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Adaption of Dinoroseobacter shibae to anaerobic conditions

ABSTRACT: To unravel the adaptation strategies of D. shibae to anaerobic conditions in microaerobic to anaerobic parts of the ocean and to define the underlying regulatory network an anaerobic shift experiment in Salt-Water-Medium in a chemostate was established. Transcriptome analyses were used to investigate the physiological status of D. shibae under this conditions.

ORGANISM(S): Dinoroseobacter shibae DFL 12 = DSM 16493 Dinoroseobacter shibae

PROVIDER: GSE47445 | GEO | 2013/08/30

SECONDARY ACCESSION(S): PRJNA205826

REPOSITORIES: GEO

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Adaption of Dinoroseobacter shibae to anaerobic conditions

Project description:To unravel the adaptation strategies of D. shibae to anaerobic conditions in microaerobic to anaerobic parts of the ocean and to define the underlying regulatory network an anaerobic shift experiment in Salt-Water-Medium in a chemostate was established. Transcriptome analyses were used to investigate the physiological status of D. shibae under this conditions. Dinoroseobacter shibae wild type strain DSM 16493T was grown in a chemostate in saltwater mininmal medium (SWM) mimicking the conditions in the marine habitat under anaerobic conditions. For growth under oxygen depletion the media were supplemented with 50 mM KNO3 to sustain anaerobic respiration. Therefore, D. shibae was grown aerobically in the chemostate until the culture reached the exponential phase, than countinuously cultivaion was started. The dilution rate was 0.1 h-1, establishing the approximate half-maximum growth rate of D. shibae in the exponential phase. The anaerobic shift was initialised after 20 hours by stopping the aeration. The samples were harvested before (as reference) and 30 minutes after stopping the airation. Three biological replica were analyzed. Comparison: Identification of genes induced or repressed under aerobic conditions in the Dinoroseobacter shibae wild type strain DSM 16493T. Here we compared the transcriptome profile of D. shibae wild type strain DSM 16493T grown aerobically in the chemostate in exponential phase with the transcriptome profile of the D. shibae wild type strain DSM 16493T which was grown without aeration for 5, 10, 15, 20, 30, 60 and 120 min.

2013-08-30 | E-GEOD-47445 | biostudies-arrayexpress

Dinoroseobacter shibae

Project description:Adaption of Dinoroseobacter shibae to anaerobic conditions

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Biogenesis and DNA cargo of Dinoroseobacter shibae outer membrane vesicles suggests vesicle formation is coupled to replication

Project description:The Gram-negative photoheterotrophic bacterium Dinoroseobacter shibae is a member of the high abundant marine Roseobacter group. In the ocean, OMVs have about the same abundance as bacteria, a distinct depth distribution, and contain DNA from a variety of marine bacterial taxa. In the present study, we determined the abundance, size, and ultrastructure of membrane vesicles of D. shibae and analysed the protein inventory of the soluble and membrane fractions of cells and vesicles in order to study the origin of OMV membranes and content. The proteomic analyses were complemented by fatty acid analyses.

2020-12-16 | PXD014351 | Pride

Adaptation of Dinoroseobacter shibae to different kinds of oxidative stress

Project description:The Gram-negative photoheterotrophic bacterium Dinoroseobacter shibae is a member of the high abundant marine Roseobacter group. Living in the photic zone environment of marine ecosystems D. shibae is frequently exposed to oxygen. Oxic environments are hazardous and therefore effective defense mechanisms are required. In the present study, the adaptation of D. shibae to different kinds of oxidative stresses was investigated. Hydrogen peroxide, diamide and paraquat were used as agents to trigger peroxide, thiol and superoxide stress. To define and compare the peroxide, superoxide and thiol stress stimulons in D. shibae, GeLC-MS/MS based proteomic data of cytosolic and surface associated proteins were used. Furthermore, a strain deficient in the rhizobial iron regulator (RirA) was used to study the global impact of RirA on peroxide dependent protein expression.

2021-03-12 | PXD013791 | Pride

Transcriptome of Dinoroseobacter shibae under changeing light regimes

Project description:D. shibae was cultivated under changing light regimes and samples for transcriptome and metabolome were taken.

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Heme coordination and nitric oxide binding by Dnr regulators are essential for adaptation of Dinoroseobacter shibae to anaerobiosis

Project description:The adaptation strategies and regulatory networks behind the adaptation of D. shibae DFL12T to nitrosative stress under anaerobic starvation was investigated. Furthermore, the role of the oxygen sensing regulator FnrL and the heme coordinating regulators DnrD and DnrF were determined under nitrosative stress conditions. Therefore transcriptional analyses were performed using regulator knock out strains.

2017-03-03 | GSE95560 | GEO

Dinoroseobacter shibae strain:DFL12

Project description:Dinoroseobacter shibae strain:DFL12 Raw sequence reads

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Transcriptomic analysis of Dinoroseobacter shibae DFL12T in response to phage infection

Project description:Dinoroseobacter shibae DFL12T was cultured with/without phage R2C, and gene expression was analyzed at 60 min and 140 min during the incubation

2018-01-20 | GSE109415 | GEO

Effect of changing light regimes on Dinoroseobacter shibae DFL12 growth

Project description:This SuperSeries is composed of the following subset Series: GSE25579: Time series analysis of the transition from dark to light growth of Dinoroseobacter shibae DFL12 GSE25581: Time series analysis of the transition from light to dark growth of Dinoroseobacter shibae DFL12 Refer to individual Series

2010-12-03 | E-GEOD-25591 | biostudies-arrayexpress

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