two post-exponential key processes have been sub- jected to extensive study for the genus Bacillus, and in particular the model system B. subtilis: genetic