Complete Genome Sequence of High Current-Producing Geobacter sulfurreducens Strain YM35, Isolated from River Sediment in Japan.
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ABSTRACT:
SUBMITTER: Fujikawa T
PROVIDER: S-EPMC8375489 | biostudies-literature |
REPOSITORIES: biostudies-literature
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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 better 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. A microarray comparison of cells accepting electrons from the electrode versus cells donating electrons to the electrode reveals that the genes previously observed to be upregulated in current-producing biofilms are not highly expressed in current-consuming biofilms.
2010-11-23 | GSE19150 | GEO
Project description:Microbial fuel cells (MFCs) are a class of ideal technologies that function via anaerobic respiration of electricigens, which bring current generation and environmental restoration together. An in-depth understanding of microbial metabolism is of great importance in engineering microbes to further improve their respiration. We employed flux balance analysis and selected Fe(iii) as a substitute for the electrode to simulate current-generating metabolism of Geobacter sulfurreducens PCA with a fixed acetate uptake rate. Simulation results indicated the fluxes of reactions directing acetate towards dissimilation to generate electrons increased under the suboptimal growth condition, resulting in an increase in the respiration rate and a decrease in the growth rate. The results revealed the competitive relationship between oxidative respiration and cell growth during the metabolism of microbe current generation. The results helped us quantitatively understand why microbes growing slowly have the potential to make good use of fuel in MFCs. At the same time, slow growth does not necessarily result in speedy respiration. Alternative respirations may exist under the same growth state due to redundant pathways in the metabolic network. The big difference between the maximum and minimum respiration mainly results from the total formate secretion. With iterative flux variability analysis, a relatively ideal model of variant of G. sulfurreducens PCA was reconstructed by deleting several enzymes in the wild model, which could reach simultaneous suboptimal growth and maximum respiration. Under this ideal condition, flux towards extracellular electron transfer rather than for biosynthesis is beneficial for the conversion of organic matter to electricity without large accumulations of biomass and electricigens may maximize utilization of limited fuel. Our simulations will provide an insight into the enhanced current-generating mechanism and identify theoretical range of respiration rates for guiding strain improvement in MFCs.
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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:State-of-the-art DNA sequencing technologies are transforming the life sciences due to their ability to generate nucleotide sequence information with a speed and quantity that is unapproachable with traditional Sanger sequencing. Genome sequencing is a principal application of this technology, where the ultimate goal is the full and complete sequence of the organism of interest. Due to the nature of the raw data produced by these technologies, a full genomic sequence attained without the aid of Sanger sequencing has yet to be demonstrated.We have successfully developed a four-phase strategy for using only next-generation sequencing technologies (Illumina and 454) to assemble a complete microbial genome de novo. We applied this approach to completely assemble the 3.7 Mb genome of a rare Geobacter variant (KN400) that is capable of unprecedented current production at an electrode. Two key components of our strategy enabled us to achieve this result. First, we integrated the two data types early in the process to maximally leverage their complementary characteristics. And second, we used the output of different short read assembly programs in such a way so as to leverage the complementary nature of their different underlying algorithms or of their different implementations of the same underlying algorithm.The significance of our result is that it demonstrates a general approach for maximizing the efficiency and success of genome assembly projects as new sequencing technologies and new assembly algorithms are introduced. The general approach is a meta strategy, wherein sequencing data are integrated as early as possible and in particular ways and wherein multiple assembly algorithms are judiciously applied such that the deficiencies in one are complemented by another.
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Project description:Gene expression in a Geobacter sulfurreducens strain overexpressing the two-component system GsuTCS1
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Project description:Previous studies have suggested that the conductive pili of Geobacter sulfurreducens are essential for extracellular electron transfer to Fe(III) oxides and for optimal long-range electron transport through current-producing biofilms. The KN400 strain of G. sulfurreducens reduces poorly crystalline Fe(III) oxide more rapidly than the more extensively studied DL-1 strain. Deletion of the gene encoding PilA, the structural pilin protein, in strain KN400 inhibited Fe(III) oxide reduction. However, low rates of Fe(III) reduction were detected after extended incubation (>30 days) in the presence of Fe(III) oxide. After seven consecutive transfers, the PilA-deficient strain adapted to reduce Fe(III) oxide as fast as the wild type. Microarray, whole-genome resequencing, proteomic, and gene deletion studies indicated that this adaptation was associated with the production of larger amounts of the c-type cytochrome PgcA, which was released into the culture medium. It is proposed that the extracellular cytochrome acts as an electron shuttle, promoting electron transfer from the outer cell surface to Fe(III) oxides. The adapted PilA-deficient strain competed well with the wild-type strain when both were grown together on Fe(III) oxide. However, when 50% of the culture medium was replaced with fresh medium every 3 days, the wild-type strain outcompeted the adapted strain. A possible explanation for this is that the necessity to produce additional PgcA, to replace the PgcA being continually removed, put the adapted strain at a competitive disadvantage, similar to the apparent selection against electron shuttle-producing Fe(III) reducers in many anaerobic soils and sediments. Despite increased extracellular cytochrome production, the adapted PilA-deficient strain produced low levels of current, consistent with the concept that long-range electron transport through G. sulfurreducens biofilms is more effective via pili.
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Project description:Sphingobium sp. strain YG1 is a lignin model dimer-metabolizing bacterium newly isolated from sediment in Kagoshima, Japan, at a depth of 102 m. Here, we report the complete genome nucleotide sequence of strain YG1.
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Project description:Biomineralization of Cu has been shown to control contaminant dynamics and transport in soils. However, very little is known about the role that subsurface microorganisms may play in the biogeochemical cycling of Cu. In this study, we investigate the bioreduction of Cu(II) by the subsurface metal-reducing bacterium Geobacter sulfurreducens Rapid removal of Cu from solution was observed in cell suspensions of G. sulfurreducens when Cu(II) was supplied, while transmission electron microscopy (TEM) analyses showed the formation of electron-dense nanoparticles associated with the cell surface. Energy-dispersive X-ray spectroscopy (EDX) point analysis and EDX spectrum image maps revealed that the nanoparticles are rich in both Cu and S. This finding was confirmed by X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analyses, which identified the nanoparticles as Cu2S. Biomineralization of CuxS nanoparticles in soils has been reported to enhance the colloidal transport of a number of contaminants, including Pb, Cd, and Hg. However, formation of these CuxS nanoparticles has only been observed under sulfate-reducing conditions and could not be repeated using isolates of implicated organisms. As G. sulfurreducens is unable to respire sulfate, and no reducible sulfur was supplied to the cells, these data suggest a novel mechanism for the biomineralization of Cu2S under anoxic conditions. The implications of these findings for the biogeochemical cycling of Cu and other metals as well as the green production of Cu catalysts are discussed.IMPORTANCE Dissimilatory metal-reducing bacteria are ubiquitous in soils and aquifers and are known to utilize a wide range of metals as terminal electron acceptors. These transformations play an important role in the biogeochemical cycling of metals in pristine and contaminated environments and can be harnessed for bioremediation and metal bioprocessing purposes. However, relatively little is known about their interactions with Cu. As a trace element that becomes toxic in excess, Cu can adversely affect soil biota and fertility. In addition, biomineralization of Cu nanoparticles has been reported to enhance the mobilization of other toxic metals. Here, we demonstrate that when supplied with acetate under anoxic conditions, the model metal-reducing bacterium Geobacter sulfurreducens can transform soluble Cu(II) to Cu2S nanoparticles. This study provides new insights into Cu biomineralization by microorganisms and suggests that contaminant mobilization enhanced by Cu biomineralization could be facilitated by Geobacter species and related organisms.
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