Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyte Azoarcus sp. strain BH72

Abstract

Endophytic colonization is a very complex process which is not yet completely understood. Molecules exuded by the plants may act as signals which influence the ability of the microbe to colonize the host or survive in the rhizosphere. Here we used the whole genome microarray approach to investigate the response of the diazotrophic model endophyte, Azoarcus sp. strain BH72, to exudates of O. sativa cv. Nipponbare in order to identify differentially regulated genes. On exposure to exudates, an overall expression of 4.4% of the 3992 protein coding genes of Azoarcus sp. strain BH72 was altered, out of which 2.4% was upregulated and 2.0% was downregulated. Genes with modulated expression included a few whose involvement in plant-microbe interaction had already been established, whereas a large fraction comprised of genes encoding proteins with putative or unknown functions. Mutational analysis of several differentially regulated genes like those encoding a minor pilin PilX, signal transduction proteins containing GGDEF domains and a serine-threonine kinase as a putative component of the type IV secretion system (T6SS), revealed their role in host colonization. Our data suggest that strain BH72 may be primed for the endophytic lifestyle by exudates, as the expression of bacterial genes relevant for endophytic colonization of roots is induced by root exudates.

Grapevine colonization by endophytic bacteria shifts secondary metabolism and suggests activation of defense pathways

“…Some studies show changes on the transcriptomic profiles in the bacterial partner during endophytic colonization (Hauberg-Lotte et al 2012;Shidore et al 2012) but only few works have focused on metabolic plant responses. For example colonization by diazotrophic bacteria and formation of nitrogen fixing structures show variation in transcriptomic profiles (Boscari et al 2013) hinting at a possible role of the metabolic constituents of the plant as drivers of endophytic symbiosis.…”

Plant-Influenced Gene Expression in the Rice Endophyte Burkholderia kururiensis M130

“…This result is in agreement with observations from transcriptome and proteomic analysis of other bacteria growing in the presence of root exudates and plant extracts. In these reports, a major change in the expression of genes related to different aspects of metabolism such as aromatic compound catabolism, energy generation, and amino acid biosynthesis and metabolism was observed (Cordeiro et al 2013;Mark et al 2005;Shidore et al 2012). In addition, differential expression of several loci encoding for families of transporter proteins have also been observed, indicating that several molecules (e.g., aromatic compounds and toxic plant metabolites) are most probably transported inside or outside bacteria when they grow in planta.…”

“…Mutations in the T6SS of the potato pathogen Pectobacterium atrosepticum led to increased virulence (Mattinen et al 2008), whereas T6SS mutations in the endophyte Azoarcus sp. strain BH72 resulted in enhanced colonization of rice plants (Shidore et al 2012). Similarly, inactivation of T6SS of Rhizobium leguminosarum enabled a strain that is normally not able to form functional nodules on pea to infect pea plants and fix nitrogen (Bladergroen et al 2003).…”

“…strain BH72 to rice root exudate. These experiments revealed that 4.4% of the total protein-coding genes of the strain were differentially regulated in the presence of the exudate, including genes for pilin, signal transduction, and type IV secretion (Shidore et al 2012). This work suggests that plant exudates may be an important switch for the endophytic lifestyle of these bacteria.…”

“…This work suggests that plant exudates may be an important switch for the endophytic lifestyle of these bacteria. Although this and a few other studies were able to identify genes differentially regulated in the rhizosphere or in the presence of plant root exudates (dos Santos et al 2010;Mark et al 2005;Rediers et al 2003;Shidore et al 2012), our knowledge of bacterial gene regulation occurring inside the plant is very limited. Cordeiro and coworkers (2013) performed proteomics experiments with endophytic Herbaspirillum seropedicae cultivated in the presence or absence of sugar cane extract (total plant macerate) and revealed a few proteins that might be differentially expressed inside the plant.…”