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

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

PROVIDER: PRJNA736403 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14766648.fastq.gz	Fastqsanger.gz
	SRR14766649.fastq.gz	Fastqsanger.gz
	SRR14766650.fastq.gz	Fastqsanger.gz
	SRR14766651.fastq.gz	Fastqsanger.gz
	SRR14766652.fastq.gz	Fastqsanger.gz

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Similar Datasets

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

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

Transcriptome comparison of wild type Azoarcus sp. strain BH72 grown under nitrogen fixation (experiment) with cells grown with combined nitrogen (ammonia) as nitrogen source

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.

2013-08-01 | GSE49394 | GEO

Transcriptome comparison of wild type Azoarcus sp. strain BH72 grown under nitrogen fixation (experiment) with cells grown with combined nitrogen (ammonia) as nitrogen source

2013-08-01 | E-GEOD-49394 | biostudies-arrayexpress

Azoarcus olearius

Project description:Azoarcus olearius overview

| PRJNA657318 | ENA

Transcriptome comparison of the wild type strain Azoarcus sp. BH72 with that of nifLA knockout strain under nitrogen fixing condition

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.

2013-08-15 | GSE49912 | GEO

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

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 .

2014-09-13 | GSE61387 | 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

Transcriptome comparison of the wild type strain Azoarcus sp. BH72 with that of nifLA knockout strain under nitrogen fixing condition

2013-08-15 | E-GEOD-49912 | biostudies-arrayexpress

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

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