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Rice roots: Non-colonized (sterile) control vs. colonized with Azoarcus olearius BH72

ABSTRACT: Rice roots: Non-colonized (sterile) control vs. colonized with Azoarcus olearius BH72

PROVIDER: PRJNA563164 | ENA |

REPOSITORIES: ENA

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Rice roots: Non-colonized (sterile) control vs. colonized with Azoarcus olearius BH72

Project description:Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post inoculation with Azoarcus olearius BH72, the goal is to understand the transcriptomic response of rice roots to colonization by bacterial endophyte

2019-09-01 | GSE136707 | GEO

The RNA-seq analysis of rice roots colonized by the endophytic bacterium Azoarcus olearius BH72 after one-, three- and seven-days post inoculation and after three days of boosted colonization.

Project description:Purpose: Transcriptional profiling of Oryza sativa japonica Nipponbare roots after one, three and seven days post inoculation with Azoarcus olearius BH72 (vs. non-inoculated controls) to understand the changes in transcriptomic response of rice roots to colonization by bacterial endophyte at initial stages of interaction; Additional set-up was included in which bacterial growth was boosted (through increasing 20-times carbon source - malic acid in the plant's hydroponic medium) to study rice roots transcriptome during enhanced colonization by the endophyte after three days post inoculation. Methods: Rice root mRNA profiles after one day, three days (including additional set-ups for boosted colonization), and seven days post inoculation with Azoarcus olearius BH72 and corresponding non-inoculated controls were generated by RNA sequencing, in triplicates, using Illumina NextSeq 500. Raw reads were then filtered, trimmed (PHRED > 33) and mapped onto IRGSP-1 version of Oryza sativa ssp. japonica cv. Nipponbare genome using CLC Genomics Workbench 8.5.1 (Qiagen, Germany). Expression of 17 selected genes was confirmed via RT-qPCR. Results: Using the RNA-Seq technology we obtained transcriptomic data from 24 sequencing libraries, with an average 46,181,160 clean reads per library, of which 87% or more were mapped onto the Oryza sativa ssp. japonica cv. Nipponbare IRGSP-1.0 genome (Fig. S3). We considered genes as differentially regulated (DEG) that exhibited at least 1.5-fold-change in expression level between Azo-colonized and non-colonized roots and FDR<0.05. Conclusions: Bacteria appeared to short-circuit the initial root defense responses for a compatible interaction during endophytic establishment, involving previously unknown putative rice candidate genes.

2021-09-01 | GSE174616 | GEO

Azoarcus olearius

Project description:Azoarcus olearius overview

| PRJNA657318 | ENA

Azoarcus olearius strain:dqs4

Project description:Azoarcus olearius strain:dqs4 Genome sequencing

| PRJNA280719 | ENA

RNA-Seq provides new insights into the nitrogen response of Azoarcus olearius BH72 during N2-fixation beyond the nitrogen fixation process

Project description:Azoarcus olearius BH72 is a diazotrophic endophyte carrying out biological nitrogen fixation (BNF) and supplying nitrogen to its host plant. Our previous microarray approach provided insights in the transcriptome of strain BH72 under N2-fixation in comparison to ammonium-grown conditions, which already indicated induction of genes not related to the BNF process. Due to the known limitations of the technique, we might have missed additional differentially regulated genes (DEGs). Thus we used directional RNA-Seq to better comprehend the transcriptional landscape under these growth conditions. RNA-Seq detected almost 24 % of the annotated genes to be regulated, twice the amount identified by microarray. In addition to confirming entire regulated operons containing known DEGs, the new approach detected induction of genes involved in carbon metabolism and flagellar and twitching motility. On the other hand, genes encoding for proteins involved in translation and vitamin biosynthesis were detected to be suppressed. Nonetheless, strain BH72 appears not to be content with N2-fixation but is primed for alternative economic N-sources, such as nitrate, urea or amino acids: we detected strong induction of machineries for uptake and assimilation.

2021-09-06 | GSE176473 | GEO

A novel repressor for expression of a type 6 protein secretion system links nitrogen signaling with beneficial plant-microbe interactions

Project description:To investigate the regulon of the novel transcriptional regulator TssR discovered in our study We then performed gene expression profiling analysis using data obtained from RNA-seq of wild type Azoarcus olearius sp. BH72 and tssR deleted mutant cultured under microaerobic conditions with additional ammonium

2022-09-01 | GSE211258 | GEO

Azoarcus olearius

Project description:Transcriptome profile of wild type Azoarcus sp. BH72 grown under microaerobic condition (0.3% oxygen) compared with that grown under aerobic condition (21% oxygen), both in presence of combined nitrogen source, respectively

| PRJNA260930 | ENA

Characterization of cell density-regulated gene expression of the grass endophyte Azoarcus sp. BH72

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.

2011-12-01 | GSE25939 | GEO

The RNA-seq analysis of rice roots colonized by the endophytic bacterium Azoarcus olearius BH72 after one-, three- and seven-days post inoculation and after three days of boosted colonization.

Project description:The RNA-seq analysis of rice roots colonized by the endophytic bacterium Azoarcus olearius BH72 after one-, three- and seven-days post inoculation and after three days of boosted colonization.

| PRJNA730797 | ENA

Characterization of cell density-regulated gene expression of the grass endophyte Azoarcus sp. BH72

2011-12-01 | E-GEOD-25939 | biostudies-arrayexpress