| genome of geobacter sulfurreducens: metal reduction in subsurface environments. | the complete genome sequence of geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. these characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface ... | 2003 | 14671304 |
| functional genome annotation through phylogenomic mapping. | accurate determination of functional interactions among proteins at the genome level remains a challenge for genomic research. here we introduce a genome-scale approach to functional protein annotation--phylogenomic mapping--that requires only sequence data, can be applied equally well to both finished and unfinished genomes, and can be extended beyond single genomes to annotate multiple genomes simultaneously. we have developed and applied it to more than 200 sequenced bacterial genomes. protei ... | 2005 | 15940241 |
| ancient lateral gene transfer in the evolution of bdellovibrio bacteriovorus. | the recently sequenced genome of the predatory delta-proteobacterium bdellovibrio bacteriovorus provides many insights into its metabolism and evolution. because its genes are reasonably uniform in g+c content, it was suggested that b. bacteriovorus actively resists recombination with foreign dna and horizontal transfer of dna from other bacteria. to investigate this further, we carried out a variety of phylogenetic and comparative genomics analyses using data from >200 microbial genomes, includ ... | 2006 | 16413191 |
| heme biosynthesis in methanosarcina barkeri via a pathway involving two methylation reactions. | the methanogenic archaeon methanosarcina barkeri synthesizes protoheme via precorrin-2, which is formed from uroporphyrinogen iii in two consecutive methylation reactions utilizing s-adenosyl-l-methionine. the existence of this pathway, previously exclusively found in the sulfate-reducing delta-proteobacterium desulfovibrio vulgaris, was demonstrated for m. barkeri via the incorporation of two methyl groups from methionine into protoheme. | 2006 | 17028275 |
| the mosaic genome of anaeromyxobacter dehalogenans strain 2cp-c suggests an aerobic common ancestor to the delta-proteobacteria. | anaeromyxobacter dehalogenans strain 2cp-c is a versaphilic delta-proteobacterium distributed throughout many diverse soil and sediment environments. 16s rrna gene phylogenetic analysis groups a. dehalogenans together with the myxobacteria, which have distinguishing characteristics including strictly aerobic metabolism, sporulation, fruiting body formation, and surface motility. analysis of the 5.01 mb strain 2cp-c genome substantiated that this organism is a myxobacterium but shares genotypic t ... | 2008 | 18461135 |
| diversity of promoter elements in a geobacter sulfurreducens mutant adapted to disruption in electron transfer. | the delta-proteobacterium, geobacter sulfurreducens, can obtain energy by coupling the oxidation of organic matter to the reduction of insoluble fe(iii) or the anode of a microbial fuel cell. because fe(iii) oxide or the anode surface, in contrast to oxygen, nitrate, or sulfate, is not soluble nor can it be reduced readily, geobacter species have developed mechanisms which allow electrons to be delivered across outer membrane to the cell surface. omcb is an outer-membrane c-type cytochrome impor ... | 2009 | 18677521 |
| influence of support material on the immobilization of biomass for the degradation of linear alkylbenzene sulfonate in anaerobic reactors. | two horizontal-flow anaerobic immobilized biomass reactors (haib) were used to study the degradation of the las surfactant: one filled with charcoal (haib1) and the other with a mixed bed of expanded clay and polyurethane foam (haib2). the reactors were fed with synthetic substrate supplemented with 14 mg l(-1)of las, kept at 30+/-2 degrees c and operated with a hydraulic retention time (hrt) of 12h. the surfactant was quantified by hplc. spatial variation analyses were done to quantify organic ... | 2009 | 18814953 |
| overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for desulfovibrio vulgaris hildenborough. | growing anaerobic microorganisms in phenotypic microarrays (pm) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. for non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a n ... | 2009 | 18996155 |
| [effects of microbial agent inoculation on bacterial community diversity in the process of pig manure composting]. | pcr-dgge method was adopted to study the effects of inoculating exogenous microbial agent on the bacterial community diversity in the process of fresh pig manure high-temperature aerobic composting. exogenous microbial agent inoculation promoted the composting process, with the high-temperature period being advanced by 2 days than that of non-inoculation. dgge pattern analysis showed that during composting, the dominant bacteria changed significantly, with the shannon-wiener index of bacterial c ... | 2009 | 19947226 |
| recording multicellular behavior in myxococcus xanthus biofilms using time-lapse microcinematography. | a swarm of the delta-proteobacterium myxococcus xanthus contains millions of cells that act as a collective, coordinating movement through a series of signals to create complex, dynamic patterns as a response to environmental cues. these patterns are self-organizing and emergent; they cannot be predicted by observing the behavior of the individual cells. using a time-lapse microcinematography tracking assay, we identified a distinct emergent pattern in m. xanthus called chemotaxis, defined as th ... | 2010 | 20729807 |
| functional genomic analysis of an uncultured δ-proteobacterium in the sponge cymbastela concentrica. | marine sponges are ancient, sessile, filter-feeding metazoans, which represent a significant component of the benthic communities throughout the world. sponges harbor a remarkable diversity of bacteria, however, little is known about the functional properties of such bacterial symbionts. in this study, we present the genomic and functional characterization of an uncultured δ-proteobacterium associated with the sponge cymbastela concentrica. we show that this organism represents a novel phylogene ... | 2011 | 20811472 |
| Negative Faradaic Resistance in Extracellular Electron Transfer by Anode-Respiring Geobacter sulfurreducens Cells. | Geobacter sulfurreducens is a Gram-negative d-proteobacterium that is capable of transferring respiratory electrons to solid-state extracellular acceptors, including anodes, via abundant c-type cytochromes expressed in the outer membrane. As extracellular electron transfer (EET) to solid-state acceptors can proceed without the addition of exogenous mediators, this microbe has attracted significant attention with respect to energy conversion between electrical and chemical energy. Here, we reveal ... | 2011 | 22047596 |
| [effects of 2-chlorophenol-acclimation on microbial community structure in anaerobic granular sludge]. | the microbial community structure in 2-chlorophenol-acclimated anaerobic granular sludge and inoculating sludge were analyzed by 16s rdna-based approach. total dna was extracted directly from the inoculating sludge and 2-cp-acclimated anaerobic sludge, and then amplified by polymerase chain reaction (pcr) technique with the specific primer pair arc21f/arc958r for archaea and 31f/907r for acidobacteria respectively. the positive pcr products were cloned and sequenced. the sequences analysis shows ... | 2008 | 18649544 |
| use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted baltic sea sediments. | the aim of this study was to enrich and identify psychrotolerant phenanthrene-degrading bacteria from polluted baltic sea sediments. polyaromatic hydrocarbon (pah)-contaminated sediments were spiked with phenanthrene and incubated for 2 months in the presence of bromodeoxyuridine that is incorporated into the dna of replicating cells. the bromodeoxyuridine-incorporated dna was extracted by immunocapture and analyzed by terminal-restriction fragment length polymorphism and 16s rrna gene cloning a ... | 2008 | 18616589 |
| roles of membrane structure and phase transition on the hyperosmotic stress survival of geobacter sulfurreducens. | geobacter sulfurreducens is a delta-proteobacterium bacteria that has biotechnological applications in bioremediation and as biofuel cells. development of these applications requires stabilization and preservation of the bacteria in thin porous coatings on electrode surfaces and in flow-through bioreactors. during the manufacturing of these coatings the bacteria are exposed to hyperosmotic stresses due to dehydration and the presence of carbohydrates in the medium. in this study we focused on qu ... | 2008 | 18602362 |
| heat-shock sigma factor rpoh from geobacter sulfurreducens. | recent studies with myxococcus xanthus have suggested that homologues of the escherichia coli heat-shock sigma factor, rpoh, may not be involved in the heat-shock response in this delta-proteobacterium. the genome of another delta-proteobacterium, geobacter sulfurreducens, which is considered to be a representative of the fe(iii)-reducing geobacteraceae that predominate in a diversity of subsurface environments, contains an rpoh homologue. characterization of the g. sulfurreducens rpoh homologue ... | 2007 | 17322204 |
| heterologous expression of dodecaheme "nanowire" cytochromes c from geobacter sulfurreducens. | multiheme cytochromes c are difficult to produce in heterologous systems. the genome of delta-proteobacterium geobacter sulfurreducens contains more than a hundred genes coding for c-type cytochromes. among those are two dodecaheme cytochromes c representing a new class of multiheme cytochromes, whose putative structure is a one-dimensional array of small highly homologous domains that contain three hemes and are covalently bound by short linkers. they are likely to form "nanowires" that are par ... | 2006 | 16403647 |
| heterologous expression of hexaheme fragments of a multidomain cytochrome from geobacter sulfurreducens representing a novel class of cytochromes c. | multiheme cytochromes c are of great interest for researchers for a variety of reasons but difficult to obtain in quantities sufficient for the majority of studies. the genome of delta-proteobacterium geobacter sulfurreducens contains more than a hundred genes coding for c-type cytochromes. three of them represent a new class of multiheme cytochromes characterized by a mixed type of heme coordination and multidomain organization. we cloned and expressed in escherichia coli three hexaheme fragmen ... | 2005 | 15642477 |
| the genome of desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold arctic sediments. | desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is able to grow at in situ temperatures below 0 degrees c. as abundant members of the microbial community in permanently cold marine sediments, d. psychrophila-like bacteria contribute to the global cycles of carbon and sulfur. here, we describe the genome sequence of d. psychrophila strain lsv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 66 ... | 2004 | 15305914 |
| redox characterization of geobacter sulfurreducens cytochrome c7: physiological relevance of the conserved residue f15 probed by site-specific mutagenesis. | the complete genome sequence of the delta-proteobacterium geobacter sulfurreducens reveals a large abundance of multiheme cytochromes. cytochrome c(7), isolated from this metal ion-reducing bacterium, is a triheme periplasmic electron-transfer protein with m(r) 9.6 kda. this protein is involved in metal ion-reducing pathways and shares 56% sequence identity with a triheme cytochrome isolated from the closely related delta-proteobacterium desulfuromonas acetoxidans (dac(7)). in this work, two-dim ... | 2004 | 15274645 |
| geobacter sulfurreducens has two autoregulated lexa genes whose products do not bind the reca promoter: differing responses of lexa and reca to dna damage. | the escherichia coli lexa protein was used as a query sequence in tblastn searches to identify the lexa gene of the delta-proteobacterium geobacter sulfurreducens from its genome sequence. the results of the search indicated that g. sulfurreducens has two independent lexa genes designated lexa1 and lexa2. a copy of a dinb gene homologue, which in e. coli encodes dna polymerase iv, is present downstream of each lexa gene. reverse transcription-pcr analyses demonstrated that, in both cases, lexa a ... | 2003 | 12670973 |
| chemosensory regulation of developmental gene expression in myxococcus xanthus. | the delta-proteobacterium myxococcus xanthus coordinates its motility during aggregation and fruiting body formation. while searching for chemotaxis genes in m. xanthus, we identified a third chemotaxis-like gene cluster, the che3 cluster, encoding homologs to two methyl-accepting chemotaxis proteins (mcps), a chew, a hybrid chea, a cheb, a cher, but no chey. mutations in mcp3a, mcp3b, and chea3 did not show obvious defects in motility or chemotaxis but did affect the timing of entry into develo ... | 2003 | 12566562 |
| symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis | we present a novel hypothesis for the origin of the eukaryotic cell, or eukaryogenesis, based on a metabolic symbiosis (syntrophy) between a methanogenic archaeon (methanobacterial-like) and a delta-proteobacterium (an ancestral sulfate-reducing myxobacterium). this syntrophic symbiosis was originally mediated by interspecies h2 transfer in anaerobic, possibly moderately thermophilic, environments. during eukaryogenesis, progressive cellular and genomic cointegration of both types of prokaryotic ... | 1998 | 9797402 |
| independent evolutionary origins of functional polyamine biosynthetic enzyme fusions catalysing de novo diamine to triamine formation. | we have identified gene fusions of polyamine biosynthetic enzymes s-adenosylmethionine decarboxylase (adometdc, sped) and aminopropyltransferase (spee) orthologues in diverse bacterial phyla. both domains are functionally active and we demonstrate the novel de novo synthesis of the triamine spermidine from the diamine putrescine by fusion enzymes from ß-proteobacterium delftia acidovorans and d-proteobacterium syntrophus aciditrophicus, in a ?spede gene deletion strain of salmonella enterica sv. ... | 2011 | 21762220 |