Genome Features of the Endophytic Actinobacterium Micromonospora lupini Strain Lupac 08: On the Process of Adaptation to an Endophytic Life Style?

Abstract

Endophytic microorganisms live inside plants for at least part of their life cycle. According to their life strategies, bacterial endophytes can be classified as “obligate” or “facultative”. Reports that members of the genus Micromonospora, Gram-positive Actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestrial to a facultative endophytic life. The aim of this work was to analyse the genome sequence of Micromonospora lupini Lupac 08 isolated from a nitrogen fixing nodule of the legume Lupinus angustifolius and to identify genomic traits that provide information on this new plant-microbe interaction. The genome of M. lupini contains a diverse array of genes that may help its survival in soil or in plant tissues, while the high number of putative plant degrading enzyme genes identified is quite surprising since this bacterium is not considered a plant-pathogen. Functionality of several of these genes was demonstrated in vitro, showing that Lupac 08 degraded carboxymethylcellulose, starch and xylan. In addition, the production of chitinases detected in vitro, indicates that strain Lupac 08 may also confer protection to the plant. Micromonospora species appears as new candidates in plant-microbe interactions with an important potential in agriculture and biotechnology. The current data strongly suggests that a beneficial effect is produced on the host-plant.

Taxonomy, Physiology, and Natural Products of Actinobacteria

“…Further, analysis of the genome of M. lupini Lupac 08 revealed a diverse array of genes that may help the bacterium to survive in the soil or in plant tissues. However, despite having many genes that encode putative plant material-degrading enzymes, this bacterium is not regarded as a plant pathogen (79). In addition, genome comparisons showed that M. lupini Lupac 08 is metabolically closely related to Frankia sp.…”

Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity

“…The use of the reverse complementary probe of EUB338 (NONEUB) as a negative control (19, figure 3g), (63, figure 4a) is not helpful in this respect because plant organelles are not targeted by this sense probe. Also, the absence of CARD-FISH signals in microbe-free, axenically grown plants after hybridization with EUB338 (19, supplementary figure 17) is problematic as a negative control because there is ample evidence that plant-associated microbes have the capacity to structurally modify plant tissues, e.g., by cell wall loosening (14,103,106), which would impact probe penetration.…”

Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer

“…The number of rRNAs and tRNAs in the LU2 strain is comparable with that of other strains listed in Table 1 and may indicate positive selection. A large number of rRNA genes is associated with a high activity of the translational apparatus, which in turn increases both the protein synthesis rate and the growth rate 19 . This phenomenon may be connected with strong competition among microorganisms located in the same ecological niche.…”