Shewanella decolorationis S12
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA271261 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1735720_1.fastq.gz | Fastqsanger.gz | |||
| SRR1735720_2.fastq.gz | Fastqsanger.gz | |||
| SRR1735721_1.fastq.gz | Fastqsanger.gz | |||
| SRR1735721_2.fastq.gz | Fastqsanger.gz | |||
| SRR1735722_1.fastq.gz | Fastqsanger.gz |
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Project description: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. Our results revealed that filamentous shift (the cells stretched to fiber-like shapes as long as 18 μm) occurred under amaranth stress. Persistent stress led to higher filamentous cell rate and decolorization ability in subcultural cells compared with parental strains. Additionally, the expression of genes involved in cell division, chemotaxi system, energy conservation, damage repair, and material transport in filamentous cells were significantly stimulated. The detailed roles of some genes with significantly elevated expressions in filamentous cells were identified by site-directed mutagenesis, such as the outer membrane porin genes ompA and ompW, the cytochrome C genes arpC and arpD, the global regulatory factor gene rpoS and methyl-accepting chemotaxis proteins genes SHD_2793 and SHD_0015. Finally, a conceptual model was proposed to help deepen our insights into both the bacterial survival strategy when toxic organics were present, and the mechanisms in which these toxic organics were biodegraded as the extracellular electron acceptors.
2019-06-18 | GSE64532 | GEO
Project description:Shewanella decolorationis S12 Genome sequencing and assembly
| PRJNA210345 | ENA
Project description: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. decolorationis S12 were significantly changed in 120 min during the ZVI-enhanced microbial azo reduction. Intriguingly, MarR transcriptional factor might play a vital role in regulating ZVI-enhanced azo reduction in the aspect of energy production, iron homeostasis, and detoxification. Further investigation showed that induced [Ni-Fe] H2ase genes (hyaABCDEF) and azoreductase genes (mtrABC-omcA) contributed to ZVI-enhanced energy production, while reduced iron uptake (hmuVCB and feoAB), induced sulfate assimilation (cysPTWA) and cysteine biosynthesis (cysM) related genes were essential to iron homeostasis and detoxification. This study disentangles underlying mechanisms of ZVI-enhanced azo reduction in S. decolorationis S12 and lays a foundation for further optimization of integrated ZVI-microbial system for efficient organic pollution treatment.
2021-10-01 | GSE160493 | GEO
Project description:De novo sequencing and analysis for Strain NBRC 103170 of Shewanella decolorationis
| PRJDB10354 | ENA
Project description:Shewanella decolorationis strain:4 | isolate:4 Genome sequencing
| PRJNA939925 | ENA
Project description:Electron acceptor redox potential (EARP) was presumed to be a determining factor for microbial metabolism in many natural and engineered processes. However, little is known about the potentially global effects of EARP on bacteria. In this study, we compared the physiological and transcriptomic properties of Shewanella decolorationis S12 respiring with different EARPs in microbial electrochemical systems to avoid the effects caused by the other physicochemical properties of real electron acceptor. Results showed that the metabolic activities of strain S12 were nonlinear responses to EARP. The tricarboxylic acid cycle for central carbon metabolism was down-regulated while glyoxylate shunt was up-regulated at 0.8 V compared to 0.2 and -0.2 V, which suggested that EARP is an important but not the only determinant for metabolic pathways of strain S12. Moreover, few cytochrome c genes were differentially expressed at different EARPs. The energy intensive flagella assembly and assimilatory sulfur metabolism pathways were significantly enriched at 0.8 V, which suggested strain S12 had stronger electrokinesis behavior and oxidative stress-response at high EARP. This study provides the first global information of EARP regulations on microbial metabolism, which will be helpful for understanding microorganism respiration.
| S-EPMC4977559 | biostudies-literature
Project description:Bacterial extracellular electron transfer (EET) plays a key role in various natural and engineering processes. Outer membrane c-type cytochromes (OMCs) are considered to be essential in bacterial EET. However, most bacteria do not have OMCs but have redox proteins other than OMCs in their extracellular polymeric substances of biofilms. We hypothesized that these extracellular non-cytochrome c proteins (ENCP) could contribute to EET, especially with the facilitation of electron mediators. This study compared the electrode respiring capacity of wild type Shewanella decolorationis S12 and an OMC-deficient mutant. Although the OMC-deficient mutant was incapable in direct electricity generation in normal cultivation, it regained electricity generation capacity (26% of the wide type) with the aid of extracellular electron mediator (riboflavin). Further bioelectrochemistry and X-ray photoelectron spectroscopy analysis suggested that the ENCP, such as proteins with Fe-S cluster, may participate in the falvin-mediated EET. The results highlighted an important and direct role of the ENCP, generated by either electricigens or other microbes, in natural microbial EET process with the facilitation of electron mediators.
| S-EPMC5476703 | biostudies-literature
Project description:Molecular mechanism of zero valent iron-enhanced microbial azo reduction in Shewanella decolorationis S12
| PRJNA673394 | ENA
Project description:Viability is a common issue of concern in almost all microbial processes. Fluorescence-based assays are extensively used in microbial viability assessment, especially for mixed-species samples or biofilms. Propidium iodide (PI) is the most frequently used fluorescence indicator for cell viability based on the membrane permeability. Our results showed that the accumulation of succinate from fumarate respiration could induce PI-permeability in Shewanella decolorationis biofilm cells. Confocal laser scanning microscope further showed that the PI-permeable membrane could be repaired in situ when the extracellular succinate was eliminated by switching fumarate respiration to electrode respiration. Simultaneously with the membrane repair, the electrode respiring capacity of the originally PI-permeable cells was recovered. Agar-colony counts suggested that a major portion of the repaired cells were viable but nonculturable (VBNC). The results evidenced that S. decolorationis S12 has the capacity to repair PI-permeable membranes which suggests a reevaluation of the fate and function of the PI-permeable bacteria and expanded our knowledge on the flexibility of bacterial survival status in harsh environments.
| S-EPMC4685271 | biostudies-literature