Figure 1.
Graphical representation of genomic features of B. amyloliquefaciens subsp. plantarum UCMB5113.
Circles display (from the outside): (1) Sites of genome plasticity. (2) Predicted CDSs transcribed in the clockwise direction. (3) Predicted CDSs transcribed in the counterclockwise direction. (4) rRNA (blue), tRNA (orange), non-coding RNA (green), and NRPS/PKS gene clusters (grey). (5,6,7) Blast comparison of UCMB5113 genome with type strain FZB42T and B. subtilis 168, respectively. (8) GC percent deviation (GC window - mean GC) in a 1000-bp window. (9) GC skew (G+C/G-C) in a 1000-bp window.
Figure 2.
Functional classification of protein-coding genes in UCMB5113.
Distibution of UCMB5113 coding sequences (93.6%) in COG functional classes. Genes that did not have any inferred COG annotation were assigned to category X.
Figure 3.
Numbers of shared and genome-specific genes.
The Venn Diagram shows the number of shared and genome-specific genes in B. amyloliquefaciens subsp. plantarum UCMB5113, B. amyloliquefaciens subsp. plantarum FZB42T, B. subtilis 168, B. amyloliquefaciens subsp. amyloliquefaciens DSM7T and B. pumilus SAFR-032.
Figure 4.
Neighbour-joining phylogenetic tree.
The position of B. amyloliquefaciens strain UCMB5113 in relation to other species within the genus Bacillus. The numbers above the branches are support values obtained from 1,000 bootstrap replicates.
Table 1.
Comparison of genomic features of B. amyloliquefaciens subsp. plantarum UCMB5113 with genomes of other Bacillus spp. belonging to the B. subtilis group.
Figure 5.
B. amyloliquefaciens UCMB5113 related activity on different substrates.
A branch pattern with massive groups of bacteria observed after 4 days of incubation period indicated swarming motility; bright pink color indicated the hydrolysis of urea to carbon dioxide and ammonia; siderophore biosynthetic cluster produced a clear zone on CAS agar; chitin degradation and utilization as carbon source; expressed hemolytic activity on blood agar; phosphate solubilization around bacteria apparent as a transparent zone; amylase activity on starch medium; aqueous drop collapse to assess production of biosurfactants.
Figure 6.
Blast comparison of NRPS/PKS clusters in UCMB5113 (above) and FZB42T(below).
Arrows indicate gene clusters; Macrolactin (light green), Bacilllaene (purple), BacillomycinD (orange), Difficidin (blue), Bacillibactin (turquoise), Surfactin (green), Bacilysin (grey), Fengycin (pink). Genes highlighted in red represent the differences where as black represent other genes flanking in each cluster.
Table 2.
NRPS and PKS gene clusters involved in synthesis of secondary metabolites in B. amyloliquefaciens.
Table 3.
Fermentation of sugars by UCMB5113 analyzed using API strips.
Figure 7.
Plant growth promotion by UCMB5113 on Arabidopsis thaliana Col-0.
(A). Plants grown on MS agar and treated with UCMB5113 display bigger leaves and increased root branching. (B) Plants grown on soil and treated with UCMB5113 have bigger leaves compared to control plants. The experiment was performed at least three times, and similar results were obtained in each case.
Figure 8.
Genomic overview of the similarity between completely sequenced B. amyloliquefaciens strains.
(A) Genomic comparison map of plant-associated B. amyloliquefaciens subsp. plantarum strains. The grey blocks indicate similarity and sequence conservation whereas gaps between the blocks show differences in genomic content between genomes. The rainbow color bar shows synteny between genomes. (B) Comparison of the plant growth promoting strain UCMB5113 (as representative of plantarum species) with non plant-associated subsp. amyloliquefaciens strains. Vertical bars (black and red) on the top show the location of plantarum group specific genes in UCMB5113, whereas red dots indicate nine of the selected plantarum-specific genes that were shown to be expressed (Figure S2).