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ecophysiological and phylogenetic studies of nevskia ramosa in pure culture.during the last 100 years, the neuston bacterium nevskia ramosa has been described several times. this bacterium forms conspicuous rosette-like microcolonies at the air-water interface. in this study, pure cultures of nevskia ramosa were obtained for the first time, from a bog lake (strain soe1, dsmz 11499t) and a freshwater ditch (strain ol1, dsmz 11500). the isolates showed special adaptations to life in the epineuston. they formed hydrophobic surface films with a dull appearance. n. ramosa is ...19989572968
phylogenetic analysis of particle-attached and free-living bacterial communities in the columbia river, its estuary, and the adjacent coastal ocean.the columbia river estuary is a dynamic system in which estuarine turbidity maxima trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. pcr-amplified 16s rrna genes from particle-attached and free-living bacteria in the columbia river, its estuary, and the adjacent coastal ocean were cloned, and 239 ...199910388721
relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer.knowledge about the relationship between microbial community structure and hydrogeochemistry (e.g., pollution, redox and degradation processes) in landfill leachate-polluted aquifers is required to develop tools for predicting and monitoring natural attenuation. in this study analyses of pollutant and redox chemistry were conducted in parallel with culture-independent profiling of microbial communities present in a well-defined aquifer (banisveld, the netherlands). degradation of organic contami ...200111571165
ammonia- and nitrite-oxidizing bacterial communities in a pilot-scale chloraminated drinking water distribution system.nitrification in drinking water distribution systems is a common operational problem for many utilities that use chloramines for secondary disinfection. the diversity of ammonia-oxidizing bacteria (aob) and nitrite-oxidizing bacteria (nob) in the distribution systems of a pilot-scale chloraminated drinking water treatment system was characterized using terminal restriction fragment length polymorphism (t-rflp) analysis and 16s rrna gene (ribosomal dna [rdna]) cloning and sequencing. for ammonia ...200211772611
culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited.the phylogenetic diversity of the intestinal bacterial community in pigs was studied by comparative 16s ribosomal dna (rdna) sequence analysis. samples were collected from a total of 24 pigs representing a variety of diets, ages, and herd health status. a library comprising 4,270 cloned 16s rdna sequences obtained directly by pcr from 52 samples of either the ileum, the cecum, or the colon was constructed. in total, 375 phylotypes were identified using a 97% similarity criterion. three hundred n ...200211823207
isolation and characterization of novel psychrophilic, neutrophilic, fe-oxidizing, chemolithoautotrophic alpha- and gamma-proteobacteria from the deep sea.we report the isolation and physiological characterization of novel, psychrophilic, iron-oxidizing bacteria (feob) from low-temperature weathering habitats in the vicinity of the juan de fuca deep-sea hydrothermal area. the feob were cultured from the surfaces of weathered rock and metalliferous sediments. they are capable of growth on a variety of natural and synthetic solid rock and mineral substrates, such as pyrite (fes(2)), basalt glass ( approximately 10 wt% feo), and siderite (feco(3)), a ...200312732565
diversity and seasonal variability of beta-proteobacteria in biofilms of polluted rivers: analysis by temperature gradient gel electrophoresis and cloning.the beta-subgroup of the proteobacteria has been shown to be important in aquatic habitats and was investigated in depth here by molecular 16s rrna techniques in biofilms of the elbe river and its polluted tributary, the spittelwasser river. the bacterial 16s rrna genes were cloned from each site, screened for beta-proteobacterial clones and sequenced. river biofilm clones from both rivers grouped into 9 clusters (rbfs). rbfs 1, 2, and 3 fell into the recently described betai cluster of cosmopol ...200312902230
diversity of microorganisms in fe-as-rich acid mine drainage waters of carnoulès, france.the acid waters (ph 2.7 to 3.4) originating from the carnoulès mine tailings contain high concentrations of dissolved arsenic (80 to 350 mg.liter(-1)), iron (750 to 2,700 mg.liter(-1)), and sulfate (2,000 to 7,500 mg.liter(-1)). during the first 30 m of downflow in reigous creek issuing from the mine tailings, 20 to 60% of the dissolved arsenic is removed by coprecipitation with fe(iii). the microbial communities along the creek have been characterized using terminal-restriction fragment length ...200616391091
macroscopic streamer growths in acidic, metal-rich mine waters in north wales consist of novel and remarkably simple bacterial communities.the microbial composition of acid streamers (macroscopic biofilms) in acidic, metal-rich waters in two locations (an abandoned copper mine and a chalybeate spa) in north wales was studied using cultivation-based and biomolecular techniques. known chemolithotrophic and heterotrophic acidophiles were readily isolated from disrupted streamers, but they accounted for only <1 to 7% of the total microorganisms present. fluorescent in situ hybridization (fish) revealed that 80 to 90% of the microbes in ...200616517651
a novel lineage of proteobacteria involved in formation of marine fe-oxidizing microbial mat communities.for decades it has been recognized that neutrophilic fe-oxidizing bacteria (feob) are associated with hydrothermal venting of fe(ii)-rich fluids associated with seamounts in the world's oceans. the evidence was based almost entirely on the mineralogical remains of the microbes, which themselves had neither been brought into culture or been assigned to a specific phylogenetic clade. we have used both cultivation and cultivation-independent techniques to study fe-rich microbial mats associated wit ...200717668050
bacterial diversity in a mine water treatment plant.we investigated the microbial community in a pilot plant for treatment of acid mine water by biological ferrous iron oxidation using clone library analysis and calculated statistical parameters for further characterization. the microbial community in the plant was conspicuously dominated by a group of betaproteobacteria affiliated with "ferribacter polymyxa".200919047391
bacterial diversity in a mine water treatment plant.we investigated the microbial community in a pilot plant for treatment of acid mine water by biological ferrous iron oxidation using clone library analysis and calculated statistical parameters for further characterization. the microbial community in the plant was conspicuously dominated by a group of betaproteobacteria affiliated with "ferribacter polymyxa".200919047391
biofilm bacterial community structure in streams affected by acid mine drainage.we examined the bacterial communities of epilithic biofilms in 17 streams which represented a gradient ranging from relatively pristine streams to streams highly impacted by acid mine drainage (amd). a combination of automated ribosomal intergenic spacer analysis with multivariate analysis and ordination provided a sensitive, high-throughput method to monitor the impact of amd on stream bacterial communities. significant differences in community structure were detected among neutral to alkaline ...200919363070
composition and activity of an autotrophic fe(ii)-oxidizing, nitrate-reducing enrichment culture.16s rrna gene libraries from the lithoautotrophic fe(ii)-oxidizing, nitrate-reducing enrichment culture described by straub et al. (k. l. straub, m. benz, b. schink, and f. widdel, appl. environ. microbiol. 62:1458-1460, 1996) were dominated by a phylotype related (95% 16s rrna gene homology) to the autotrophic fe(ii) oxidizer sideroxydans lithotrophicus. the libraries also contained phylotypes related to known heterotrophic nitrate reducers comamonas badia, parvibaculum lavamentivorans, and rho ...200919749073
significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. we combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(vi) reduction in the subsurface of a uranium contamination plume at the oak ridge field research center in tennessee. remediati ...201020729318
lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation.neutrophilic fe-oxidizing bacteria (feob) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by gallionella ferruginea or mariprofundus ferrooxydans. similar filaments preserved in silica are often identified as feob fossils in rocks. although it is assumed that twisted iron stalks are indicative of feob, the stalk's metabolic role has not been established. to this end, we studied the marine feob m. ferrooxydans by light, x-ray and ...201021107443
lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation.neutrophilic fe-oxidizing bacteria (feob) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by gallionella ferruginea or mariprofundus ferrooxydans. similar filaments preserved in silica are often identified as feob fossils in rocks. although it is assumed that twisted iron stalks are indicative of feob, the stalk's metabolic role has not been established. to this end, we studied the marine feob m. ferrooxydans by light, x-ray and ...201021107443
neutrophilic iron-oxidizing "zetaproteobacteria" and mild steel corrosion in nearshore marine environments.microbiologically influenced corrosion (mic) of mild steel in seawater is an expensive and enduring problem. little attention has been paid to the role of neutrophilic, lithotrophic, iron-oxidizing bacteria (feob) in mic. the goal of this study was to determine if marine feob related to mariprofundus are involved in this process. to examine this, field incubations and laboratory microcosm experiments were conducted. mild steel samples incubated in nearshore environments were colonized by marine ...201021131509
neutrophilic iron-oxidizing "zetaproteobacteria" and mild steel corrosion in nearshore marine environments.microbiologically influenced corrosion (mic) of mild steel in seawater is an expensive and enduring problem. little attention has been paid to the role of neutrophilic, lithotrophic, iron-oxidizing bacteria (feob) in mic. the goal of this study was to determine if marine feob related to mariprofundus are involved in this process. to examine this, field incubations and laboratory microcosm experiments were conducted. mild steel samples incubated in nearshore environments were colonized by marine ...201021131509
distribution and diversity of gallionella-like neutrophilic iron oxidizers in a tidal freshwater marsh.microbial iron oxidation is an integral part of the iron redox cycle in wetlands. nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. in this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (feob) and to link their distributions to the geochemical properties of the sediments. we applied recently designed 16s rrna primers targeting g ...201121317256
nanometer-scale visualization and structural analysis of the inorganic/organic hybrid structure of gallionella ferruginea twisted stalks.the so-called fe/mn-oxidizing bacteria have long been recognized for their potential to form extracellular iron hydroxide or manganese oxide structures in aquatic environments. bacterial species belonging to the genus gallionella, one type of such bacteria, oxidize iron and produce uniquely twisted extracellular stalks consisting of iron oxide-encrusted inorganic/organic fibers. this paper describes the ultrastructure of gallionella cells and stalks and the visualized structural and spatial loca ...201121378050
microbial communities and chemosynthesis in yellowstone lake sublacustrine hydrothermal vent waters.five sublacustrine thermal spring locations from 1 to 109ôçëm water depth in yellowstone lake were surveyed by 16s ribosomal rna gene sequencing in relation to their chemical composition and dark co(2) fixation rates. they harbor distinct chemosynthetic bacterial communities, depending on temperature (16-110-¦c) and electron donor supply (h(2)s <1 to >100ôçë++m; nh(3) <0.5 to >10ôçë++m). members of the aquificales, most closely affiliated with the genus sulfurihydrogenibium, are the most frequen ...201121716640
Structural and spatial associations between Fe, O, and C in the network structure of the Leptothrix ochracea sheath surface.The structural and spatial associations of Fe with O and C in the outer coat fibers of the Leptothrix ochracea sheath were shown to be substantially similar to the stalk fibers of Gallionella ferruginea, i.e., a central C core, probably of bacterial origin, and aquatic Fe interacting with O at the surface of the core.201121926209
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 ...201121998695
Silicon and Phosphorus Linkage with Iron via Oxygen in the Amorphous Matrix of Gallionella ferruginea Stalks.Bacterial species belonging to the genus Gallionella are Fe-oxidizing bacteria that produce uniquely twisted extracellular stalks consisting of iron-oxide-encrusted inorganic/organic fibers in aquatic environments. This paper describes the degree of crystallinity of Gallionella stalks and the chemical linkages of constituent elements in the stalk fibers. Transmission electron microscopy revealed that the matrix of the fiber edge consisted of an assembly of primary particles of approximately 3 nm ...201222020519
comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques.comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16s rrna gene clone library and improved cultivation-based techniques. our study demonstrated that the use of gellan gum as a gelling reagent instead of agar was more effective at increasing culturability, cultivating a diverse array of novel microbes, and reducing the gaps of the results between molecular and cultivation-based analyses.200515812052
composition and dynamics of bacterial communities of a drinking water supply system as assessed by rna- and dna-based 16s rrna gene fingerprinting.bacterial community dynamics of a whole drinking water supply system (dwss) were studied from source to tap. raw water for this dwss is provided by two reservoirs with different water characteristics in the harz mountains of northern germany. samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. rna and dna were extracted from the sampled water. the 16s rrna or its gen ...200616517632
metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from guaymas basin.deep-sea hydrothermal vent chimneys contain a high diversity of microorganisms, yet the metabolic activity and the ecological functions of the microbial communities remain largely unexplored. in this study, a metagenomic approach was applied to characterize the metabolic potential in a guaymas hydrothermal vent chimney and to conduct comparative genomic analysis among a variety of environments with sequenced metagenomes. complete clustering of functional gene categories with a comparative metage ...201323785357
isolation and metabolic characteristics of previously uncultured members of the order aquificales in a subsurface gold mine.culture-dependent and -independent techniques were combined to characterize the physiological properties and the ecological impacts of culture-resistant phylotypes of thermophiles within the order aquificales from a subsurface hot aquifer of a japanese gold mine. thermophilic bacteria phylogenetically associated with previously uncultured phylotypes of aquificales were successfully isolated. 16s ribosomal dna clone analysis of the entire microbial dna assemblage and fluorescence in situ whole-ce ...200212039766
comparative genomics of freshwater fe-oxidizing bacteria: implications for physiology, ecology, and systematics.the two microaerophilic, fe-oxidizing bacteria (feob) sideroxydans es-1 and gallionella es-2 have single circular chromosomes of 3.00 and 3.16 mb that encode 3049 and 3006 genes, respectively. multi-locus sequence analysis (mlsa) confirmed the relationship of these two organisms to one another, and indicated they may form a novel order, the gallionellalaes, within the betaproteobacteria. both are adapted for chemolithoautotropy, including pathways for co2-fixation, and electron transport pathway ...201324062729
microbial diversity and metabolic networks in acid mine drainage habitats.acid mine drainage (amd) emplacements are low-complexity natural systems. low-ph conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. this natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhab ...201526074887
characterization of mtod from sideroxydans lithotrophicus: a cytochrome c electron shuttle used in lithoautotrophic growth.the autotrophic sideroxydans lithotrophicus es-1 can grow by coupling the oxidation of ferrous iron to the reduction of oxygen. soluble ferrous iron is oxidized at the surface of the cell by an mtoab porin-cytochrome complex that functions as an electron conduit through the outer membrane. electrons are then transported to the cytoplasmic membrane where they are used to generate proton motive force (pmf) (for atp synthesis) and nadh for autotrophic processes such as carbon fixation. as part of t ...201525972843
microbes: mini iron factories.microbes have flourished in extreme habitats since beginning of the earth and have played an important role in geological processes like weathering, mineralization, diagenesis, mineral formation and destruction. biotic mineralization is one of the most fascinating examples of how microbes have been influencing geological processes. iron oxidizing and reducing bacteria are capable of precipitating wide varieties of iron oxides (magnetite), carbonates (siderite) and sulphides (greigite) via contro ...201425320452
influence of seasonal and geochemical changes on the geomicrobiology of an iron carbonate mineral water spring.fuschna spring in the swiss alps (engadin region) is a bicarbonate iron(ii)-rich, ph-neutral mineral water spring that is dominated visually by dark green microbial mats at the side of the flow channel and orange iron(iii) (oxyhydr)oxides in the flow channel. gradients of o(2), dissolved iron(ii), and bicarbonate establish in the water. our goals were to identify the dominating biogeochemical processes and to determine to which extent changing geochemical conditions along the flow path and seaso ...201222865064
high voltage electrochemiluminescence (ecl) as a new method for detection of pah during screening for pah-degrading microbial consortia.the search for new bacterial consortia capable of removing pah from the environment is associated with the need to employ novel, simple, and economically efficient detection methods. a fluorimetric method (fl) as well as high voltage electrochemiluminescence (ecl) on a modified surface of an aluminum electrode were used in order to determine the changes in the concentrations of pah in the studied aqueous solutions. the ecl signal (the spectrum and emission intensity for a given wavelength) was d ...201526213425
oxygen isotope ratios of po4: an inorganic indicator of enzymatic activity and p metabolism and a new biomarker in the search for life.the distinctive relations between biological activity and isotopic effect recorded in biomarkers (e.g., carbon and sulfur isotope ratios) have allowed scientists to suggest that life originated on this planet nearly 3.8 billion years ago. the existence of life on other planets may be similarly identified by geochemical biomarkers, including the oxygen isotope ratio of phosphate (delta(18)o(p)) presented here. at low near-surface temperatures, the exchange of oxygen isotopes between phosphate and ...200111226207
neutrophilic fe-oxidizing bacteria are abundant at the loihi seamount hydrothermal vents and play a major role in fe oxide deposition.a number of hydrothermal vent sites exist on the summit of the loihi seamount, a shield volcano that is part of the hawaiian archipelago. the vents are 1,100 to 1,325 m below the surface and range in temperature from slightly above ambient (10 degrees c) to high temperature (167 degrees c). the vent fluid is characterized by high concentrations of co2 (up to 17 mm) and fe(ii) (up to 268 microm), but there is a general paucity of h2s. most of the vents are surrounded by microbial mats that have a ...200212039770
phylogenetic diversity of archaea and bacteria in the anoxic zone of a meromictic lake (lake pavin, france).the compositions of archaeal and bacterial populations at different depths (60 m [mixolimnion-chemocline interface], 70 m [chemocline-subchemocline interface], 90 m, and 92 m [the water-sediment interface]) in the anoxic zone of the water column in lake pavin, a freshwater permanently stratified mountain lake in france, were determined. phylogenetic trees were constructed from sequences to assess archaeal and bacterial diversity at the four sites.200717261512
metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics.by their metabolic activities, microorganisms have a crucial role in the biogeochemical cycles of elements. the complete understanding of these processes requires, however, the deciphering of both the structure and the function, including synecologic interactions, of microbial communities. using a metagenomic approach, we demonstrated here that an acid mine drainage highly contaminated with arsenic is dominated by seven bacterial strains whose genomes were reconstructed. five of them represent y ...201121562598
microbial lithotrophic oxidation of structural fe(ii) in biotite.microorganisms are known to participate in the weathering of primary phyllosilicate minerals through the production of organic ligands and acids and through the uptake of products of weathering. here we show that the lithotrophic fe(ii)-oxidizing, nitrate-reducing enrichment culture described by straub et al. (k. l. straub, m. benz, b. schink, and f. widdel, appl. environ. microbiol. 62:1458-1460, 1996) can grow via oxidation of structural fe(ii) in biotite, a fe(ii)-rich trioctahedral mica foun ...201222685132
microbial transformations of nitrogen, sulfur, and iron dictate vegetation composition in wetlands: a review.the majority of studies on rhizospheric interactions focus on pathogens, mycorrhizal symbiosis, or carbon transformations. although the biogeochemical transformations of n, s, and fe have profound effects on vegetation, these effects have received far less attention. this review, meant for microbiologists, biogeochemists, and plant scientists includes a call for interdisciplinary research by providing a number of challenging topics for future ecosystem research. firstly, all three elements are p ...201222539932
two types of morphologically distinct fibers comprising gallionella ferruginea twisted stalks.two morphologically distinct extracellular stalk fibers produced by gallionella ferruginea were compared by electron microscopy and elemental analysis. the thick- and fine-fiber stalks were different in structure on a micrometer scale and in the site on the mother cell to which they were attached, but on a nanometer scale they were similar in ultrastructure and in the elemental composition of their basic fiber matrix.201222452845
molecular underpinnings of fe(iii) oxide reduction by shewanella oneidensis mr-1.in the absence of o(2) and other electron acceptors, the gram-negative bacterium shewanella oneidensis mr-1 can use ferric [fe(iii)] (oxy)(hydr)oxide minerals as the terminal electron acceptors for anaerobic respiration. at circumneutral ph and in the absence of strong complexing ligands, fe(iii) oxides are relatively insoluble and thus are external to the bacterial cells. s. oneidensis mr-1 and related strains of metal-reducing shewanella have evolved machinery (i.e., metal-reducing or mtr path ...201222363328
ecological succession among iron-oxidizing bacteria.despite over 125 years of study, the factors that dictate species dominance in neutrophilic iron-oxidizing bacterial (feob) communities remain unknown. in a freshwater wetland, we documented a clear ecological succession coupled with niche separation between the helical stalk-forming gallionellales (for example, gallionella ferruginea) and tubular sheath-forming leptothrix ochracea. changes in the iron-seep community were documented using microscopy and cultivation-independent methods. quantific ...201324225888
ecological succession among iron-oxidizing bacteria.despite over 125 years of study, the factors that dictate species dominance in neutrophilic iron-oxidizing bacterial (feob) communities remain unknown. in a freshwater wetland, we documented a clear ecological succession coupled with niche separation between the helical stalk-forming gallionellales (for example, gallionella ferruginea) and tubular sheath-forming leptothrix ochracea. changes in the iron-seep community were documented using microscopy and cultivation-independent methods. quantific ...201324225888
functional gene analysis of freshwater iron-rich flocs at circumneutral ph and isolation of a stalk-forming microaerophilic iron-oxidizing bacterium.iron-rich flocs often occur where anoxic water containing ferrous iron encounters oxygenated environments. culture-independent molecular analyses have revealed the presence of 16s rrna gene sequences related to diverse bacteria, including autotrophic iron oxidizers and methanotrophs in iron-rich flocs; however, the metabolic functions of the microbial communities remain poorly characterized, particularly regarding carbon cycling. in the present study, we cultivated iron-oxidizing bacteria (feob) ...201323811518
chemolithotrophic nitrate-dependent fe(ii)-oxidizing nature of actinobacterial subdivision lineage tm3.anaerobic nitrate-dependent fe(ii) oxidation is widespread in various environments and is known to be performed by both heterotrophic and autotrophic microorganisms. although fe(ii) oxidation is predominantly biological under acidic conditions, to date most of the studies on nitrate-dependent fe(ii) oxidation were from environments of circumneutral ph. the present study was conducted in lake grosse fuchskuhle, a moderately acidic ecosystem receiving humic acids from an adjacent bog, with the obj ...201323514778
arsenic contamination of groundwater: a review of sources, prevalence, health risks, and strategies for mitigation.arsenic contamination of groundwater in different parts of the world is an outcome of natural and/or anthropogenic sources, leading to adverse effects on human health and ecosystem. millions of people from different countries are heavily dependent on groundwater containing elevated level of as for drinking purposes. as contamination of groundwater, poses a serious risk to human health. excessive and prolonged exposure of inorganic as with drinking water is causing arsenicosis, a deteriorating an ...201425374935
invited commentary: lubricating the rusty wheel, new insights into iron oxidizing bacteria through comparative genomics. 201425126088
microbial iron oxidation in the arctic tundra and its implications for biogeochemical cycling.the role that neutrophilic iron-oxidizing bacteria play in the arctic tundra is unknown. this study surveyed chemosynthetic iron-oxidizing communities at the north slope of alaska near toolik field station (tfs) at toolik lake (lat 68.63, long -149.60). microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. some fe-oxidizing bacteria (feob) produce easily recogniz ...201526386054
novel and unexpected microbial diversity in acid mine drainage in svalbard (78° n), revealed by culture-independent approaches.svalbard, situated in the high arctic, is an important past and present coal mining area. dozens of abandoned waste rock piles can be found in the proximity of longyearbyen. this environment offers a unique opportunity for studying the biological control over the weathering of sulphide rocks at low temperatures. although the extension and impact of acid mine drainage (amd) in this area is known, the native microbial communities involved in this process are still scarcely studied and uncharacteri ...201527682111
crystals: animal, vegetable or mineral?the morphologies of biological materials, from body shapes to membranes within cells, are typically curvaceous and flexible, in contrast to the angular, facetted shapes of inorganic matter. an alternative dichotomy has it that biomolecules typically assemble into aperiodic structures in vivo, in contrast to inorganic crystals. this paper explores the evolution of our understanding of structures across the spectrum of materials, from living to inanimate, driven by those naive beliefs, with partic ...201526464788
preserved filamentous microbial biosignatures in the brick flat gossan, iron mountain, california.a variety of actively precipitating mineral environments preserve morphological evidence of microbial biosignatures. one such environment with preserved microbial biosignatures is the oxidized portion of a massive sulfide deposit, or gossan, such as that at iron mountain, california. this gossan may serve as a mineralogical analogue to some ancient martian environments due to the presence of oxidized iron and sulfate species, and minerals that only form in acidic aqueous conditions, in both envi ...201526247371
the kallisti limnes, carbon dioxide-accumulating subsea pools.natural co2 releases from shallow marine hydrothermal vents are assumed to mix into the water column, and not accumulate into stratified seafloor pools. we present newly discovered shallow subsea pools located within the santorini volcanic caldera of the southern aegean sea, greece, that accumulate co2 emissions from geologic reservoirs. this type of hydrothermal seafloor pool, containing highly concentrated co2, provides direct evidence of shallow benthic co2 accumulations originating from sub- ...201526179858
microscale characterization and trace element distribution in bacteriogenic ferromanganese coatings on sand grains from an intertidal zone of the east china sea.an ancient wood layer dated at about 5600 yr bp by accelerator mass spectrometry (ams) 14c was discovered in an intertidal zone of the east china sea. extensive and horizontally stratified sediments with black color on the top and yellowish-red at the bottom, and some nodule-cemented concretions with brown surface and black inclusions occurred in this intertidal zone. microscale analysis methods were employed to study the microscale characterization and trace element distribution in the stratifi ...201525786213
microbial iron mats at the mid-atlantic ridge and evidence that zetaproteobacteria may be restricted to iron-oxidizing marine systems.chemolithoautotrophic iron-oxidizing bacteria play an essential role in the global iron cycle. thus far, the majority of marine iron-oxidizing bacteria have been identified as zetaproteobacteria, a novel class within the phylum proteobacteria. marine iron-oxidizing microbial communities have been found associated with volcanically active seamounts, crustal spreading centers, and coastal waters. however, little is known about the presence and diversity of iron-oxidizing communities at hydrotherma ...201525760332
geochemical niches of iron-oxidizing acidophiles in acidic coal mine drainage.a legacy of coal mining in the appalachians has provided a unique opportunity to study the ecological niches of iron-oxidizing microorganisms. mine-impacted, anoxic groundwater with high dissolved-metal concentrations emerges at springs and seeps associated with iron oxide mounds and deposits. these deposits are colonized by iron-oxidizing microorganisms that in some cases efficiently remove most of the dissolved iron at low ph, making subsequent treatment of the polluted stream water less expen ...201525501473
self-assembly of biomorphic carbon/sulfur microstructures in sulfidic environments.in natural and laboratory-based environments experiencing sustained counter fluxes of sulfide and oxidants, elemental sulfur (s(0))-a key intermediate in the sulfur cycle-can commonly accumulate. s(0) is frequently invoked as a biomineralization product generated by enzymatic oxidation of hydrogen sulfide and polysulfides. here we show the formation of s(0) encapsulated in nanometre to micrometre-scale tubular and spherical organic structures that self-assemble in sulfide gradient environments i ...201627628108
size dependent microbial oxidation and reduction of magnetite nano- and micro-particles.the ability for magnetite to act as a recyclable electron donor and acceptor for fe-metabolizing bacteria has recently been shown. however, it remains poorly understood whether microbe-mineral interfacial electron transfer processes are limited by the redox capacity of the magnetite surface or that of whole particles. here we examine this issue for the phototrophic fe(ii)-oxidizing bacteria rhodopseudomonas palustris tie-1 and the fe(iii)-reducing bacteria geobacter sulfurreducens, comparing mag ...201627492680
the architecture of iron microbial mats reflects the adaptation of chemolithotrophic iron oxidation in freshwater and marine environments.microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. despite much research on chemolithotrophic fe-oxidizing bacteria, fe mat architecture has not been visualized because these delicate structures are easily disrupted. there are striking similarities between the biominerals that comprise freshwater and marine fe mats, made by beta- and zetaproteobacteria, respectivel ...201627313567
surprising abundance of gallionella-related iron oxidizers in creek sediments at ph 4.4 or at high heavy metal concentrations.we identified and quantified abundant iron-oxidizing bacteria (feob) at three iron-rich, metal-contaminated creek sites with increasing sediment ph from extremely acidic (r1, ph 2.7), to moderately acidic (r2, ph 4.4), to slightly acidic (r3, ph 6.3) in a former uranium-mining district. the geochemical parameters showed little variations over the 1.5 year study period. the highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water a ...201324385973
comparison of microbial community compositions of two subglacial environments reveals a possible role for microbes in chemical weathering processes.viable microbes have been detected beneath several geographically distant glaciers underlain by different lithologies, but comparisons of their microbial communities have not previously been made. this study compared the microbial community compositions of samples from two glaciers overlying differing bedrock. bulk meltwater chemistry indicates that sulfide oxidation and carbonate dissolution account for 90% of the solute flux from bench glacier, alaska, whereas gypsum/anhydrite and carbonate di ...200516269734
composition and diversity of microbial communities recovered from surrogate minerals incubated in an acidic uranium-contaminated aquifer.our understanding of subsurface microbiology is hindered by the inaccessibility of this environment, particularly when the hydrogeologic medium is contaminated with toxic substances. in this study, surrogate geological media contained in a porous receptacle were incubated in a well within the saturated zone of a pristine region of an aquifer to capture populations from the extant communities. after an 8-week incubation, the media were recovered, and the microbial community that developed on each ...200415466548
comparative genomic insights into ecophysiology of neutrophilic, microaerophilic iron oxidizing bacteria.neutrophilic microaerophilic iron-oxidizing bacteria (feob) are thought to play a significant role in cycling of carbon, iron and associated elements in both freshwater and marine iron-rich environments. however, the roles of the neutrophilic microaerophilic feob are still poorly understood due largely to the difficulty of cultivation and lack of functional gene markers. here, we analyze the genomes of two freshwater neutrophilic microaerophilic stalk-forming feob, ferriphaselus amnicola oyt1 an ...201526617599
life at the energetic edge: kinetics of circumneutral iron oxidation by lithotrophic iron-oxidizing bacteria isolated from the wetland-plant rhizosphere.batch cultures of a lithotrophic fe(ii)-oxidizing bacterium, strain brt, isolated from the rhizosphere of a wetland plant, were grown in bioreactors and used to determine the significance of microbial fe(ii) oxidation at circumneutral ph and to identify abiotic variables that affect the partitioning between microbial oxidation and chemical oxidation. strain brt grew only in the presence of an fe(ii) source, with an average doubling time of 25 h. in one set of experiments, fe(ii) oxidation rates ...200212147500
the influence of human settlement on the distribution and diversity of iron-oxidizing bacteria belonging to the gallionellaceae in tropical streams.among the neutrophilic iron-oxidizing bacteria (feob), gallionella is one of the most abundant genera in freshwater environments. by applying qpcr and dgge based on 16s rrna gene-directed primers targeting gallionellaceae, we delineated the composition and abundance of the gallionellaceae-related feob community in streams differentially affected by metal mining, and explored the relationships between these community characteristics and environmental variables. the sampling design included stream ...201425505456
reconstruction of the metabolic potential of acidophilic sideroxydans strains from the metagenome of an microaerophilic enrichment culture of acidophilic iron-oxidizing bacteria from a pilot plant for the treatment of acid mine drainage reveals metabolic versatility and adaptation to life at low ph.bacterial community analyses of samples from a pilot plant for the treatment of acid mine drainage (amd) from the lignite-mining district in lusatia (east germany) had previously demonstrated the dominance of two groups of acidophilic iron oxidizers: the novel candidate genus "ferrovum" and a group comprising gallionella-like strains. since pure culture had proven difficult, previous studies have used genome analyses of co-cultures consisting of "ferrovum" and a strain of the heterotrophic acido ...201628066396
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