Figure 1.
. Neighbour-joining tree based on 16S rRNA gene sequences showing the relationship of Micromonospora species and other members of the family Micromonosporaceae. Strains isolated from plant related sources are indicated by a green arrow.
Figure 2.
Circular representation of Micromonospora lupini Lupac 08.
Circles displayed from the outside in: 1. Cellulose-binding genes in black, chitin-binding genes in red, lectin genes in lavender blue; 2. Genome coordinates; 3. MW; 4. GC% (linear range between 65 and 80%); 5. Regions of genome plasticity according to the RGP_Finder method (Mage platform) based on synteny breaks between the query genome (Lupac 08) and close genomes (Micromonospora aurantiaca ATCC 27029T, Micromonospora sp. L5 and Verrucosispora maris AB-18-032T) correlated with HGT features (tRNA hotspot, DNA repeats, mobility genes), and compositional bias and GC deviation computation. C1 to C15 indicate the position of the 15 clusters of genes coding for secondary metabolites of Table 4.
Table 1.
Comparative genomic characteristics of M. lupini Lupac 08 and three Micromonospora genomes publicly available.
Figure 3.
MAUVE alignment of the genome sequences of Micromonospora lupini Lupac 08, Micromonospora sp. L5, Micromonospora aurantiaca ATCC 27029T and Micromonospora sp. ATCC 39149.
When boxes have the same colour, this indicates syntenic regions. Boxes below the horizontal line indicate inverted regions. Rearrangements are shown by coloured lines. Scale is in nucleotides.
Figure 4.
Venn diagram showing the number of clusters of orthologous genes, shared and unique, between M. lupini Lupac 08, Micromonospora sp. L5 and M. aurantiaca ATCC 27029T.
Figure 5.
Bicluster plot of the metabolic profiles of M lupini Lupac 08 and 20 other bacterial genomes.
Table 2.
Transporters identified in the genome of M. lupini Lupac 08 and comparison with other bacteria with a plant/soil associated life styles.
Table 3.
Secretion system genes present in the genome of M. lupini Lupac 08.
Figure 6.
Expression of cellulose, starch, xylan and chitin degrading genes in Micromonospora lupini Lupac 08.
(A) carboxymetheylcellulose hydrolysis at 4 (left) and 14 (right) days after inoculation. (B), starch hydrolysis at 4 days after inoculation. (C), chitin degradation at 7 days after inoculation. (D), xylan degradation at 4 (left) and 14 (right) days after inoculation.
Figure 7.
Plant growth promotion and biological control features of M. lupini Lupac 08.
(A) Siderophore, (B) indole-3-acetic acid [a, negative control E. coli DH5α; b, Lupac 08] and pectinase production (D) by M. lupini strain Lupac 08;. (C) Plant growth promoting effect of M. lupini Lupac 08 on clover plantlets. a) control; b) inoculated with Rhizobium sp. E11; c) co-inoculated with Rhizobium sp. E11 and M. lupini Lupac 08.
Table 4.
Comparison of secondary metabolite clusters found in the genome of M. lupini Lupac 08 and other related microorganisms.