GEO DataSets

(Submitter supplied) To investigate how cell elongation impacts extracellular electron transfer (EET) of electroactive microorganisms (EAMs), the division of model EAM Shewanella oneidensis MR-1 was engineered by reducing the formation of cell divisome. Specially, by blocking the translation of division proteins via anti-sense RNAs or expressing division inhibitors, the cellular length and output power density were all increased. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33796

12 Samples

Download data: XLSX

(Submitter supplied) Shewanella oneidensis MR-1 is a facultative anaerobe that grows by respiration using a variety of electron acceptors. This organism serves as a model to study how bacteria thrive in redox-stratified environments. A glucose-utilizing engineered derivative of MR-1 has been reported to be unable to grow in glucose minimal medium (GMM) in the absence of electron acceptors, despite this strain having a complete set of genes for reconstructing glucose to lactate fermentative pathways. more...

Organism:

Shewanella oneidensis; Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL27952

8 Samples

Download data: TXT

(Submitter supplied) Purpose : Identification of the regulons directly and indirectly affected by the main regulators of flagellation in Shewanella putrefaciens CN-32 Methods : mRNA profiles were generated for Shewanella putrefaciens CN-32 samples by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . more...

Organism:

Shewanella putrefaciens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32422

8 Samples

Download data: XLSX

(Submitter supplied) Here, we established a successive Fe0-enhanced microbe system to remove azo dye (a typical organic pollutant) by Shewanella decolorationis S12 (S. decolorationis S12, an effective azo dye degradation bacterium) and examined the gene expression time course (10, 30, 60, and 120 min) in whole genome transcriptional level. Comparing with the treatment without ZVI, approximately 8% genes affiliated with 10 different gene expression profiles in S. more...

Organism:

Shewanella decolorationis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29324

24 Samples

Download data: TXT

(Submitter supplied) Transcriptomic analysis used to understand the influence of elevated intracellular cyclic-di-GMP in Shewanella oneidensis on expression of c-type cytochrome at transcript level.

Organism:

Shewanella oneidensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24121

12 Samples

Download data: XLSX

(Submitter supplied) Shewanella spp. possess a broad respiratory versatility, which contributes to the occupation of hypoxic/anoxic environmental or host-associated niches. Here we observed a strain-specific induction of biofilm formation in response to supplementation with the anaerobic electron acceptors dimethyl sulfoxide (DMSO) and nitrate in a panel of Shewanella algae isolates. The respiration-driven biofilm response is not observed in DMSO and nitrate reductase deletion mutants of the type strain S. more...

Organism:

Shewanella algae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26874

9 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Shewanella oneidensis; Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL27952

16 Samples

Download data: TXT

(Submitter supplied) Shewanella oneidensis MR-1 was grown on electrodes in electrochemical flow cells (EFC), and the transcriptome profiles of electrode-attached MR-1 cells were compared under electrolyte-flow and static (non-flow) conditions. The results revealed that the SO_3096 gene encoding a putative extracytoplasmic function (ECF) sigma factor, as well as genes related to cyclic-di-guanosine monophosphate and flagella synthesis (e.g., SO_3556 and flrC) and c-type cytochrome maturation (dsbD), was significantly up-regulated under the electrolyte-flow condition. more...

Organism:

Shewanella oneidensis; Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL27952

8 Samples

Download data: TXT

(Submitter supplied) Shewanella oneidensis MR-1 was grown on electrodes in electrochemical flow cells (EFC), and the transcriptome profiles of electrode-attached MR-1 cells were compared under electrolyte-flow and static (non-flow) conditions. The results revealed that the SO_3096 gene encoding a putative extracytoplasmic function (ECF) sigma factor, as well as genes related to cyclic-di-guanosine monophosphate and flagella synthesis (e.g., SO_3556 and flrC) and c-type cytochrome maturation (dsbD), was significantly up-regulated under the electrolyte-flow condition. more...

Organism:

Shewanella oneidensis; Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL27952

8 Samples

Download data: TXT

(Submitter supplied) In this work we analyzed changes in gene espression in Shewanella baltica upon cold stress. In order to imitate natural environment, we cultured bacteria in the Instant Ocean medium in a chemostat. Samples were collected after 90 and 180 minutes of cold stress and analyzed by RNA sequencing. The transcriptomic response could be characterized as global downregulation of gene expression (613 genes downregulated) and we found only 242 genes which were upregulated. more...

Organism:

Shewanella baltica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28560

5 Samples

Download data: TXT, WIG

(Submitter supplied) Purpose: The goals of this study are to find out the differential expression genes in the fadR mutant strain(ΔfadR) compared with wild-type (WT) and to further explore the regulation mechanisms of fadR. Methods: Shewanella oneidensis MR-1 WT and ΔfadR were collected in log phage(OD~0.6). RNA extraction was performed using the RNeasy minikit (Qiagen) and the RNA was quantified by using a NanoVue spectrophotometer (GE Healthcare). more...

Organism:

Shewanella oneidensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26851

2 Samples

Download data: XLS

(Submitter supplied) Electrochemically active bacteria (EAB) are capable of electrochemical interactions with electrodes via extracellular electron transfer (EET) pathways and serve as essential components in bioelectrochemical systems. Previous studies have suggested that EAB, such as Shewanella oneidensis MR-1, use cyclic AMP (cAMP) receptor proteins for coordinately regulating the expression of catabolic and EET-related genes, allowing us to hypothesize that the intracellular cAMP concentration is an important factor determining electrochemical activities of EAB. more...

Organism:

Shewanella oneidensis; Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL17650

8 Samples

Download data: TXT

(Submitter supplied) Bacterial anaerobic respiration using extracellular electron acceptor plays a predominant role in global biogeochemical cycles. However, the bacterial adaptive mechanisms to the toxic organic pollutant as the extracellular electron acceptor during anaerobic respiration is not clear, which limits us to optimize the strategies for the bioremediation of contaminated environment. Here, we report the physiological characteristics and the global gene expression of an ecologically successful bacterium Shewanella decolorationis S12 when using a typical toxic organic pollutant, amaranth, as the extracellular electron acceptor. more...

Organism:

Shewanella decolorationis S12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19591

6 Samples

Download data: TXT

(Submitter supplied) CGH of 46 Shewanella baltica strains using customized oligonucleotide microarrays

Organism:

Shewanella baltica

Type:

Genome variation profiling by array

Platform:

GPL23607

46 Samples

Download data: GPR, TXT

(Submitter supplied) Shewanella algae C6G3 can conduct dissimilative nitrate reduction into ammonium and MnIV reduction. This bacteria have the unusual ability to produce anaerobically nitrite from ammonium in the presence of MnIV. This property may explain NO2/3- accumulation observed in some anaerobic zones of marine sediments. To gain insight into their metabolic capabilities, global mRNA expression patterns were investigated by RNA-seq and qRT-PCR in cells growing with lactate and ammonium as carbon and nitrogen sources and with MnIV or nitrate as electron acceptors. more...

Organism:

Shewanella algae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24512

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Electrochemically active bacteria (EAB) receive considerable attention for their utility in bioelectrochemical processes. Although electrode potentials are known to affect the metabolic activity of EAB, it is unclear whether EAB are able to sense and respond to electrode potentials. Here, we show that, in the presence of a high-potential electrode, a model EAB Shewanella oneidensis MR-1 can utilize NADH-dependent catabolic pathways and a background formate-dependent pathway to achieve high growth yield. more...

Organism:

Shewanella oneidensis; Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL17650

22 Samples

Download data: TXT

(Submitter supplied) Cyclic 3',5'-adenosine monophosphate (cAMP) phosphodiesterase (CPD) is an enzyme that catalyzes the hydrolysis of cAMP, a signaling molecule affecting diverse cellular and metabolic processes in bacteria. Some CPDs are also known to function in cAMP-independent manners, while their physiological roles remain largely unknown. Here, we investigated physiological roles of CPD in Shewanella oneidensis MR-1, a model environmental bacterium, and report that CPD is involved in amino-acid metabolism. more...

Organism:

Shewanella oneidensis MR-1; Shewanella oneidensis

Type:

Expression profiling by array

Platform:

GPL17650

8 Samples

Download data: TXT

(Submitter supplied) Study of the roles played by Fur and RyhB in Shewanella oneidensis

Organism:

Shewanella oneidensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24121

15 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of Shewanella OS185 and OS195 strains grown under aerobic, anaerobic thiosulfate and nitrate respiratory conditions.

Organism:

Shewanella baltica

Type:

Expression profiling by array

Platform:

GPL23607

18 Samples

Download data: GPR

(Submitter supplied) Purpose: The goal is to investigate how to enhance the adaptability of deep-sea bacterium Shewanella piezotolerans WP3 to low temperature and high pressure by experimental evolution with H2O2 stress

Organism:

Shewanella piezotolerans WP3

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17267

6 Samples

Download data: TXT