| detection and in situ identification of representatives of a widely distributed new bacterial phylum. | 16s rrna gene libraries were prepared by polymerase chain reaction amplification and cloning from soil samples taken periodically from a field with genetically modified plants. sequence analyses of the cloned rdnas indicated that 140 of them clustered apart from known bacterial phyla. based on 31 full sequences a new phylum could be defined. it includes holophaga foetida, 'geothrix fermentans' and acidobacterium capsulatum as the only cultured species so far. therefore, this line of descent was ... | 1997 | 9252585 |
| microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. | microbial community composition associated with benzene oxidation under in situ fe(iii)-reducing conditions in a petroleum-contaminated aquifer located in bemidji, minn., was investigated. community structure associated with benzene degradation was compared to sediment communities that did not anaerobically oxidize benzene which were obtained from two adjacent fe(iii)-reducing sites and from methanogenic and uncontaminated zones. denaturing gradient gel electrophoresis of 16s rdna sequences ampl ... | 1999 | 10388703 |
| geothrix fermentans gen. nov., sp. nov., a novel fe(iii)-reducing bacterium from a hydrocarbon-contaminated aquifer. | in an attempt to understand better the micro-organisms involved in anaerobic degradation of aromatic hydrocarbons in the fe(iii)-reducing zone of petroleum-contaminated aquifers, fe(iii)-reducing micro-organisms were isolated from contaminated aquifer material that had been adapted for rapid oxidation of toluene coupled to fe(iii) reduction. one of these organisms, strain h-5t, was enriched and isolated on acetate/fe(iii) medium. strain h-5t is a gram-negative strict anaerobe that grows with var ... | 1999 | 10555343 |
| enrichment of geobacter species in response to stimulation of fe(iii) reduction in sandy aquifer sediments. | engineered stimulation of fe(iii) has been proposed as a strategy to enhance the immobilization of radioactive and toxic metals in metal-contaminated subsurface environments. therefore, laboratory and field studies were conducted to determine which microbial populations would respond to stimulation of fe(iii) reduction in the sediments of sandy aquifers. in laboratory studies, the addition of either various organic electron donors or electron shuttle compounds stimulated fe(iii) reduction and re ... | 2000 | 10833228 |
| humics as an electron donor for anaerobic respiration. | the possibility that microorganisms might use reduced humic substances (humics) as an electron donor for the reduction of electron acceptors with a more positive redox potential was investigated. all of the fe(iii)- and humics-reducing microorganisms evaluated were capable of oxidizing reduced humics and/or the reduced humics analogue anthrahydroquinone-2,6,-disulphonate (ahods), with nitrate and/or fumarate as the electron acceptor. these included geobacter metallireducens, geobacter sulphurred ... | 1999 | 11207721 |
| microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds. | we studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (wadi gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory. phormidium- and oscillatoria-like cyanobacterial morphotypes were dominant in the field. bacteria belonging to different groups, mainly the cytophaga-flavobacterium-bacteriodes group, the gamma and beta subclasses of the class p ... | 2002 | 11916684 |
| mechanisms for accessing insoluble fe(iii) oxide during dissimilatory fe(iii) reduction by geothrix fermentans. | mechanisms for fe(iii) oxide reduction were investigated in geothrix fermentans, a dissimilatory fe(iii)-reducing microorganism found within the fe(iii) reduction zone of subsurface environments. culture filtrates of g. fermentans stimulated the reduction of poorly crystalline fe(iii) oxide by washed cell suspensions, suggesting that g. fermentans released one or more extracellular compounds that promoted fe(iii) oxide reduction. in order to determine if g. fermentans released electron-shuttling ... | 2002 | 11976100 |
| diversity and ubiquity of bacteria capable of utilizing humic substances as electron donors for anaerobic respiration. | previous studies have demonstrated that reduced humic substances (hs) can be reoxidized by anaerobic bacteria such as geobacter, geothrix, and wolinella species with a suitable electron acceptor; however, little is known of the importance of this metabolism in the environment. recently we investigated this metabolism in a diversity of environments including marine and aquatic sediments, forest soils, and drainage ditch soils. most-probable-number enumeration studies were performed using 2,6-anth ... | 2002 | 11976120 |
| anaerobic biodegradation of tce in laboratory columns of fractured saprolite. | an experiment was conducted to determine if biodegradation of trichloroethylene (tce) can occur in previously uncontaminated ground water in saturated fractured saprolite (highly weathered material derived from sedimentary rocks). two undisturbed columns (0.23 m diameter by 0.25 m long) of fractured saprolite were collected from approximately 2 m depth at an uncontaminated site on the oak ridge reservation, oak ridge, tennessee. natural, uncontaminated ground water from the site, which was degas ... | 2004 | 15318776 |
| dissimilatory fe(iii) and mn(iv) reduction. | dissimilatory fe(iii) and mn(iv) reduction has an important influence on the geochemistry of modern environments, and fe(iii)-reducing microorganisms, most notably those in the geobacteraceae family, can play an important role in the bioremediation of subsurface environments contaminated with organic or metal contaminants. microorganisms with the capacity to conserve energy from fe(iii) and mn(iv) reduction are phylogenetically dispersed throughout the bacteria and archaea. the ability to oxidiz ... | 2004 | 15518832 |
| microbial communities associated with electrodes harvesting electricity from a variety of aquatic sediments. | the microbial communities associated with electrodes from underwater fuel cells harvesting electricity from five different aquatic sediments were investigated. three fuel cells were constructed with marine, salt-marsh, or freshwater sediments incubated in the laboratory. fuel cells were also deployed in the field in salt marsh sediments in new jersey and estuarine sediments in oregon, usa. all of the sediments produced comparable amounts of power. analysis of 16s rrna gene sequences after 3-7 mo ... | 2004 | 15546038 |
| biological soil crusts of sand dunes in cape cod national seashore, massachusetts, usa. | biological soil crusts cover hundreds of hectares of sand dunes at the northern tip of cape cod national seashore (massachusetts, usa). although the presence of crusts in this habitat has long been recognized, neither the organisms nor their ecological roles have been described. in this study, we report on the microbial community composition of crusts from this region and describe several of their physical and chemical attributes that bear on their environmental role. microscopic and molecular a ... | 2004 | 15546040 |
| evidence for involvement of an electron shuttle in electricity generation by geothrix fermentans. | in experiments performed using graphite electrodes poised by a potentiostat (+200 mv versus ag/agcl) or in a microbial fuel cell (with oxygen as the electron acceptor), the fe(iii)-reducing organism geothrix fermentans conserved energy to support growth by coupling the complete oxidation of acetate to reduction of a graphite electrode. other organic compounds, such as lactate, malate, propionate, and succinate as well as components of peptone and yeast extract, were utilized for electricity prod ... | 2005 | 15812057 |
| biological control of hog waste odor through stimulated microbial fe(iii) reduction. | odor control and disposal of swine waste have inhibited expansion of swine production facilities throughout the united states. swine waste odor is associated primarily with high concentrations of volatile fatty acids (vfas). here, we demonstrate that stimulated fe(iii) reduction in hog manure can rapidly remove the malodorous compounds and enhance methane production by 200%. as part of these studies, we enumerated the indigenous fe(iii)-reducing population in swine waste and identified members o ... | 2005 | 16085869 |
| application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. | reduction of soluble uranium u(vi) to less-soluble uranium u(iv) is a promising approach to minimize migration from contaminated aquifers. it is generally assumed that, under constant reducing conditions, u(iv) is stable and immobile; however, in a previous study, we documented reoxidation of u(iv) under continuous reducing conditions (wan et al., environ. sci. technol. 2005, 39:6162-6169). to determine if changes in microbial community composition were a factor in u(iv) reoxidation, we employed ... | 2006 | 16957256 |
| influence of bicarbonate, sulfate, and electron donors on biological reduction of uranium and microbial community composition. | a microcosm study was performed to investigate the effect of ethanol and acetate on uranium(vi) biological reduction and microbial community changes under various geochemical conditions. each microcosm contained an uranium-contaminated sediment (up to 2.8 g u/kg) suspended in buffer with bicarbonate at concentrations of either 1 or 40 mm and sulfate at either 1.1 or 3.2 mm. ethanol or acetate was used as an electron donor. results indicate that ethanol yielded in significantly higher u(vi) reduc ... | 2007 | 17874092 |
| in situ bioreduction of uranium (vi) to submicromolar levels and reoxidation by dissolved oxygen. | groundwater within area 3 of the u.s. department of energy (doe) environmental remediation sciences program (ersp) field research center at oak ridge, tn (orfrc) contains up to 135 microm uranium as u(vi). through a series of experiments at a pilot scale test facility, we explored the lower limits of groundwater u(vi) that can be achieved by in-situ biostimulation and the effects of dissolved oxygen on immobilized uranium. weekly 2 day additions of ethanol over a 2-year period stimulated growth ... | 2007 | 17874778 |
| influence of nitrate on microbial reduction of pertechnetate. | factors influencing microbial reduction of tc(vii) in nitrate and radionuclide contaminated aquifer sediments were investigated using sediment microcosms containing organic electron donor, nitrate and tc(vii). microcosms underwent nitrate reduction followed by tc(vii) reduction. during this transition, the microbial community changed from being dominated by bacteria affiliated with the genus paenibacillus during the nitrate reduction phase, to those affiliated with genera agrobacterium, geothrix ... | 2008 | 18409612 |
| edaphobacter modestus gen. nov., sp. nov., and edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. | the phylum acidobacteria is currently represented mostly by environmental 16s rrna gene sequences, and the phylum so far contains only four species with validly published names, holophaga foetida, geothrix fermentans, acidobacterium capsulatum and terriglobus roseus. in the present study, two novel strains of acidobacteria were isolated. high-throughput enrichments were set up with the microdrop technique using an alpine calcareous soil sample and a mixture of polymeric carbon compounds suppleme ... | 2008 | 18450699 |
| microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels. | microbial enumeration, 16s rrna gene clone libraries, and chemical analysis were used to evaluate the in situ biological reduction and immobilization of uranium(vi) in a long-term experiment (more than 2 years) conducted at a highly uranium-contaminated site (up to 60 mg/liter and 800 mg/kg solids) of the u.s. department of energy in oak ridge, tn. bioreduction was achieved by conditioning groundwater above ground and then stimulating growth of denitrifying, fe(iii)-reducing, and sulfate-reducin ... | 2008 | 18456853 |
| acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of acanthopleuribacteraceae fam. nov., acanthopleuribacterales ord. nov., holophagaceae fam. nov., holophagales ord. nov. and holophagae classis nov. in the phylum 'acidobacteria'. | strain fyk2218(t) was isolated from a specimen of the chiton acanthopleura japonica, which had been collected from a beach on the boso peninsula in japan. phylogenetic analyses based on 16s rrna gene sequences revealed that the strain belonged to the phylum 'acidobacteria'. the most closely related type strains to strain fyk2218(t) were holophaga foetida tmbs4(t) (83.6 % 16s rrna gene sequence similarity) and geothrix fermentans h-5(t) (83.6 %) in subdivision 8 of the 'acidobacteria'. cells of f ... | 2008 | 18984699 |
| effect of dechlorination and sulfate reduction on the microbial community structure in denitrifying membrane-biofilm reactors. | recent studies showed that the chlorinated solvents trichloroethene (tce), 1,1,1-trichloroethane (tca), and chloroform (cf) were reductively dehalogenated in a h(2)-based membrane biofilm reactor (mbfr) under denitrifying conditions. here, we describe a detailed phylogenetic characterization of mbfr biofilm communities having distinctly different metabolic functions with respect to electron-acceptor reduction. using massively parallel pyrosequencing of the v6 region of the 16s rrna gene, we dete ... | 2010 | 20524654 |
| Influence of uranium on bacterial communities: a comparison of natural uranium-rich soils with controls. | This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing ... | 2011 | 21998695 |