Abstract
Plant root secreted compounds alter the gene expression of associated microorganisms by acting as signal molecules that either stimulate or repel the interaction with beneficial or harmful species, respectively. However, it is still unclear whether two distinct groups of beneficial bacteria, non-plant-associated (soil) strains and plant-associated (endophytic) strains, respond uniformly or variably to the exposure with root exudates. Therefore, Bacillus mycoides, a potential biocontrol agent and plant growth-promoting bacterium, was isolated from the endosphere of potatoes and from soil of the same geographical region. Confocal fluorescence microscopy of plants inoculated with GFP-tagged B. mycoides strains showed that the endosphere isolate EC18 had a stronger plant colonization ability and competed more successfully for the colonization sites than the soil isolate SB8. To dissect these phenotypic differences, the genomes of the two strains were sequenced and the transcriptome response to potato root exudates was compared. The global transcriptome profiles evidenced that the endophytic isolate responded more pronounced than the soil-derived isolate and a higher number of significant differentially expressed genes were detected. Both isolates responded with the alteration of expression of an overlapping set of genes, which had previously been reported to be involved in plant–microbe interactions; including organic substance metabolism, oxidative reduction, and transmembrane transport. Notably, several genes were specifically upregulated in the endosphere isolate EC18, while being oppositely downregulated in the soil isolate SB8. These genes mainly encoded membrane proteins, transcriptional regulators or were involved in amino acid metabolism and biosynthesis. By contrast, several genes upregulated in the soil isolate SB8 and downregulated in the endosphere isolate EC18 were related to sugar transport, which might coincide with the different nutrient availability in the two environments. Altogether, the presented transcriptome profiles provide highly improved insights into the life strategies of plant-associated endophytes and soil isolates of B. mycoides.
Highlights
The rhizosphere harbors an enormous pool of soil microorganisms and is considered as the ‘hot spot’ for microbial colonization and activity (Prashar et al, 2013)
In order to compare the rhizosphere competence of the B. mycoides EC18 cells expressing green fluorescent protein (GFP) (Figure 1A) and of the SB8 cells expressing red fluorescent protein (RFP) (Figure 1B), a 1:1 mixture of the strains was inoculated into the hydroponic plant interaction model, and strain competition experiments were performed (Figure 1C)
Endophytic bacteria have emerged as a valuable source of biocontrol agents and metabolites, which has great potential in sustainable agricultural application
Summary
The rhizosphere harbors an enormous pool of soil microorganisms and is considered as the ‘hot spot’ for microbial colonization and activity (Prashar et al, 2013). Some of the rhizobacteria even have the capacity of multiplying inside roots and begin an endophytic lifestyle (Hardoim et al, 2008). Rhizobacteria and plants naturally interact in various ways. Beneficial plant–microbial interactions in the rhizosphere can result in the promotion of plant health and development (Mark et al, 2005). A number of plant growth-promoting rhizobacteria (PGPR) have been commercially used as adjuncts to agricultural practice and show great promise (Glick, 2012). The mechanisms of PGPR and plant root interaction have drawn considerable attention (Kuiper et al, 2004; Santos et al, 2014; Pangesti et al, 2015). Only a few studies on plants and their interaction with endophytic bacteria have been reported so far
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