Complete genome sequencing of Bacillus sp. TK-2, analysis of its cold evolution adaptability

Abstract

To date, a large number of Bacillus species from different sources have been identified. However, there are few investigations on genome information and evolutionary insights of Bacillus species from cold environments. Bacillus sp. TK-2, isolated from the soil of Changbai Mountain, is a gram-positive bacterium with cold adaptation characteristics. In this study, we present the annotated complete genome sequence of Bacillus sp. TK-2. The genome comprised 5,286,177 bp with a GC content of 35.88%, 5293 protein-encoding genes, 32 rRNA, and 77 tRNA. Numerous genes related to cold adaptation were detected in the genome of Bacillus sp. TK-2, mainly involving in energy supply, regulation of cell membrane fluidity, antioxidant, and molecular chaperones. In addition, the strain TK-2 classified in the Bacillus groups was distributed on a terminal branch with Bacillus cereus A1 by Blastn and phylogenetic analysis in NCBI database. Complete genome sequences of the strain TK-2 and Bacillus cereus A1 were compared by the online tool "Average Nucleotide Identity", showing that the average nucleotide identity of these two strains was 98.26%. In parallel, A comparative analysis of the genomes of both Bacillus sp. TK-2 and Bacillus cereus A1 was conducted. Through the analysis of core and specific genes with cd-hit, it was found that the two strains had 5691 pan gene, 4524 core gene, and 1167 specific gene clusters. Among the 624 specific gene clusters of Bacillus sp. TK-2, some cold tolerance genes were detected, which implied the unique adaptability of Bacillus sp. TK-2 in long-term low temperature environments. Importantly, enzyme-encoding genes related to the degradation of polysaccharides such as cellulose and hemicellulose were detected in the 477 CAZyme genes of this genome. This work on sequencing and bioinformatics analysis of the complete sequence of Bacillus sp. TK-2 promote the application and in-depth research of low-temperature biotechnology.

Figure 1

(a) The growth curve of the strain TK-2 at different temperatures. (b) The morphology of TK-2 on the medium. (c,d) The optical photos of the strain TK-2 under microscope and SEM.

Figure 2

(a) Genomic circle diagram of Bacillus sp. TK-2. The genome circle diagram has seven circles, from the outer circle to the inner circle, and the information displayed in each circle is the genome position, GC content, and coding gene on the positive strand. (Red), the coding gene on the negative strand (green mark), the ncRNA information on the positive strand (blue), and the ncRNA information on the negative strand (purple), which are the long-segment repetitive sequence information in the genome (orange). (b) Details of KEGG of Bacillus sp. TK-2. There are six categories, as shown on the right side of Fig. 2b, each category is divided into secondary classification system, X-axis is the number of genes, Y-axis is biological pathway Secondary classification, different colors are used to distinguish the primary classification of biological pathways.

Figure 3

(a) GO function classification of Bacillus sp. TK-2. The X-axis is the number of genes, Y-axis is GO term, and different colors are used to distinguish biological processes, cell components, and molecular functions. (b) COG functional classification of genes, the X-axis is the functional classification of COG, the Y-axis is the number of genes annotated in each classification, and the explanation of each classification is marked on the right side of (b).

Figure 4

Strategies diagram for predicting cold tolerance of Bacillus sp. TK-2.

Figure. 5

ML phylogenetic tree reconstruction containing the 16S rDNA genomes of 30 strains of bacteria. Escherichia coli was set as the outgroup.

Figure 6

(a) Venn diagram of common and unique genes analysis. (b,c) Detection and annotation of SNPindel and structure.

Figure 7

Gene distribution picture of CAZymes in Bacillus sp. TK-2.