Rice paddy metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB15601 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR455986_1.fastq.gz | Fastqsanger.gz | |||
| DRR455986_2.fastq.gz | Fastqsanger.gz | |||
| DRR455987_1.fastq.gz | Fastqsanger.gz | |||
| DRR455987_2.fastq.gz | Fastqsanger.gz | |||
| DRR455988_1.fastq.gz | Fastqsanger.gz |
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Project description:G. sulfurreducens (ATCC #51573) was obtained from the laboratory culture collection of Dr. Derek Lovley. Cells were grown under strict anaerobic conditions at 23 °C in batch culture. Both control and experimental populations were grown with 10mM acetate as the electron donor while Fe(III) as 55 mM ferric citrate served as the electron acceptor for the control populations and graphite anodes as the electron acceptor for the experimental populations. Controls populations were harvested at a concentration of 30 mM Fe(II). Fuel cell power output was monitored by measuring the voltage across a known resistance in the fuel cell and experimental populations were harvested when current production reached a steady state of 0.6 milliamperes. Cells were harvested at log phase by centrifugation at 4 °C and the cell pellet was flash-frozen in liquid nitrogen and then stored at -80 °C prior to RNA extraction. Three cultures of control and experimental populations were collected. Each culture vessel was harvested and extracted for total RNA separately to produce three biological replicates for this experiment. Additional information regarding the fuel cell experimental set up and culture conditions for this experiment can be found in both the current reference and the following reference: Bond DR and Lovley DR. Electricity production by Geobacter sulfurreducens attached to electrodes. 2003. Applied and Environmental Microbiology 69: 1548-1555.
2007-07-02 | E-TIGR-5001 | biostudies-arrayexpress
Project description:G. sulfurreducens (ATCC #51573) was obtained from the laboratory culture collection of Dr. Derek Lovley. Cells were grown under strict anaerobic conditions at 23 �Â�°C in batch culture. Both control and experimental populations were grown with 10mM acetate as the electron donor while Fe(III) as 55 mM ferric citrate served as the electron acceptor for the control populations and graphite anodes as the electron acceptor for the experimental populations. Controls populations were harvested at a concentration of 30 mM Fe(II). Fuel cell power output was monitored by measuring the voltage across a known resistance in the fuel cell and experimental populations were harvested when current production reached a steady state of 0.6 milliamperes. Cells were harvested at log phase by centrifugation at 4 �Â�°C and the cell pellet was flash-frozen in liquid nitrogen and then stored at -80 �Â�°C prior to RNA extraction. Three cultures of control and experimental populations were collected. Each culture vessel was harvested and extracted for total RNA separately to produce three biological replicates for this experiment. Additional information regarding the fuel cell experimental set up and culture conditions for this experiment can be found in both the current reference and the following reference: Bond DR and Lovley DR. Electricity production by Geobacter sulfurreducens attached to electrodes. 2003. Applied and Environmental Microbiology 69: 1548-1555.
2006-01-26 | E-TIGR-83 | biostudies-arrayexpress
Project description:. In this study we show successful use of SWATH-MS for quantitative proteomic analysis of a microbial electrochemically active biofilm. Shewanella oneidensis MR-1 was grown on carbon cloth electrodes under continuous anodic electrochemical polarizations in a bioelectrochemical system. Using lactate as the electron donor, anodes serving as terminal microbial electron acceptors were operated at three different electrode potentials (+0.71V, +0.21V & -0.19V vs. SHE) and the development of catalytic activity was monitored by measuring the current traces over time. Once maximum current was reached (usually within 21-29 hours) the electrochemical systems were shut off and biofilm proteins were extracted from the electrodes for proteomic assessment.
2016-08-10 | PXD001472 | Pride
Project description:The formation of electroactive biofilms is a crucial process for the generation of bioelectricity and bioremediation. G. sulfurreducens is a dissimilatory metal-reducing microorganism that can couple oxidation of organic matter with extracellular electron transfer to different insoluble electron acceptors. It has the capability to form biofilms in insoluble metal oxides and electroconductive biofilms in electrodes in bioelectrochemical systems. The formation of electroactive biofilms in this microorganism is a process that has been studied from a physiological, genetic, physical, and electrochemical approach. In G. sulfurreducens, we found that the transcriptional regulator GSU1771 participates in the gene expression of essential genes involved in electron transfer and biofilm formation. Strains deficient in GSU1771 increases Fe(III) reduction, produces more c-type cytochromes and exopolysaccharides. Furthermore, the biofilms produced are thicker and more electroactive than wild-type. In this work, we investigate the global gene expression profile performing RNA-seq comparing Δgsu1771 mutant biofilm grown in non-conductive support (glass) and respiring-graphite electrode. RNA-seq analysis of Δgsu1771 biofilm grown in glass support revealed a total of 467 (167 upregulated and 300 downregulated) differentially expressed genes versus the wild-type biofilm. Meanwhile, in Δgsu1771 biofilm developed in respiring-electrode graphite, we detect 119 (79 upregulated and 40 downregulated) differentially expressed genes with respect to wild-type biofilm. Moreover, transcriptional changes of 67 (56 with the same regulation and in 11 counterregulation) genes were shared in Δgsu1771 biofilm developed in glass and graphite electrodes. We locate upregulated in Δgsu1771 biofilms potential target genes, involved in exopolysaccharide synthesis (gsu1961-63, gsu1959, gsu1972-73, gsu1976-77). We confirmed the upregulation of gsu1979, gsu0972, gsu0783, pgcA, omcM, aroG, panC gnfK, gsu2507, and the downregulation of asnA, ato-1, gsu0810, pilA, csrA, ppcD, and gsu3356 genes by RT-qPCR. DNA-protein binding assay shows direct binding of the GSU1771 regulator to the promoter region of pgcA, pulF, relA, and gsu3356. Also, heme-staining and western blotting revealed an increase of c-type cytochromes in Δgsu1771 biofilms such as OmcS and OmcZ. In general, our data shows that GSU1771 is a global regulator involved in controlling the extracellular electron transfer and exopolysaccharide synthesis, processes required for electroconductive biofilm development.
2023-06-19 | GSE223184 | GEO
Project description:There is a wide diversity of potential applications for direct electron transfer from electrodes to microorganisms, which might be better optimized if the mechanisms for this novel electrode-biofilm interaction were further understood. Geobacter sulfurreducens is one of the few microorganisms available in pure culture that is known to be capable of directly accepting electrons from a negatively poised electrode. Gene transcript abundance in cells of G. sulfurreducens using electrons delivered from a graphite electrode as the sole electron donor for fumarate reduction was compared with transcript abundance in cells growing on the same graphite material, but without an electrical connection and acetate as the electron donor.
2010-11-23 | GSE19149 | GEO
Project description: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. The present study constructed an MR-1 mutant, cyaC-OE that overexpressed cyaC, a gene encoding a membrane-bound class III adenylate cyclase, and examined its electrochemical and transcriptomic characteristics. We show that intracellular cAMP concentration in cyaC-OE is more than double that in wild-type MR-1, and cya-OE generates approximately two-fold higher current in BES than the wild type. In addition, the expression of genes involved in EET and anaerobic carbon catabolism is up-regulated in cya-OE as compared to that in the wild type. These results suggest that enhancement of the intracellular cAMP level is a promising approach for constructing an EAB with high catabolic and electrochemical activities.
2019-11-01 | GSE129679 | GEO
Project description:Bioaugmentation of microbial fuel cells with Geobacter sulfurreducens strain 60473 for boosting power outputs from food wastes
| PRJDB19628 | ENA
Project description:Metagenomic analysis of microbes attached to fuel cell electrodes
| PRJEB19676 | ENA
Project description:Desulfovibrio ferrophilus IS5 was incubated on indium-tin oxide (ITO) electrodes poised at −0.4 V and −0.5 V (versus standard hydrogen electrode) in H-type reactors for 10 days. Total RNA was extracted from cells after incubation, and RNA fragments were purified and transcribed into cDNA. cDNA was sequenced by NovaSeq 6000 System.
2020-08-11 | GSE133931 | GEO
Project description:Desulfovibrio vulgaris Hildenoborough was incubated in an H-type electrochemical reactor for 7 days on an indium-tin doped oxide electrode poised at −0.2 V (versus standard hydrogen electrode), which served as the sole electron donor. As a negative open circuit (without electrode) control, cells were incubated in a glass vial in the absence of an electrode. Total RNA was extracted from cells after incubation, and RNA fragments were purified and transcribed into cDNA. cDNA was sequenced by NovaSeq 6000 System.
2023-08-04 | GSE155721 | GEO