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 investigated whether root exudates of the host might play a role in initiating the endophyte-rice interaction. The whole genome microarray approach was used 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. Azoarcus sp. strain BH72 was grown in the presence or absence of root exudates of Oryza sativa cv. Nipponbare for two different time points, and differences in the gene expression profile were monitored. RNA from cells grown on synthetic medium for 1 and 4 hours respectively in presence (experiment) and absence (control) of exudates was used for two color whole genome microarray approach.
Project description:Azoarcus sp. BH72 is able to communicate via cell density-dependent gene regulation. Here, the impact of cell-free conditioned culture supernatants, obtained from stationary phase Azoarcus wild type cultures, on gene expression was investigated determining changes in transcript profiles when early exponential aerobic cultures were incubated with cell-free culture supernatants for one and four hours. Bacterial communication via quorum sensing (QS) is involved in the regulation of several cellular mechanisms such as metabolic processes, microbe-host interactions or biofilm formation. The nitrogen-fixing model endophyte of grasses Azoarcus sp. strain BH72 shows density-dependent gene regulation in the absence of common hydrophobic autoinducers for pilA encoding the structural protein of type IV pili that are essential for plant colonization. Here, we used a transcriptomic approach to identify target genes differentially regulated under QS conditions in conditioned supernatants in comparison to standard growth conditions. Analysis used RNA from the early exponential growth phase as control samples for comparison to the quorum-sensing condition samples taken at one hour and four hours after incubation with cell-free culture supernatants.
Project description:Root exudates play an important role in plant-microbe interaction. The transcriptional profilings of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 in response to maize root exudates under static condition, were investigated by an Illumina RNA-seq for understanding the regulatory roles of the root exudates. 4 treatments, including 2 blank control (24 h and 48 h-post inoculation, named as 5 and 15, respectively), and 2 treatments with maize root exudates (24 h and 48 h-post inoculation, named as 7 and 17, respectively)
Project description:Low oxygen tensions are often encountered in flooded soils of rice fields by root-associated, strictly respiratory, beta proteobacterium, Azoarcus sp. BH72 which fixes nitrogen only under microaerobic condition. In this study, genome wide oligonucleotide microarrays were used compare the global transcription profile of Azoarcus sp. BH72 under microaerobic condition with cells grown under aerobic condition, both with ammonia as sole nitrogen source. The outcome of this study will provide a better insight about the establishment of this endophyte in the microaerobic environment, probably prevailing inside of the rice root niche . RNA from cells grown under microaerobic condition with 0.3% oxygen (experiment) and aerobic condition with 21% oxygen (control), respectively was used for two color whole genome microarray approach.
Project description:Insect pathogenic fungus Beauveria bassiana in one of the best studied insect biocontrol fungus, which infects insects by cuticle penetration. After breaking the cuticles, the fungus will propagate in insect hemocoel and kill insect hosts. It has also been found that the mycelia of B. bassiana can penetrate plant tissues to reach insect inside plant, e.g. corn borer (Ostrinia furnacalis), but do not cause damage to plants. The mechanism of fungal physiological plasticity is poorly understood. To accompany our genome sequencing work of B. bassiana strain ARSEF 2860, fungal transcriptional responses to different niches were studied using an Illumina RNA_seq technique. To examine fungal response to insect cuticle, conidia were inoculated on locust hind wings for 24 hours before used for RNA extraction. To evaluate fungal adaptation to insect hemocole, the fifth instar larvae of cotton bollworms were injected with spore suspension and fungal cells isolated by centrifugation in a step gradient buffer. To unveil the mechanism of interaction with plants, the fungus was grown in corn root exudates for 24 hours. After RNA sequencing, around three million tags were acquired for each sample and fungal transcriptional profiles were compared. Unveiling gene differential expression patterns when the insect biocontrol fungus Beauveria bassiana grown in insect hemocoel, corn root exudates and on insect cuticles.
Project description:We analysed the transcriptomic response of 3 rhizobial symbionts of Mimosa pudica (Rhizobium mesoamericanum STM3625, Cupriavidus taiwanensis LMG19424 and Burkholderia phymatum STM815) when cultivated in a minimum culture medium (control condition) versus induced by root exudates of their host plant Mimosa pudica. We used RNAseq using illumina technology.
Project description:Azoarcus sp. BH72 is known to express nitrogenase genes endophytically in rice seedlings in gnotobiotic culture. Availability of fixed nitrogen is one of the important signals regulating the transcription of nitrogenase genes and hence nitrogen fixing activity. NifA is the essential transcription activator of nif genes. RNA isolated from the nifA knockout mutant of strain BH72 was compared with the transcriptome of wild type under nitrogen fixing condition using a global genome wide microarray approach and the differences in the gene expression profile were monitered. RNA isolated from wild type strain BH72 and nifLA mutant strain BHLAO grown respectively under microaerobic nitrogen fixing condition with glutamate as poor nitrogen source was used for two color whole genome microarray approach
Project description:Transcription profiles of Bacillus amyloliquefacs FZB42 (cultured to an optical densit of 1.0 or 3.0) in response to root exudates from nutrient-sufficient maize plants and plants starved of nitrogen, phosphorus, potassium or iron.
Project description:Model endophyte Azoarcus sp. BH72 is known to contribute fixed nitrogen to its host Kallar grass by nitrogen fixation and also expresses nitrogenase genes endophytically in rice seedlings in gnotobiotic culture. Availability of fixed nitrogen is one of the important signals regulating the transcription of nitrogenase genes and hence nitrogen fixing activity. Therefore, we analysed global transcription in response to differences in the nitrogen source. Transcription profiles of cells grown microaerobically (0.6% oxygen) on minimal medium with nitrogen (N2-fixing) versus ammonium (combined nitrogen) were compared using a genome-wide microarray approach and differences in the gene expression profile were monitored. RNA from cells grown on nitrogen-free synthetic medium under nitrogen fixation (experiment) and combined nitrogen source as ammonium chloride (control) was used for two-color whole-genome microarray approach.
Project description:Although proteins and peptides encoded in small open reading frames (ORFs < 100 AA) in microbial genomes can play critical roles as toxins, bacteriocins, transcriptional regulators, signaling molecules, and chaperones, many such ORFs remain annotated as “hypothetical proteins”. In the genome of the hyperthermophilic bacterium, Thermotoga maritima, nearly 2/3 of the 167 small ORFs have no known function. As a strategy for investigating the potential significance of specific small ORFs, growth conditions that could trigger the expression of genes encoding small ORFs were sought. A defined medium supplemented with either 1 or 5 g/L yeast extract was used to track transcriptional response during the transition from exponential to stationary phase. RNA derived from exponential (1E) and stationary (1S) phase cultures grown on 1 g/l yeast extract was compared to RNA derived from exponential (5E) and stationary (5S) phase cultures grown on 5 g/l yeast extract using a four-slide loop design.