Article

Characterization of a Neutrophilic, Chemolithoautotrophic Fe(II)Oxidizing ??-Proteobacterium from Freshwater Wetland Sediments

January 2004
Geomicrobiology 21(1):1-10

January 2004
21(1):1-10

Authors:

University of Wisconsin–Madison

A neutrophilic Fe(II)-oxidizing bacterium (FeOB) isolated from Fe-rich freshwater wetland sediments has been phylogenetically and physiologically characterized. The 16S rRNA gene sequence of this organism (designated strain TW2) places it among the Rhodocyclus group within the β-proteobacteria. The closest known relative to strain TW2 is the heterotrophic perchlorate reducer Dechlorosoma suillum, with 94% 16S rRNA gene identity. TW2 grows chemolithoautotrophically with Fe(II) as an electron donor and O2 as an electron acceptor. Inorganic carbon fixation during growth on Fe(II) was demonstrated via HCO3 fixation experiments. The organism can also grow organotrophically with acetate as the sole carbon and energy source, and can utilize acetate as an auxiliary source of fixed carbon which enhances cell yield (2–3-fold) during lithotrophic growth on Fe(II). No other electron donors and no electron acceptors other than O2 were utilized. The organism's ability to grow with Fe(II) and acetate, along with its limitations with respect to electron acceptor utilization, suggests a specific adaptation to microaerobic niches in redox interfacial environments. The unique metabolism of strain TW2, together with the 16S rRNA sequence data, suggests that this organism represents a novel taxonomic group at the genus level.

Characterization of Neutrophilic Fe(II)-Oxidizing Bacteria Isolated from the Rhizosphere of Wetland Plants and Description of Ferritrophicum radicicola gen. nov. sp. nov., and Sideroxydans paludicola sp. nov

Article

Full-text available

Dec 2007

Iron deposits (Fe plaque) on wetland plant roots contain abundant microbial populations, including Fe(II)-oxidizing bacteria (FeOB) that have not been cultured previously. In this study, 4 strains of Fe plaque-associated FeOB were isolated from 4 species of wetland plants. All 4 isolates grew in tight association with Fe-oxides, but did not form any identifiable Fe-oxide structures. All strains were obligate lithotrophic Fe(II)-oxidizers that were microaerobic, and were unable to use other inorganic or organic energy sources. One strain, BrT, was shown to fix 14CO2 at a rate consistent with its requirement for total cell carbon. The doubling times for the strains varied between 9.5 and 15.8 hours. The fatty acid methyl ester (FAME) profiles of 2 strains, BrT and CCJ, revealed that 16:0, 15:1 isoG, and 14:0 were dominant fatty acids. Phylogenetic analysis of the 16S rRNA gene indicated that all the strains were Betaproteobacteria. Two of the strains, BrT and Br-1 belong to a new species, Sideroxydans paludicola; a third strain, LD-1, is related to Sideroxydans lithotrophicus, a recently described species of FeOB. The fourth isolate, Ferritrophicum radicicola, represented a new genus in a new order of Betaproteobacteria, the Ferritrophicales. There are no other cultured isolates in this order. A small subunit rRNA gene-based, cultivation-independent analysis of Typha latifolia collected from a wetland revealed terminal restriction fragment profiles (tRFLP) consistent with the presence of these bacteria in the rhizosphere. These novel organisms likely play an important role in Fe(II) oxidation kinetics and Fe cycling within many terrestrial and freshwater environments.

In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer

Article

Mar 2024
SCI TOTAL ENVIRON

Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ∼3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.

Ferruginous casts of bromolites in kaolin beds: microbial ferrihydrite-goethite transformation as early stage taphonomy in lacustrine and riparian sediments

Article

Dec 2021

Paul L. Broughton

Two spatiotemporally distant deposits in western North America on differing sides of the K-Pg boundary are recognized to have accumulated innumerable ferruginous faecal-like specimens consisting of 3-D casts suspended in kaolin clay fills of lacustrine and riparian areas proximal to fluvial channels. Evidence presented interprets these specimens as organic in origin, consisting of coprolites and other bromalites (cololites), at the Readlyn deposit of the Whitemud Formation (Maastrichtian) in southern Saskatchewan and the Salmon Creek deposit of the Wilkes Formation (Miocene) near Toledo, Washington State. Comparable taphonomic processes at each deposit are suggested by preservation of identical, metre-long, enigmatic casts of the digestive system (cololites) of an unknown animal associated with the innumerable coprolites. Micro-fabrics of specimen interiors suggest that microbial mats entombed faecal and other organic entities in kaolin-rich lacustrine muds. This research proposes that microbial-induced ferrihydrite precipitation rapidly transformed into thin encrustations of goethite, encasing faecal droppings and other organic remains. Ferrihydrite-goethite-hematite biomineral sequencing cemented kaolin and quartz silt grains at the interface with the organic remains, precluding significant decay and thereby preserving external surface morphologies as encrustations. The mm-thick layers of the cemented sediment enveloped the organic droppings as rigid goethite moulds, preventing the collapse of the encasement morphologies as the organic residues were replaced by biominerals. Concentric growth layers of microbial mat-induced ferrihydrite-goethite cement progressed inward, resulting in 3-D casts. Only external morphologies were preserved, but often with finely detailed surface textures. The interiors of the casts preserve evidence of interconnected fabrics of pseudomorphed bacterial cell walls consisting of radially arranged jackets of acicular (Readlyn deposit) or platy (Salmon Creek deposit) goethite crystallites. Concretionary siderite replacement fabrics in some specimens resulted in the obliteration of the earlier microbial induced biomineral fabrics. Previous interpretations that the Wilkes Formation specimens resulted from inorganic processes only, thereby pseudo-coprolites, have been reappraised as faecal droppings comparable to coprolites of the Whitemud Formation.

Characteristics and possible formation process of ferromanganese beachrock in an intertidal zone of East China Sea influenced by buried ancient woods

Article

Nov 2021
MAR GEOL

The ferromanganese (FeMn) deposits could be found in many shallow water and deep-ocean places. Lots of studies have been performed to explore the occurrence, formation and economic value of FeMn nodules or crusts on the deep ocean floor. However, the occurrence and formation of FeMn beachrocks at the coastal zones has rarely been reported. In the present study, we collected two types of dendritic FeMn beachrock samples from an intertidal zone of Zhoushan Archipelago, East China Sea, where was significantly amended by an ancient wood layer formed during 6200–8540 cal. yr B.P.. Then the microscale analysis including electron microprobe analyzer (EMPA), X-ray powder diffraction (XRD), and scanning electron microscopy-energy dispersive X-ray spectrometer (SEM-EDS) were performed to study the microscale characteristics on these FeMn beachrocks. Combined with our previous studies, a possible formation process was proposed: (1) Buried ancient woods produced enough organic acids to accelerate the weathering of nearby bedrock via chemical or biological reactions; (2) The seepage water could be regarded as a bridge to connect the ancients woods and the intertidal zones, and large amounts of dissolved Fe²⁺ and Mn²⁺ can be transported to the sandy beach and intertidal zones; (3) Precipitation of insoluble FeMn oxides occurred with the involvement of microbial processes and direct inorganic chemical sorption under mixing of seepage water and seawater; (4) After that, these FeMn oxides would experience nucleation, crystallization growth, and then diagenetic process to form the FeMn beachrocks. The present study spotted a light on the microscale features, formation process and biogeochemical cycling of nearshore/coastal diagenetic Fe-Mn deposits.

Nitrate Removal by a Novel Lithoautotrophic Nitrate-Reducing, Iron(II)-Oxidizing Culture Enriched from a Pyrite-Rich Limestone Aquifer

Article

Full-text available

Jul 2021
APPL ENVIRON MICROB

Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially mediated nitrate reduction by Fe(II)-oxidizing (NRFeOx) microorganisms. However, lithoautotrophic NRFeOx cultures have never been enriched from any aquifer and as such there are no model cultures available to study the physiology and geochemistry of this potentially environmentally relevant process. Using iron(II) as an electron donor, we enriched a lithoautotrophic NRFeOx culture from nitrate-containing groundwater of a pyrite-rich limestone aquifer. In the enriched NRFeOx culture that does not require additional organic co-substrates for growth, within 7-11 days 0.3-0.5 mM of nitrate was reduced and 1.3-2 mM of iron(II) was oxidized leading to a stoichiometric NO 3 ⁻ /Fe(II) ratio of 0.2, with N 2 and N 2 O identified as the main nitrate reduction products. Short-range ordered Fe(III) (oxyhydr)oxides were the product of iron(II) oxidation. Microorganisms were observed to be closely associated with formed minerals but only few cells were encrusted, suggesting that most of the bacteria were able to avoid mineral precipitation at their surface. Analysis of the microbial community by long-read 16S rRNA gene sequencing revealed that the culture is dominated by members of the Gallionellaceae family that are known as autotrophic, neutrophilic, microaerophilic iron(II)-oxidizers. In summary, our study suggests that NRFeOx mediated by lithoautotrophic bacteria can lead to nitrate removal in anthropogenically impacted aquifers. Importance Removal of nitrate by microbial denitrification in groundwater is often limited by low concentrations of organic carbon. In these carbon-poor ecosystems, nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate removal. However, no lithoautotrophic NRFeOx culture has been successfully isolated or enriched from this type of environment and as such there are no model cultures available to study the rate-limiting factors of this potentially important process. Here we present the physiology and microbial community composition of a novel lithoautotrophic NRFeOx culture enriched from a fractured aquifer in southern Germany. The culture is dominated by a putative Fe(II)-oxidizer affiliated with the Gallionellaceae family and performs nitrate reduction coupled to Fe(II) oxidation leading to N 2 O and N 2 formation without the addition of organic substrates. Our analyses demonstrate that lithoautotrophic NRFeOx can potentially lead to nitrate removal in nitrate-contaminated aquifers.

Iron-bound carbon increases along a freshwater−oligohaline gradient in a subtropical tidal wetland

Article

Jan 2021
SOIL BIOL BIOCHEM

Globally, a vast extent of tidal wetlands will be threatened by sea-level-rise-induced salinization. Because ferric (hydro)oxides [Fe(III)] play a crucial role in soil organic carbon (SOC) preservation, understanding the responses of the Fe-bound C pool to increasing salinity could assist in accurate prediction of the changes in C stocks in the tidal wetland soils facing imminent sea-level rise. In this study, we investigated pools of Fe-bound C and SOC, C-degrading enzyme activity, Fe species contents and Fe-cycling bacteria, and plant properties along a salinity gradient from freshwater (0.0±0.1 ppt; part per thousand) to oligohaline (2.6±0.6 ppt) in a subtropical tidal wetland. Overall, the belowground biomass and the content of root Fe(III) plaque (a proxy of root oxygen loss potential) rose with the increasing salinity. Along the salinity gradient, the abundance of Gallionella (Fe-oxidizing bacteria) increased, but the abundance of Geobacter (Fe-reducing bacteria) decreased. The Fe(II):Fe(III) ratios decreased as salinity increased, implying that more Fe(II) was oxidized and immobilized into Fe(III) closer to the sea. Fe sulfides contents also elevated close to sea. The co-existence of Fe(III) and Fe sulfides at the oligohaline sites implied a high spatial heterogeneity of Fe distribution. During the growing season, the SOC pool generally decreased with increasing salinity, probably due to a reduction in aboveground-C input and enhanced activity of the C-degrading enzyme. The Fe-bound C pool was positively affected by the amorphous Fe(III) content and negatively related to the activity of phenol oxidase. The Fe-bound C pool generally rose along the salinity gradient, with the importance of Fe-bound C to SOC increasing from 18% to 29%. Altogether, our findings implied that when the imminent sea-level-rise-induced salinization occurs, the total soil C stock may generally decrease, but Fe-bound C will become increasingly important in protecting the rest of the C stocks in tidal wetland soils.

Microbial chemolithotrophy mediates oxidative weathering of granitic bedrock

Article

Dec 2019

The flux of solutes from the chemical weathering of the continental crust supplies a steady supply of essential nutrients necessary for the maintenance of Earth’s biosphere. Promotion of weathering by microorganisms is a well-documented phenomenon and is most often attributed to heterotrophic microbial metabolism for the purposes of nutrient acquisition. Here, we demonstrate the role of chemolithotrophic ferrous iron [Fe(II)]-oxidizing bacteria in biogeochemical weathering of subsurface Fe(II)-silicate minerals at the Luquillo Critical Zone Observatory in Puerto Rico. Under chemolithotrophic growth conditions, mineral-derived Fe(II) in the Rio Blanco Quartz Diorite served as the primary energy source for microbial growth. An enrichment in homologs to gene clusters involved in extracellular electron transfer was associated with dramatically accelerated rates of mineral oxidation and adenosine triphosphate generation relative to sterile diorite suspensions. Transmission electron microscopy and energy-dispersive spectroscopy revealed the accumulation of nanoparticulate Fe–oxyhydroxides on mineral surfaces only under biotic conditions. Microbially oxidized quartz diorite showed greater susceptibility to proton-promoted dissolution, which has important implications for weathering reactions in situ. Collectively, our results suggest that chemolithotrophic Fe(II)-oxidizing bacteria are likely contributors in the transformation of rock to regolith.

浙江舟山海岸带渗漏水沉淀铁泥中的微生物矿化作用

Article

Mar 2008

东海潮间带埋藏古木影响下的Fe-S矿物特征

Article

Apr 2009

Contribution of Microaerophilic Iron(II)-Oxidizers to Iron(III) Mineral Formation

Article

Jun 2019

Neutrophilic microbial aerobic oxidation of ferrous iron (Fe(II)) is restricted to pH-circumneutral environments characterized by low oxygen where microaerophilic Fe(II)-oxidizing microorganisms successfully compete with abiotic Fe(II) oxidation. However, accumulation of ferric (bio)minerals increases competition by stimulating abiotic surface-catalyzed heterogeneous Fe(II) oxidation. Here, we present an experimental approach that allows quantification of microbial and abiotic contribution to Fe(II) oxidation in the presence or initial absence of ferric (bio)minerals. We found that at 20 µM O2 and the initial absence of Fe(III) minerals, an iron(II)-oxidizing enrichment culture (99.6% similarity to Sideroxydans spp.) contributed 40% to the overall Fe(II) oxidation within approx. 26 hours and oxidized up to 3.6∙10-15 mol Fe(II) cell-1 h-1. Optimum O2 concentrations at which enzymatic Fe(II) oxidation can compete with abiotic Fe(II) oxidation ranged from 5-20 µM. Lower O2 levels limited biotic Fe(II) oxidation, while at higher O2 levels abiotic Fe(II) oxidation dominated. The presence of ferric (bio)minerals induced surface-catalytic heterogeneous abiotic Fe(II) oxidation and reduced the microbial contribution to Fe(II) oxidation from 40% to 10% at 10 µM O2. The obtained results will help to better assess the impact of microaerophilic Fe(II) oxidation on the biogeochemical iron cycle in a variety of environmental natural and anthropogenic settings.

Microaerobic Fe(II) oxidation coupled to carbon assimilation processes driven by microbes from paddy soil

Article

Mar 2019

Microaerobic Fe(II) oxidation process at neutral pH, driven by microbes can couple to carbon assimilation process in iron-rich freshwater and marine environments; however, few studies report such coupled processes in paddy soil of the critical zone in South China. In this study, rhizosphere soil from flooded paddy field was used as the inoculum to enrich the microaerophilic Fe(II)-oxidizing bacteria (FeOB) in gradient tubes with different Fe(II) substrates (FeS and FeCO3) and 13C-biocarbonate as inorganic carbon source to track the carbon assimilation. Kinetics of Fe(II) oxidation and biomineralization were analyzed, and the composition and abundance of the microbial community were profiled using 16S rRNA gene-based high-throughput sequencing. Results showed that microbial cell bands were formed 0.5–1.0 cm below the medium surface in the inoculated tubes with Fe(II) substances, while no cell band was found in the non-inocula controls. The protein concentrations in the cell bands reached the highest values at 18.7–22.9 mg mL-1 on 6 d in the inocula tubes with Fe(II) substrates. A plateau of the yields of 13C-biocarbonate incorporation was observed during 6–15 d at 0.44–0.54% and 1.61–1.98% in the inocula tubes with FeS and FeCO3, respectively. The inocula tube with FeS showed a higher Fe(II) oxidation rate of 0.156 mmol L-1 d-1 than that with FeCO3 (0.106 mmol L-1 d-1). Analyses of X-ray diffraction and scanning electron microscopy with energy-dispersive X-ray spectroscopy revealed that amorphous iron oxide was formed on the surface of rod-shaped bacteria after Fe(II) oxidation. Relative to the agar only control, the abundances of Clostridium and Pseudogulbenkiania increased in the inocula tube with FeS, while those of Vogesella, Magnetospirillum, Solitalea, and Oxalicibacterium increased in the inocula tube with FeCO3, all of which might be the potential microaerophilic FeOB in paddy soil. The findings in this study suggest that microbes that couple microaerobic Fe(II) oxidation to carbon assimilation existed in the paddy soil, which provides an insight into the iron-carbon coupling transformation under microaerobic conditions in the critical zone of the iron-rich red soil.

5. Geomicrobiological Cycling of Iron

Chapter

Dec 2005

Insights into the Fundamental Physiology of the Uncultured Fe-Oxidizing Bacterium Leptothrix ochracea

Article

Full-text available

Apr 2018
APPL ENVIRON MICROB

Leptothrix ochracea is known for producing large volumes of iron oxyhydroxide sheaths that alter wetland biogeochemistry. For over a century, these delicate structures have fascinated microbiologists and geoscientists. Because L. ochracea still resists long-term in vitro culture, the debate regarding its metabolic classification dates back to 1885. We developed a novel culturing technique for L. ochracea using in situ natural waters and coupled this with single-cell genomics and nanoscale secondary-ion mass spectrophotometry (nanoSIMS) to probe L. ochracea's physiology. In microslide cultures L. ochracea doubled every 5.7 h and had an absolute growth requirement for ferrous iron, the genomic capacity for iron oxidation, and a branched electron transport chain with cytochromes putatively involved in lithotrophic iron oxidation. Additionally, its genome encoded several electron transport chain proteins, including a molybdopterin alternative complex III (ACIII), a cytochrome bd oxidase reductase, and several terminal oxidase genes. L. ochracea contained two key autotrophic proteins in the Calvin-Benson-Bassham cycle, a form II ribulose bisphosphate carboxylase, and a phosphoribulose kinase. L. ochracea also assimilated bicarbonate, although calculations suggest that bicarbonate assimilation is a small fraction of its total carbon assimilation. Finally, L. ochracea's fundamental physiology is a hybrid of those of the chemolithotrophic Gallionella-type iron-oxidizing bacteria and the sheathed, heterotrophic filamentous metal-oxidizing bacteria of the Leptothrix-Sphaerotilus genera. This allows L. ochracea to inhabit a unique niche within the neutrophilic iron seeps. IMPORTANCE Leptothrix ochracea was one of three groups of organisms that Sergei Winogradsky used in the 1880s to develop his hypothesis on chemolithotrophy. L. ochracea continues to resist cultivation and appears to have an absolute requirement for organic-rich waters, suggesting that its true physiology remains unknown. Further, L. ochracea is an ecological engineer; a few L. ochracea cells can generate prodigious volumes of iron oxyhydroxides, changing the ecosystem's geochemistry and ecology. Therefore, to determine L. ochracea's basic physiology, we employed new single-cell techniques to demonstrate that L. ochracea oxidizes iron to generate energy and, despite having predicted genes for autotrophic growth, assimilates a fraction of the total CO2 that autotrophs do. Although not a true chemolithoautotroph, L. ochracea's physiological strategy allows it to be flexible and to extensively colonize iron-rich wetlands.

A novel organotrophic nitrate-reducing Fe(II)-oxidizing bacterium isolated from paddy soil and draft genome sequencing indicate its metabolic versatility

Article

Full-text available

Dec 2017

The extensive application of fertilizers for growing rice results in a large input of nitrogen into paddy soils. During rice growth, iron is exposed to periodic transition under different redox conditions. Nitrate (NO3⁻) reduction coupled to Fe(II) oxidation (NRCFO) links the iron and nitrogen cycles. However, little is known about the biogeochemical mechanism and microorganisms involved in NRCFO in paddy soil. In the present study, we isolated an anaerobic, NO3⁻-reducing Fe(II) oxidizer known as strain Paddy-1 from paddy soil. After 6 days of culture in 5 mM acetate, this strain reduced 97% of NO3⁻ and oxidized 86% of Fe(II) from initial concentrations of 9.3 and 5.1 mM, respectively. A phylogenetic analysis of the 16S rRNA gene sequence placed strain Paddy-1 in a clade within the order Rhodocyclales. In accordance with other NRCFO species, Fe(III) oxides produced by strain Paddy-1 were in the form of amorphous Fe(III) oxides. The reported draft genome of strain Paddy-1 predicts the presence of genes involved in denitrification, outer membrane electron transport, and iron homeostasis as well as candidate Fe(II) oxidation genes. The physiological and genomic information on this strain provide a basis for investigating the mechanism of NRCFO in microorganisms from paddy soil.

Microaerophilic Fe(II)-oxidizing Zetaproteobacteria isolated from low-Fe marine coastal sediments – physiology and characterization of their twisted stalks

Article

Full-text available

Mar 2017
APPL ENVIRON MICROB

Importance: So far only few isolates of benthic marine microaerophilic Fe(II)-oxidizers belonging to the Zetaproteobacteria exist and most isolates were obtained from habitats containing elevated Fe concentrations. Consequently, it was thought that these microorganisms are important mainly in habitats with high Fe concentrations. The two novel isolates of Zetaproteobactera that are presented in the present study were isolated from typical coastal marine sediments that do not contain elevated Fe concentrations. This increases the knowledge about possible habitats in which Zetaproteobacteria can exist. Furthermore, we showed that the physiology and the typical organo-mineral structures (twisted stalks) that are produced by the isolates do not notably differ from the physiology and the cell-mineral structures of isolates from environments with high Fe concentrations. We also showed that the organo-mineral structures can function as a sink for trace metals.

Study on the Composition of Biogenic Iron-Containing Materials Obtained Under Cultivation of the Leptothrix sp. on Different Media

Article

Full-text available

Mar 2017
APPL BIOCHEM BIOTECH

The biogenic iron oxide/hydroxide materials possess useful combination of physicochemical properties and are considered for application in various areas. Their production does not require special investments because these compounds are formed during cultivation of neurophilic iron bacteria. Bacteria from genus Leptothrix develop intensively in the Sphaerotilus-Leptothrix group of bacteria isolation medium and feeding media of Fedorov and Lieske. These media are different in their composition which determined the present study as an attempt to clear up the reasons that define the differences in the composition of the laboratory-obtained biomasses and the natural biomass finds. FTIRS, Mössbauer spectroscopy, and XRD were used in the research. Comparative analysis showed that the biomass and control samples contain iron compounds (α-FeOOH, γ-FeOOH, β-FeOOH, γ-Fe2O3) in different ratios. The biomass samples were enriched in oxyhydroxides of higher dispersion. Organic residuals of bacterial origin, SO4, CO3, and PO4 groups were registered in the biogenic materials.

The role of microaerophilic Fe-oxidizing micro-organisms in producing banded iron formations

Article

Jul 2016
GEOBIOLOGY

Despite the historical and economic significance of banded iron formations (BIFs), we have yet to resolve the formation mechanisms. On modern Earth, neutrophilic microaerophilic Fe-oxidizing micro-organisms (FeOM) produce copious amounts of Fe oxyhydroxides, leading us to wonder whether similar organisms played a role in producing BIFs. To evaluate this, we review the current knowledge of modern microaerophilic FeOM in the context of BIF paleoenvironmental studies. In modern environments wherever Fe(II) and O2 co-exist, microaerophilic FeOM proliferate. These organisms grow in a variety of environments, including the marine water column redoxcline, which is where BIF precursor minerals likely formed. FeOM can grow across a range of O2 concentrations, measured as low as 2 μm to date, although lower concentrations have not been tested. While some extant FeOM can tolerate high O2 concentrations, many FeOM appear to prefer and thrive at low O2 concentrations (~3-25 μm). These are similar to the estimated dissolved O2 concentrations in the few hundred million years prior to the 'Great Oxidation Event' (GOE). We compare biotic and abiotic Fe oxidation kinetics in the presence of varying levels of O2 and show that microaerophilic FeOM contribute substantially to Fe oxidation, at rates fast enough to account for BIF deposition. Based on this synthesis, we propose that microaerophilic FeOM were capable of playing a significant role in depositing the largest, most well-known BIFs associated with the GOE, as well as afterward when global O2 levels increased.

The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

Article

Full-text available

Jun 2016

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, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to chemolithotrophic Fe oxidation, including (1) removing Fe oxyhydroxide waste without entombing cells or clogging flow paths through the mat and (2) colonizing niches where Fe(II) and O2 overlap. This work improves our understanding of Fe mat developmental history and how mat morphology links to metabolism. We can use these results to interpret biogenicity, metabolism, and paleoenvironmental conditions of Fe microfossil mats, which would give us insight into Earth's Fe and O2 history.

The interplay of hydrological, chemical and microbial processes in the formation of iron-rich floating films in aquatic environments at a circumneutral pH

Article

Full-text available

Dec 2015

The direct contribution of microbial activity to the formation of iron-oxide minerals is difficult to prove in wetlands due to the high reactivity of solid iron phases with different compounds and the variety of redox processes that may occur at each oxic-anoxic boundary. Here, we propose an explanation for the formation of iron-oxide films in wetlands and groundwater seepage areas fed by sandy aquifers based on the interaction of hydrological, chemical and microbiological processes under circumneutral conditions. The presence of a floating iron-oxide film was found to create a boundary at the air-water interface that maintains a suboxic and slightly acidic environment below the film compared with the environments obtained in other free-film wetland areas. The water trapped below this film had an average pH of 6.1, was particularly poor in O2, HCO–3, Na+, Ca2+, Mg2+, K+, and Tot-S, and has high concentrations of Tot-P, Tot-Fe, NH+4 and Zn. The formation of a floating iron-oxide film was reproduced under anaerobic conditions after progressive enrichment through the incubation of natural sediment samples in the laboratory. Heterotrophic bacteria belonging to the genus Enterobacter were the dominant bacteria in the enrichments that resulted in the formation of a floating iron-oxide film. The X-ray diffraction patterns showed that the presence of two-line ferrihydrite was common to the iron-oxide films collected in both the natural environment and the laboratory cultures, whereas other iron-oxides (goethite and low-crystalline lepidocrocite) were observed only in the natural environment. This study highlights the role of ubiquitous bacteria, which are generally considered unimportant participants in iron-transformation processes in the environment, and the contribution of both biological and non-biological processes to iron oxidation in natural systems under circumneutral conditions.

Biogenic Iron-Rich Filaments in the Quartz Veins in the Uppermost Ediacaran Qigebulake Formation, Aksu Area, Northwestern Tarim Basin, China: Implications for Iron Oxidizers in Subseafloor Hydrothermal Systems

Article

Full-text available

Jul 2015
ASTROBIOLOGY

Fe-(oxyhydr)oxide-encrusted filamentous microstructures produced by microorganisms have been widely reported in various modern and ancient extreme environments; however, the iron-dependent microorganisms preserved in hydrothermal quartz veins have not been explored in detail because of limited materials available. In this study, abundant well-preserved filamentous microstructures were observed in the hydrothermal quartz veins of the uppermost dolostones of the terminal-Ediacaran Qigebulake Formation in the Aksu area, northwestern Tarim Basin, China. These filamentous microstructures were permineralized by goethite and hematite as revealed by Raman spectroscopy and completely entombed in chalcedony and quartz cements. Microscopically, they are characterized by biogenic filamentous morphologies (commonly 20-200 μm in length and 1-5 μm in diameter) and structures (curved, tubular sheath-like, segmented, and mat-like filaments), similar to the Fe-oxidizing bacteria (FeOB) living in modern and ancient hydrothermal vent fields. A previous study revealed that quartz-barite vein swarms were subseafloor channels of low-temperature, silica-rich, diffusive hydrothermal vents in the earliest Cambrian, which contributed silica to the deposition of the overlying bedded chert of the Yurtus Formation. In this context, this study suggests that the putative filamentous FeOB preserved in the quartz veins might have thrived in the low-temperature, silica- and Fe(II)-rich hydrothermal vent channels in subseafloor mixing zones and were rapidly fossilized by subsequent higher-temperature, silica-rich hydrothermal fluids in response to waning and waxing fluctuations of diffuse hydrothermal venting. In view of the occurrence in a relatively stable passive continental margin shelf environment in Tarim Block, the silica-rich submarine hydrothermal vent system may represent a new and important geological niche favorable for FeOB colonization, which is different from their traditional habitats reported in hydrothermal vent systems at oceanic spreading centers or volcanic seamounts. Thus, these newly recognized microfossils offer a new clue to explore the biological signatures and habitat diversity of microorganisms on Earth and beyond. Key Words: Filamentous microfossils-Fe-oxidizing bacteria-Uppermost Ediacaran-Quartz vein-Submarine hydrothermal feeder system-The earliest Cambrian. Astrobiology 15, 523-537.

Microbial biomineralization of iron seepage water: Implication for the iron ores formation in intertidal zone of Zhoushan Archipelago, East China Sea

Article

Jan 2009

The biogeochemcical reactions responsible for fossilized minerals preservation in ancient geological conditions are very often debatable, because little is known about the in situ processes at geo-historical period. in the present study, we describe the formation of iron ores collected in the intertidal zone of the Zhujiajian island, Zhoushan Archipelago in the East China Sea. Morphological, mineralogical and geochemical analyses were performed on the iron ores and the surrounding geological materials. The results show that the iron ores, composed of spherical ferrihydrite and fibrous aggregates of goethite, presented morphological characteristics reminiscent of bacterial activity. The biominerization process in the seepage system is believed to represent an analogue mechanism for the biogenic formation of iron ores. The degradation of the ancient wood layer provided humic substances which accelerated the leaching process of iron from the surrounding bedrock and soils. The abundant leaching iron not only provided the sufficient iron material source, but also created the ideal conditions for the survival of the iron-oxidizing bacteria. The presence of Leptothrix-like sheaths and Gallionella-like stalks in the present-day seepage environment promoted the oxidization of Fe2+ to Fe3+ and the rapid precipitation of bacteriogenic iron oxides (BIOS) on bacterial sheaths and stalks, allowing the preservation of the morphological characteristics of the bacteria. As time went by, the amorphous biomineralization product (ferrihydrite) can further transfer to more crystalline goethite and therefore be preserved in the ores permanently, representing as the imprints of bacterial activity during the formation of iron ores. The present findings should help elucidate the role of bacteria in the formation of biogenic iron ores in different environments during geo-historical context.

Geomicrobiological Cycling of Iron

Article

Full-text available

Jan 2005

Andreas Kappler

Iron is the most abundant element on Earth and the most frequently utilized transition metal in the biosphere. It is a component of many cellular compounds and is involved in numerous physiological functions. Hence, iron is an essential micronutrient for all eukaryotes and the majority of prokaryotes. Prokaryotes that need iron for biosynthesis require micromolar concentrations, levels that are often not available in neutral pH oxic environments. Therefore, prokaryotes have evolved specific acquisition molecules, called siderophores, to increase iron bioavailability. Acquisition of iron by siderophores is a complex process and is discussed in detail by Kraemer et al. (2005). Here we focus on prokaryotes that generate energy for growth by oxidation or reduction of iron. In both processes single electron transfers are involved. Hence, for a significant extent of energy generation, turnover of iron in the millimolar rather than the micromolar range is necessary. Iron metabolizing organisms have therefore a strong influence on iron cycling in the environment. Microbial iron oxidation and reduction will be discussed, with emphasis on circumneutral pH environments that prevail on Earth. The active metabolic processes outlined above have to be distinguished from indirect biologically induced iron mineral formation in which prokaryotic cell surfaces simply act as passive templates (“passive iron biomineralization”) (e.g., Konhauser 1997). ### General aspects of the iron cycle On our planet, iron is ubiquitous in the hydrosphere, lithosphere, biosphere and atmosphere, either as particulate ferric [Fe(III)] or ferrous [Fe(II)] iron-bearing minerals or as dissolved ions. Redox transformations of iron, as well as dissolution and precipitation and thus mobilization and redistribution, are caused by chemical and to a significant extent by microbial processes (Fig. 1⇓). Microorganisms catalyze the oxidation of Fe(II) under oxic or anoxic conditions as well as the reduction of Fe(III) in anoxic habitats. Microbially influenced transformations of iron are often much faster than the …

QPCR Analysis of Functional Genes in Iron-Rich Microbial Mats at an Active Hydrothermal Vent System Lō'ihi Seamount, Hawaii.

Article

Full-text available

Apr 2015
APPL ENVIRON MICROB

The chemolithotrophic Zetaproteobacteria represent a novel class of Proteobacteria which oxidize Fe(II) to Fe(III) and are the dominant bacterial population in iron-rich microbial mats. Zetaproteobacteria were first discovered at Lō'ihi Seamount, located 35 km southeast off the big island of Hawaii, which is characterized by low-temperature diffuse hydrothermal venting. Novel non-degenerate QPCR assays for genes associated with microbial nitrogen fixation, denitrification, arsenic detoxification, Calvin Benson Bassham (CBB), and reductive tricarboxylic acid (rTCA) cycles were developed using selected microbial mat community-derived metagenomes. Nitrogen fixation genes were not detected but all other functional genes were present. This suggests that arsenic detoxification and denitrification processes are likely co-occurring in addition to two modes of carbon fixation. Two groups of microbial mat community types were identified by T-RFLP and were further described based on QPCR data for Zetaproteobacterial abundance and carbon fixation mode preference. QPCR variance was associated with mat morphology, but not for temperature or sample site. Geochemistry data was significantly associated with sample site and mat morphology. Together, these QPCR assays constitute a 'functional gene signature' for iron microbial mat communities across a broad array of temperatures, mat types, chemistries, and sampling sites at Lō'ihi Seamount. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Formation of biogenic sheath-like Fe oxyhydroxides in a near-neutral pH hot spring: Implications for the origin of microfossils in high-temperature, Fe-rich environments

Article

Full-text available

Dec 2013

[1] A small hot spring that is informally called “Fe-waterfall spring” and is located in the Rehai geothermal area discharges hot (42 to 73°C), near-neutral (pH = 7.65) Fe-rich water. Submerged reddish precipitates are composed largely of ferrihydrite, goethite, lepidocrocite, opal-A, quartz, and anorthite, as revealed by X-ray diffraction (XRD) and Mössbauer spectroscopy. Molecular phylogenetic analysis demonstrates that the bacterial community in these precipitates is mainly composed of Cyanobacteria, Planctomycetes, β-proteobacteria, Deinococci-Thermus, and Chlorobi. Scanning electron microscopy and high-resolution transmission electron microscopy examinations show that abundant sheath-like Fe oxyhydroxides, which exhibit different morphologies and sizes, are present in Fe-rich precipitates. These sheath-like structures are composed of ferrihydrite rather than more crystalline lepidocrocite or goethite. Energy-dispersive X-ray spectrometer, scanning transmission electron microscopy, and nano secondary ion mass spectrometry reveal that they are mainly composed of Fe, Si, and O, together with some trace elements. Most of the sheath-like structures are not morphologically comparable to biogenic Fe oxyhydroxides produced by known chemolithotrophic Fe oxidizers, which is consistent with the fact that no chemolithotrophic Fe oxidizers were identified by molecular analysis in the precipitates. We suggest that the sheath-like Fe oxyhydroxides are formed through passive Fe sorption and nucleation onto the cell walls of various thermophiles rather than by the direct metabolic activities of chemolithotrophic Fe oxidizers. Biogenic sheath-like Fe oxyhydroxides in Fe-waterfall spring have important implications for geochemical cycles driven by microorganisms, the origin of microfossils, and the formation of banded iron formations (BIFs) in the Archean ocean.

Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations

Article

Full-text available

Dec 2013

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 at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic “Ferrovum myxofaciens” was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and “Ferrovum myxofaciens” revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments.

Fe-phyllosilicate redox cycling organisms from a redox transition zone in Hanford 300 Area sediments

Article

Full-text available

Dec 2013

Microorganisms capable of reducing or oxidizing structural iron (Fe) in Fe-bearing phyllosilicate minerals were enriched and isolated from a subsurface redox transition zone at the Hanford 300 Area site in eastern Washington, USA. Both conventional and in situ “i-chip” enrichment strategies were employed. One Fe(III)-reducing Geobacter (G. bremensis strain R1, Deltaproteobacteria) and six Fe(II) phyllosilicate-oxidizing isolates from the Alphaproteobacteria (Bradyrhizobium japonicum strains 22, is5, and in8p8), Betaproteobacteria (Cupriavidus necator strain A5-1, Dechloromonas agitata strain is5), and Actinobacteria (Nocardioides sp. strain in31) were recovered. The G. bremensis isolate grew by oxidizing acetate with the oxidized form of NAu-2 smectite as the electron acceptor. The Fe(II)-oxidizers grew by oxidation of chemically reduced smectite as the energy source with nitrate as the electron acceptor. The Bradyrhizobium isolates could also carry out aerobic oxidation of biotite. This is the first report of the recovery of a Fe(II)-oxidizing Nocardioides, and to date only one other Fe(II)-oxidizing Bradyrhizobium is known. The 16S rRNA gene sequences of the isolates were similar to ones found in clone libraries from Hanford 300 sediments and groundwater, suggesting that such organisms may be present and active in situ. Whole genome sequencing of the isolates is underway, the results of which will enable comparative genomic analysis of mechanisms of extracellular phyllosilicate Fe redox metabolism, and facilitate development of techniques to detect the presence and expression of genes associated with microbial phyllosilicate Fe redox cycling in sediments.

Review on iron availability in soil: Interaction of Fe minerals, plants, and microbes

Article

Full-text available

Nov 2013

The rationale of this paper is to review the state of the art regarding the biotic and abiotic reactions that can influence Fe availability in soils. In soil, the management-induced change from oxic to anoxic environment results in temporal and spatial variations of redox reactions, which, in turn, affect the Fe dynamics and Fe mineral constituents. Measuring the Fe forms in organic complexes and the interaction between bacteria and Fe is a major challenge in getting a better quantitative understanding of the dynamics of Fe in complex soil ecosystems.We review the existing literature on chemical and biochemical processes in soils related with the availability of Fe that influences plant nutrition. We describe Fe acquisition by plant and bacteria, and the different Fe–organic complexes in order to understand their relationships and the role of Fe in the soil carbon cycle.Although total Fe is generally high in soil, the magnitude of its available fraction is generally very low and is governed by very low solubility of Fe oxides. Plants and microorganisms can have different strategies in order to improve Fe uptake including the release of organic molecules and metabolites able to form complexes with FeIII. Microorganisms appear to be highly competitive for Fe compared with plant roots. Crystalline Fe and poorly crystalline (hydro)oxides are also able to influence the carbon storage in soil.The solubility of crystalline Fe minerals in soil is usually very low; however, the interaction with plant, microbes, and organic substance can improve the formation of soluble FeIII complexes and increase the availability of Fe for plant growth. Microbes release siderophores and plant exudates (e.g., phytosiderophores, organic acids, and flavonoids), which can bind and solubilize the Fe present in minerals. The improved understanding of this topic can enable the identification of effective solutions for remedying Fe deficiency or, alternatively, restricting the onset of its symptoms and yield’s limitations in crops. Therefore, development and testing of new analytical techniques and an integrated approach between soil biology and soil chemistry are important prerequisites.

Acetyl Coumarin effect on iron availability in some types of Egyptian soils - تأثير الأسيتيل كومارين علي صلاحية عنصر الحديد في بعض أنواع الأراضي المصرية

Technical Report

Sep 2023

Saeed Gwally

Reduction of Chromate via Biotic and Abiotic Pathways in the Presence of Three Co-contaminating Electron Acceptors

Article

Dec 2023

Photoferrotrophy, BIF deposition, and iron-free oxygen oases in the Archean surface ocean

Preprint

Full-text available

Nov 2023

Banded Iron Formations (BIFs) are both the world’s largest ore deposits and important geological archives that record the early evolution of the Earth-Life system. BIFs were likely deposited as the result of ferrous iron [Fe(II)] oxidation, precipitation, and sedimentation from iron-rich (ferruginous) seawater, mostly during the Archean Eon. Proposed mechanisms for iron oxidation include abiotic reactions with photosynthetic oxygen, reaction with oxygen catalyzed by iron-oxidizing bacteria (IOB), and anoxic oxidation by anoxygenic iron-oxidizing phototrophic bacteria (photoferrotrophs). These iron oxidation processes may have operated concurrently, but their relative contributions to BIF deposition have not been considered. Here, we developed a 1-D ferruginous ocean model incorporating abiotic iron cycling and the physiology of oxygenic phototrophs, microaerophilic IOB, photoferrotrophs, and iron-reducing bacteria. Our model shows that, under Archean ocean conditions, most iron oxidation and precipitation would have been driven by photoferrotrophy, with a small fraction by microaerophilic IOB and a negligible contribution from abiotic reactions. The combined activities of these pathways led to BIF deposition at rates in line with geological records and, importantly, allowed the development of an Fe(II)-free surface ocean conducive to the formation of oxygen oases and the proliferation of oxygenic phototrophs. Teaser Archean ocean simulation shows that photoferrotrophs dominated the precipitation of BIFs and promoted the formation of marine oxygen oases.

Hydrologic fluxes of iron in groundwater ecosystems: Implications for global risks and challenges

Chapter

Nov 2023

Iron (Fe) is ranked as the second most abundant metallic element in the Earth’s crust and functions as an essential micronutrient for all living organisms. Both bioavailability and the redox sensitivity of iron are well documented in a variety of environmental ecosystems. The cycling of iron influences various global reservoirs including sediments, soil, lakes, and groundwater via abiotic and biotic processes. In groundwater, the occurrence of iron is predominantly in the form of complexes, such as ferrous bicarbonate, Fe(OH)3, and Fe3O4, which form as a result of dissolved iron content and percolation from underlying soil and rock structures. In groundwater systems, iron speciation is shaped by critical factors including chemical composition, addition and removal of iron, and internal recycling. Several studies conducted around the world highlighted that in comparison to WHO standards, concentrations exceeding 0.3 μg/mL level pose a serious threat because groundwater is contaminated by iron. Long-term assessments suggest that the reductive dissolution of iron (hydr)oxide minerals and complexes in groundwater contribute to sources of dissolved Fe concentrations. The reducing conditions, residence time, depth, and salinity contribute to dissolution and migration of Fe to groundwater. Moreover, diverse microbial species representing heterotrophic iron-oxidizing (FeOB) and iron-reducing (FeRB) phylogenetic groups greatly influence the fate of ion cycling and bioavailability in groundwater. With these issues in mind, this chapter seeks to outline global iron flux, highlighting microbial and biochemical intervention in the transition processes and possible issues and challenges that need to be resolved for combating iron contamination in groundwater systems.

Increase in iron-bound organic carbon content under simulated sea-level rise: A “marsh organ” field experiment

Article

Oct 2023
SOIL BIOL BIOCHEM

Corrosion of X65 steel by Pseudomonas sp. in planktonic and sessile states and inhibition effect of cathodic polarization

Article

Nov 2022

In harsh marine environment, corrosion is a serious problem, among which microbiologically influenced corrosion is particularly common and complex. This work studied corrosion of X65 steel by planktonic and sessile iron oxidizing bacteria (IOB), i.e. Pseudomonas sp. isolated from coastal water of Qingdao, and inhibition effect of cathodic polarization. Results demonstrate that both the planktonic and sessile IOB caused the corrosion of X65 steel by promoting the oxidation of ferrous ions, but the contribution of sessile cells was far greater than that of planktonic cells. Cathodic polarization kills sessile cells on the metal surface and prevent attachment of IOB. With a negative shift of the cathodic potential, the inhibition effect was enhanced. Cathodic polarization altered interface properties of X65 steel, affecting adhesion and corrosion process of IOB cells. However, when X65 steel was sufficiently polarized to −1050 mV vs. SCE, IOB produced more extracellular polymeric substances to resist stimulation by an external electric field. Therefore, cathodic polarization could not completely remove sessile IOB cells, and pitting corrosion existed on the metal surface.

Microbial Metal Cycling in Aquatic Environments

Chapter

May 2007

Microbially Mediated Anaerobic Iron(II) Oxidation at Circumneutral pH

Chapter

May 2007

Microorganisms and Bioprocessing, General

Chapter

Oct 2022

Mingming Zhang

Bioprocesses have been developed for an enormous range of commercial applications, from production of industrial alcohol and organic solvents, specialty chemicals such as antibiotics, therapeutic proteins, and vaccines to bioleaching of gold, copper, and uranium. Successful bioprocess begins with an effective biocatalyst which involves knowledge in microbiology, biochemistry, and molecular biology relevant to bioprocess design, operation, and scale-up, and the significance of these subjects in defining optimum bioprocess performance. To this end, this chapter focuses on the microbiology, biochemistry, and molecular biology which underpin bioprocessing, and gives the readers an introduction to microbes which includes their classification, morphology, internal structures, and nutrient and energy requirements.KeywordsBioprocessesMicroorganismsBacteriaIron oresMetal extraction

Activity of Autotrophic Fe(II)-Oxidizing Denitrifiers in Freshwater Lake Sediments

Article

May 2021

Orange leads to black: evaluating the efficacy of co‐culturing iron‐oxidizing and sulfate‐reducing bacteria to discern ecological relationships

Article

Feb 2021

Two global cycles, iron and sulfur, are critically interconnected in estuarine environments by microbiological actors. To this point, the methods of laboratory study of this interaction have been limited. Here we propose a methodology for co-culturing from numerous coastal environments, from the same source inocula, iron-oxidizing and sulfate-reducing bacteria. The use of same source inocula is largely beneficial to understand real-world interactions that are likely occurring in situ. Through the use of this methodology, the ecological interactions between these groups can be studied in a more controlled environment. Here, we characterize the oxygen and hydrogen sulfide concentrations using microelectrode depth profiling in the co-cultures of iron-oxidizing bacteria and sulfate-reducing bacteria. These results suggest that while oxygen drives the relationship between these organisms and sulfate-reducers are reliant on iron-oxidizers in this culture to create an anoxic environment, there is likely another environmental driver that also influences the interaction as the two remain spatially distinct, as trends in FeS precipitation changed within the anoxic zone relative to the presence of Fe(III) oxyhydroxides. Understanding the relationship between iron-oxidizing and sulfate-reducing bacteria will ultimately have implications for understanding microbial cycling in estuarine environments as well as in processes such as controlling microbially influenced corrosion.

The Weathering Microbiome of an Outcropping Granodiorite

Article

Full-text available

Dec 2020

Microorganisms have long been recognized for their capacity to catalyze the weathering of silicate minerals. While the vast majority of studies on microbially mediated silicate weathering focus on organotrophic metabolism linked to nutrient acquisition, it has been recently demonstrated that chemolithotrophic ferrous iron [Fe(II)] oxidizing bacteria (FeOB) are capable of coupling the oxidation of silicate mineral Fe(II) to metabolic energy generation and cellular growth. In natural systems, complex microbial consortia with diverse metabolic capabilities can exist and interact to influence the biogeochemical cycling of essential elements, including iron. Here we combine microbiological and metagenomic analyses to investigate the potential interactions among metabolically diverse microorganisms in the near surface weathering of an outcrop of the Rio Blanco Quartz Diorite (DIO) in the Luquillo Mountains of Puerto Rico. Laboratory based incubations utilizing ground DIO as metabolic energy source for chemolithotrophic FeOB confirmed the ability of FeOB to grow via the oxidation of silicate-bound Fe(II). Dramatically accelerated rates of Fe(II)-oxidation were associated with an enrichment in microorganisms with the genetic capacity for iron oxidizing extracellular electron transfer (EET) pathways. Microbially oxidized DIO displayed an enhanced susceptibility to the weathering activity of organotrophic microorganisms compared to unoxidized mineral suspensions. Our results suggest that chemolithotrophic and organotrophic microorganisms are likely to coexist and contribute synergistically to the overall weathering of the in situ bedrock outcrop.

稻田土壤微生物驱动的微好氧亚铁氧化耦合碳同化过程

Article

Dec 2019

Distinguishing Biotic and Abiotic Iron Oxidation at Low Temperatures

Article

May 2019

The rates of microbial and abiotic iron oxidation were determined in a variety of cold (T= 9-12°C), circumneutral (pH = 5.5-9) environments in the Swiss Alps. These habitats include iron-bicarbonate springs, iron-arsenic-bicarbonate springs, and alpine lakes. Rates of microbial iron oxidation were measured up to a pH of 7.4, with only abiotic processes detected at higher pH values. Iron oxidizing bacteria (FeOB) were responsible for 39-89% of the net oxidation rate at locations where biological iron oxidation was detected. Members of putative iron oxidizing genera, especially Gallionella, are abundant in systems where biological iron oxidation was measured. Geochemical sampling suites accompanying each experiment include field data (temperature, pH, conductivity, dissolved oxygen, redox sensitive solutes), solute concentrations, and sediment composition. Dissolved inorganic carbon concentrations indicate that bicarbonate and carbonate are typically the most abundant anions in these systems. Speciation calculations reveal that ferrous iron typically exists as FeCO3 (aq), FeHCO3+, FeSO4 (aq) or Fe2+ in these systems. The abundance of ferrous carbonate and bicarbonate species appears to lead to a dramatic increase in the abiotic rate of reaction compared to the rate expected from chemical oxidation in dilute solution. This approach, integrating geochemistry, rates, and community composition, reveals locations and geochemical conditions that permit microbial iron oxidation, and locations where the abiotic rate is too fast for the biotic process to compete.

Evidence for the Existence of Autotrophic Nitrate-Reducing Fe(II)-Oxidizing Bacteria in Marine Coastal Sediment

Article

Full-text available

Sep 2016
APPL ENVIRON MICROB

Importance: Twenty years after the discovery of nitrate-reducing Fe(II)-oxidizers it is still controversially discussed if autotrophic nitrate-reducing Fe(II)-oxidizing microorganisms exist and to what extent Fe(II) oxidation in this process is enzymatically catalyzed or which role abiotic side reactions of Fe(II) with reactive N-species play. Most pure cultures of nitrate-reducing Fe(II)-oxidizers are mixotrophic i.e., they need an organic co-substrate to maintain their activity over several cultural transfers. For the few existing autotrophic isolates and enrichment cultures either the mechanism of nitrate-reducing Fe(II) oxidation is not known or the evidence for their autotrophic lifestyle is controversial. In the present study, we provide the first evidence for the existence of autotrophic nitrate-reducing Fe(II)-oxidizers in coastal marine sediments. The evidence is based on stoichiometries of nitrate reduction and Fe(II) oxidation determined in microcosm incubations and the incorporation of carbon from CO2 under conditions that favor the activity of nitrate-reducing Fe(II) oxidizers.

Sedimentary facies analyses from nano- to millimetre scale exploring past microbial activity in a high-altitude lake (Lake Son Kul, Central Asia)

Article

Full-text available

Mar 2015
GEOL MAG

The fabric of sedimentary rocks in lacustrine archives usually contains long and continuous proxy records of biological, chemical and physical parameters that can be used to study past environmental and climatic variability. Here we propose an innovative approach to sedimentary facies analysis based on a coupled geomicrobiological and sedimentological study using high-resolution microscopic techniques in combination with mineralogical analyses. We test the applicability of this approach on Lake Son Kul, a high alpine lake in central Tien Shan (Kyrgyzstan) by looking at the mineral fabric and microbial communities observed down to the nanoscale. The characterization of microbe–mineral interactions allows the origin of four carbonate minerals (e.g. aragonite, dolomite, Mg-calcite, calcite) to be determined as primary or diagenetic phases in Lake Son Kul. Aragonite was mainly of primary origin and is driven by biological activity in the epilimnion, whereas diagenetic minerals such as Mg-calcite, calcite, dolomite and pyrite were triggered by bacterial sulphate reduction and possibly by methanotrophic archaea. A new morphotype of aragonite (i.e. spherulite-like precursor) occurs in Unit IV (c. 7100–5000 cal. BP) associated with microbial mat structures. The latter enhanced the preservation of viral relics, which have not yet been reported in Holocene lacustrine sediments. This study advocates that microbe–mineral interactions screened down to the nanoscale (e.g. virus-like particles) can be used successfully for a comprehensive description of the fabric of laminated lake sediments. In this sense, they complement traditional facies sedimentology tools and offer valuable new insights into: (1) the study of microbial and viral biosignatures in Quaternary sediments; and (2) palaeoenvironmental reconstructions.

Ecophysiology and the energetic benefit of mixotrophic Fe(II) oxidation by various strains of nitrate-reducing bacteria

Article

Full-text available

Jan 2009

In order to assess the importance of nitrate-dependent Fe(II) oxidation and its impact on the growth physiology of dominant Fe oxidizers, we counted these bacteria in freshwater lake sediments and studied their growth physiology. Most probable number counts of nitrate-reducing Fe(II)-oxidizing bacteria in the sediment of Lake Constance, a freshwater lake in Southern Germany, yielded about 10 5 cells mL À1 of the total heterotrophic nitrate-reducing bacteria, with about 1% (10 3 cells mL À1) of nitrate-reducing Fe(II) oxidizers. We investigated the growth physiology of Acidovorax sp. strain BoFeN1, a dominant nitrate-reducing mixotrophic Fe(II) oxidizer isolated from this sediment. Strain BoFeN1 uses several organic compounds (but no sugars) as substrates for nitrate reduction. It also reduces nitrite, dinitrogen monoxide, and O 2 , but cannot reduce Fe(III). Growth experiments with cultures amended either with acetate plus Fe(II) or with acetate alone demonstrated that the simultaneous oxidation of Fe(II) and acetate enhanced growth yields with acetate alone (12.5 g dry mass mol À1 acetate) by about 1.4 g dry mass mol À1 Fe(II). Also, pure cultures of Pseudomonas stutzeri and Para-coccus denitrificans strains can oxidize Fe(II) with nitrate, whereas Pseudomonas fluorescens and Thiobacillus denitrificans strains did not. Our study demonstrates that nitrate-dependent Fe(II) oxidation contributes to the energy metabolism of these bacteria, and that nitrate-dependent Fe(II) oxidation can essentially contribute to anaerobic iron cycling.

Neutrophilic Bacteria in Iron Mineral Transformation and Their Applications

Chapter

Aug 2015

Iron, being the fourth abundant metal, is widely distributed in the earth. Iron is a redox-active transition metal existing in both the oxidation states in the form of ferric iron minerals (goethite, ferrihydrite, hematite) and ferrous iron minerals (pyrite, siderite, vivianite). At circumneutral pH, ferrous [Fe (II)] ion is unstable and is rapidly oxidized to ferric [Fe (III)] under aerobic conditions. Conversely, Fe (III) reduction takes place under anaerobic/anoxic conditions at circumneutral pH. Iron mineral transformations to a larger extent are microbially mediated by chemolithotrophic microorganisms that utilize iron as electron acceptor or donor to generate energy for their growth resulting in numerous mineral transformations. Hence, according to the pH of the environmental niches in the oxic–anoxic soils and freshwater sediments, neutrophilic iron-oxidizing bacteria (IOB) and iron-reducing bacteria (IRB) play active roles in mineral transformations. These bacteria have phylogenetic origins within different proteobacteria. The natural biogenic transformations by the neutrophilic bacteria with suitable eco-engineering can be adopted in the field of bioremediation to combat the increasing environmental pollution.

Recent progress in research on neutrophilic, microaerophilic iron(II)-oxidizing bacteria

Article

Jan 2012

Neutrophilic, microaerophilic iron(II)-oxidizing bacteria (FeOB) can oxidize iron(II) for energy via O2 - dependent mechanisms under suboxic, slightly-acidic to circumneutral conditions. This biological oxidation process commonly produces copious amorphous iron (III) oxyhydroxides, a preferential substrate for dissimilatory iron (III) reduction (iron respiration). Such oxyhydroxides have the potential to accelerate iron geochemical cycling at redox interfaces in terrestrial and aquatic systems. Despite reports on neutrophilic, microaerophilic FeOB since the 1830s, associated research progress has been slow, largely due to difficulty in laboratory cultivation and isolation of these organisms. Until the mid-1990s, modified FeS gradient methods were used for isolation of novel obligate FeOB from diverse habitats and substantial progress was achieved in understanding bacterial iron(II) oxidation. Representative neutrophilic, microaerophilic FeOB include stalked Gallionella and Mariprofundus, sheathed Leptothrix and Sphaerotilus, and several non- stalk-forming, unicellular species such as Sideroxidans, Ferritrophicum and Ferrocurvibacter. Related species have frequently been found in redox transition zones of circumneutral-pH, iron-rich environments such as groundwater seeps, wetland rhizosphere soils and deep-sea hydrothermal vents. Bacterial iron (II) oxidation is of global significance to biogeochemical iron cycling and other elements such as C, N, P, S and Mn. Bacterially-mediated iron cycling also influences the fate and transport of organic compounds and several trace metals. There is growing interest in understanding the role of neutrophilic, microaerophilic FeOB in biomineralization, geologic evolution, global climate change, and other fundamental geochemical processes. Here we review recent findings regarding bacterial iron(II) oxidation under suboxic, circumneutral-pH conditions, and summarize associated methodologies for studying the ecology of neutrophilic, microaerophilic FeOB. Recommendations are provided regarding future study of these organisms and associated biogeochemical processes.

Relating Microbial Community Structure and Geochemistry in Deep Regolith Developed on Volcaniclastic Rock in the Luquillo Mountains, Puerto Rico

Article

Full-text available

Sep 2014

Fe oxidation is often the first chemical reaction that initiates weathering and disaggregation of intact bedrock into regolith. Here we explore the use of pyrosequencing tools to test for evidence that bacteria participate in these reactions in deep regolith. We analyze regolith developed on volcaniclastic rocks of the Fajardo formation in a ridgetop within the rainforest of the Luquillo Mountains of Puerto Rico. In the 9 meter-deep regolith profile, the primary minerals chlorite, feldspar, and pyroxene are detected near 8.3 m but weather to kaolinite and Fe oxides found at shallower depths. Over the regolith profile, both total and heterotrophic bacterial cell counts generally increase from the bedrock to the surface. Like other soil microbial studies, the dominant phyla detected are Proteobacteria, Acidobacteria, Planctomycetes, and Actinobacteria. Proteobacteria (a, b, g and d) were the most abundant at depth (6.8 - 9 m, 41 - 44%), while Acidobacteria were the most abundant at the surface (1.4 - 4.4 m, 37 - 43%). Despite the fact that Acidobacteria dominated surficial communities while Proteobacteria dominated near bedrock, the near-surface and near-bedrock communities were not statistically different in structure but were statistically different from mid-depth communities. Approximately 21% of all sequences analyzed did not match known sequences: the highest fraction of unmatched sequences was greatest at mid-depth (45% at 4.4 m).

Neutrophilic lithotrophic iron-oxidizing prokaryotes and their role in the biogeochemical processes of the iron cycle

Article

Nov 2014

Biology of lithotrophic neutrophilic iron-oxidizing prokaryotes and their role in the processes of the biogeochemical cycle of iron are discussed. This group of microorganisms is phylogenetically, taxonomically, and physiologically heterogeneous, comprising three metabolically different groups: aerobes, nitratedependent anaerobes, and phototrophs; the latter two groups have been revealed relatively recently. Their taxonomy and metabolism are described. Materials on the structure and functioning of the electron transport chain in the course of Fe(II) oxidation by members of various physiological groups are discussed. Occurrence of iron oxidizers in freshwater and marine ecosystems, thermal springs, areas of hydrothermal activity, and underwater volcanic areas are considered. Molecular genetic techniques were used to determine the structure of iron-oxidizing microbial communities in various natural ecosystems. Analysis of stable isotope fractionation of 56/54Fe in pure cultures and model experiments revealed a predominance of biological oxidation over abiotic ones in shallow aquatic habitats and mineral springs, which was especially pronounced under microaerobic conditions at the redox zone boundary. Discovery of anaerobic bacterial Fe(II) oxidation resulted in development of new hypotheses concerning the possible role of microorganisms and the mechanisms of formation of the major iron ore deposits during Precambrian era until the early Proterozoic epoch. Paleobiological data are presented on the microfossils and specific biomarkers retrieved from ancient ore samples and confirming involvement of anaerobic biogenic processes in their formation.

Bacterial consortia in iron-deposited colonies formed on paddy soil surface under microaerobic conditions

Article

Jun 2013

The present study observed bacterial consortia in iron-deposited colonies formed on the surface of paddy soils. Plow layer soils under reduced condition, which were collected from a paddy field in Japan and paddy fields located at two sites in Mekong Delta, Vietnam, were incubated at 25 and 30°C in test tubes under a nitrogen (N2) atmosphere with sleeve stoppers made from a synthetic rubber. The sleeve stopper enabled the establishment of microaerobic conditions because of gradual diffusion of oxygen (O2) into the tube (29.2 nmol mL−1 day−1). Many colonies were observed on the soil surface in the test tubes after 2–3 weeks of incubation from both Japanese and Vietnam paddy soils. Bright orange and blood red colonies, which had 0.5–1-mm diameters and circular shapes, were observed. Micro X-ray fluorescence analysis of the colonies showed deposition of iron (Fe) in the colonies, indicating bacteria were enriched in the Fe oxidation. Microscopic observation showed acicular, floc and concentric crystal structures of Fe oxides in the colonies. Long- and short-rod bacterial cells mainly existed inside (or interspace) and outside surface of the colonies. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and clone library analysis of bacterial 16S rRNA genes showed that most of the obtained sequences belonged to Betaproteobacteria, in which bacteria related to “Sideroxydans lithotrophicus” and “S. paludicola” in Gallionellales, known as microaerobic, neutrophilic Fe-oxidizers, were predominant. The sequences related to Thiobacillus spp. and Dechloromonas spp., some strains of which are known to be anaerobic, nitrate-dependent neutrophilic Fe-oxidizers, were also obtained. The present study showed proliferation of bacteria related to neutrophilic Fe-oxidizers in paddy soils under microaerobic condition.

A Novel Autotrophic Bacterium Isolated from an Engineered Wetland System Links Nitrate-Coupled Iron Oxidation to the Removal of As, Zn and S

Article

Full-text available

Apr 2013

A neutrophilic, autotrophic bacterium that couples iron oxidation to nitrate reduction (iron-oxidizing bacteria [IOB]) under anoxic conditions was isolated from a working bioremediation site in Trail, British Columbia. The site was designed and developed primarily to treat high concentrations of Zn and As that originate from capped industrial landfill sites. The system consisted of two upflow biochemical reactor cells (BCR) followed by three vegetated wetland polishing cells with sub-surface flow and a holding pond. During a 5-year period (2003–2007), the system treated more than 19,100 m3 of contaminated water, removing and sequestering more than 10,700 kg of As, Zn and sulfate at average input water concentrations of: As, 58.6 mg l−1 (±39.9 mg l−1); Zn, 51.9 mg l−1 (±35.4 mg l−1) and SO42−, 781.5 mg l−1 (±287.8 mg l−1). The bacterium was isolated in order to better understand the mechanisms underlying the consistent As removal that took place in the system. Analysis using Basic Local Alignment Search Tool (BLAST) database showed that the closest homologies are to Candidatus accumulibacterphosphatis (95 % homology), Dechloromonas aromatica (94 %), and Sideroxydans lithotrophicus ES-1 (92 %) Within the BCR cells, the IOB oxidized Fe2+ generated by iron-reducing bacteria (IRB); the source of the iron was most likely biosolids and coatings of iron oxide on locally available sand used in the matrix. We have provisionally designated the novel bacterium as TR1.

Hallbeck L, Pedersen K.. Autotrophic and mixotrophic growth of Gallionella ferruginea. J Gen Microbiol 137: 2657-2661

Article

Full-text available

Nov 1991
J Gen Microbiol

C02 fixation and uptake of sugars by Gaffioneffa ferrughea were demonstrated by liquid scintillation and microautoradiographic techniques. The theoretical carbon content of a G. ferruginea cell in the exponential and stationary growth phases was calculated from size measurements of images of acridine-orange-stained cells. The carbon content of a cell in the exponential phase was 1.25 x mol and for a cell in the stationary phase it was 5 x 10-l5 mol. G. ferruginea was shown to obtain all of its cell carbon from C02 fixation when it was cultured under aerobic gradient conditions in a mineral salt solution with iron sulphide. Uptake experiments were performed with 1.6 pM-( 14C)glucose, 1.6 pM-( 4C)fructose and 1.3 pM-( 14C)sucrose. There was significant uptake of all three sugars. Measurements of respired 14C02 showed that 48%, 25% and 32% of the total amount of incorporated sugar was respired for glucose, fructose and sucrose, respectively. The uptake of glucose increased when the glucose concentration in the growth medium was increased. At a glucose concentration of 10 p~ or higher, the cell carbon was derived exclusively from glucose, within the errors of estimation. Mixotrophic growth with 20 p~- glucose decreased the COz fixation to 0-4 x 10-14 mol carbon per cell, compared to autotrophically grown cells with 1.0 x 10-14 mol carbon per cell. The addition of 20 pM-glucose gave an increase in cell number in the stationary phase from 1 x lo6 to 5 x lo6 cells ml-l.

Gapped BLAST and PSI-BLAST: A new generation of protein database search programs

Article

Full-text available

Sep 1997

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic, and statistical refinements permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is described for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position Specific Iterated BLAST (PSLBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities.

Phylogenetic affiliations of Rhodoferax fermentans and related species of phototrophic bacteria as determined by automated 16S rDNA sequencing

Article

Full-text available

Feb 1994

Akira Hiraishi

16S rDNA sequences of strains of Rhodoferax fermentans were analyzed and compared with those of species of the genera Rubrivivax and Rhodocyclus. Approximately 1.5-kb fragments of 16S rDNA from crude cell lysates were amplified by the polymerase chain reaction (PCR) and sequenced directly by using Tth DNA polymerase with the linear PCR sequencing protocol, followed by on-line detection with an automated laser fluorescent DNA sequencer. Pairwise sequence comparisons and distance matrix tree analysis showed that Rhodoferax fermentans, Rubrivivax gelatinosus, and Rhodocyclus species belong to three separate lineages within the beta subclass of the Proteobacteria, thereby confirming the phylogenetic validity of the genus Rhodoferax, as well as of the genera Rubrivivax and Rhodocyclus.

Profiling complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA

Article

Full-text available

Apr 1993

We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.

DNA recovery from Soils of Diverse Composition

Article

Full-text available

Feb 1996

A simple, rapid method for bacterial lysis and direct extraction of DNA from soils with minimal shearing was developed to address the risk of chimera formation from small template DNA during subsequent PCR. The method was based on lysis with a high-salt extraction buffer (1.5 M NaCl) and extended heating (2 to 3 h) of the soil suspension in the presence of sodium dodecyl sulfate (SDS), hexadecyltrimethylammonium bromide, and proteinase K. The extraction method required 6 h and was tested on eight soils differing in organic carbon, clay content, and pH, including ones from which DNA extraction is difficult. The DNA fragment size in crude extracts from all soils was > 23 kb. Preliminary trials indicated that DNA recovery from two soils seeded with gram-negative bacteria was 92 to 99%. When the method was tested on all eight unseeded soils, microscopic examination of indigenous bacteria in soil pellets before and after extraction showed variable cell lysis efficiency (26 to 92%). Crude DNA yields from the eight soils ranged from 2.5 to 26.9 micrograms of DNA g-1, and these were positively correlated with the organic carbon content in the soil (r = 0.73). DNA yields from gram-positive bacteria from pure cultures were two to six times higher when the high-salt-SDS-heat method was combined with mortar-and-pestle grinding and freeze-thawing, and most DNA recovered was of high molecular weight. Four methods for purifying crude DNA were also evaluated for percent recovery, fragment size, speed, enzyme restriction, PCR amplification, and DNA-DNA hybridization. In general, all methods produced DNA pure enough for PCR amplification. Since soil type and microbial community characteristics will influence DNA recovery, this study provides guidance for choosing appropriate extraction and purification methods on the basis of experimental goals.

Gapped BLAST and PSI-BLAST: A new generation of protein database search programs

Article

Full-text available

Sep 1997

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH

Article

Full-text available

Jan 1998

A gel-stabilized gradient method that employed opposing gradients of Fe2+ and O2 was used to isolate and characterize two new Fe-oxidizing bacteria from a neutral pH, Fe(2+)-containing groundwater in Michigan. Two separate enrichment cultures were obtained, and in each the cells grew in a distinct, rust-colored band in the gel at the oxic-anoxic interface. The cells were tightly associated with the ferric hydroxides. Repeated serial dilutions of both enrichments resulted in the isolation of two axenic strains, ES-1 and ES-2. The cultures were judged pure based on (i) growth from single colonies in tubes at dilutions of 10(-7) (ES-2) (ES-2) and 10(-8) (ES-1); (ii) uniform cell morphologies, i.e., ES-1 was a motile long thin, bent, or S-shaped rod and ES-2 was a shorter curved rod; and (iii) no growth on a heterotrophic medium. Strain ES-1 grew to a density of 10(8) cells/ml on FeS with a doubling time of 8 h. Strain ES-2 grew to a density of 5 x 10(7) cells/ml with a doubling time of 12.5 h. Both strains also grew on FeCO3. Neither strain grew without Fe2+, nor did they grow with glucose, pyruvate, acetate, Mn, or H2S as an electron donor. Studies with an oxygen microelectrode revealed that both strains grew at the oxic-anoxic interface of the gradients and tracked the O2 minima when subjected to higher O2 concentrations, suggesting they are microaerobes. Phylogenetically the two strains formed a novel lineage within the gamma Proteobacteria. They were very closely related to each other and were equally closely related to PVB OTU 1, a phylotype obtained from an iron-rich hydrothermal vent system at the Loihi Seamount in the Pacific Ocean, and SPB OTU 1, a phylotype obtained from permafrost soil in Siberia. Their closest cultivated relative was Stenotrophomonas maltophilia. In total, this evidence suggests ES-1 and ES-2 are members of a previously untapped group of putatively lithotrophic, unicellular iron-oxidizing bacteria.

Changes in Bacterial Species Composition in Enrichment Cultures with Various Dilutions of Inoculum as Monitored by Denaturing Gradient Gel Electrophoresis

Article

Full-text available

Jan 1999

Denaturing gradient gel electrophoresis revealed changes in the bacterial species obtained from enrichment cultures with different inoculum dilutions. This inoculum dilution enrichment approach may facilitate the detection and isolation of a greater number of bacterial species than traditional enrichment techniques.

NOTE Phylogenetic analysis of Formivibrio citricus, Propionivibrio dicarboxylicus, Anaerobiospirillum thomasii, Succinimonas amylolytica and Succinivibrio dextrinosolvens and proposal of Succinivibrionaceae fam. nov.

Article

Full-text available

May 1999

The phylogenetic position of Gram-negative, strictly anaerobic, non-spore-forming bacteria, representing four different genera, was determined by analysis of their 16S rDNA sequences. Formivibrio citricus and Propionivibrio dicarboxylicus are members of the beta-subclass of the class Proteobacteria. While Formivibrio citricus stands phylogenetically isolated, Propionivibrio dicarboxylicus is moderately related to members of the genus Rhodocyclus. Succinimonas amylolytica and Succinivibrio dextrinosolvens are members of the gamma-subclass of the class Proteobacteria in which they, together with members of the genus Anaerobiospirillum and Ruminobacter amylophilus, form a separate line of descent. This phylogenetic group is described as Succinivibrionaceae fam. nov.

Ubiquity and Diversity of Dissimilatory (Per)chlorate-Reducing Bacteria

Article

Full-text available

Jan 2000

Environmental contamination with compounds containing oxyanions of chlorine, such as perchlorate or chlorate [(per)chlorate] or chlorine dioxide, has been a constantly growing problem over the last 100 years. Although the fact that microbes reduce these compounds has been recognized for more than 50 years, only six organisms which can obtain energy for growth by this metabolic process have been described. As part of a study to investigate the diversity and ubiquity of microorganisms involved in the microbial reduction of (per)chlorate, we enumerated the (per)chlorate-reducing bacteria (ClRB) in very diverse environments, including pristine and hydrocarbon-contaminated soils, aquatic sediments, paper mill waste sludges, and farm animal waste lagoons. In all of the environments tested, the acetate-oxidizing ClRB represented a significant population, whose size ranged from 2.31 x 10(3) to 2.4 x 10(6) cells per g of sample. In addition, we isolated 13 ClRB from these environments. All of these organisms could grow anaerobically by coupling complete oxidation of acetate to reduction of (per)chlorate. Chloride was the sole end product of this reductive metabolism. All of the isolates could also use oxygen as a sole electron acceptor, and most, but not all, could use nitrate. The alternative electron donors included simple volatile fatty acids, such as propionate, butyrate, or valerate, as well as simple organic acids, such as lactate or pyruvate. Oxidized-minus-reduced difference spectra of washed whole-cell suspensions of the isolates had absorbance maxima close to 425, 525, and 550 nm, which are characteristic of type c cytochromes. In addition, washed cell suspensions of all of the ClRB isolates could dismutate chlorite, an intermediate in the reductive metabolism of (per)chlorate, into chloride and molecular oxygen. Chlorite dismutation was a result of the activity of a single enzyme which in pure form had a specific activity of approximately 1,928 micromol of chlorite per mg of protein per min. Analyses of the 16S ribosomal DNA sequences of the organisms indicated that they all belonged to the alpha, beta, or gamma subclass of the Proteobacteria. Several were closely related to members of previously described genera that are not recognized for the ability to reduce (per)chlorate, such as the genera Pseudomonas and Azospirllum. However, many were not closely related to any previously described organism and represented new genera within the Proteobacteria. The results of this study significantly increase the limited number of microbial isolates that are known to be capable of dissimilatory (per)chlorate reduction and demonstrate the hitherto unrecognized phylogenetic diversity and ubiquity of the microorganisms that exhibit this type of metabolism.

Identification of Polyphosphate-Accumulating Organisms and Design of 16S rRNA-Directed Probes for Their Detection and Quantitation

Article

Full-text available

Mar 2000
APPL ENVIRON MICROB

Laboratory-scale sequencing batch reactors (SBRs) as models for activated sludge processes were used to study enhanced biological phosphorus removal (EBPR) from wastewater. Enrichment for polyphosphate-accumulating organisms (PAOs) was achieved essentially by increasing the phosphorus concentration in the influent to the SBRs. Fluorescence in situ hybridization (FISH) using domain-, division-, and subdivision-level probes was used to assess the proportions of microorganisms in the sludges. The A sludge, a high-performance P-removing sludge containing 15.1% P in the biomass, was comprised of large clusters of polyphosphate-containing coccobacilli. By FISH, >80% of the A sludge bacteria were beta-2 Proteobacteria arranged in clusters of coccobacilli, strongly suggesting that this group contains a PAO responsible for EBPR. The second dominant group in the A sludge was the Actinobacteria. Clone libraries of PCR-amplified bacterial 16S rRNA genes from three high-performance P-removing sludges were prepared, and clones belonging to the beta-2 Proteobacteria were fully sequenced. A distinctive group of clones (sharing >/=98% sequence identity) related to Rhodocyclus spp. (94 to 97% identity) and Propionibacter pelophilus (95 to 96% identity) was identified as the most likely candidate PAOs. Three probes specific for the highly related candidate PAO group were designed from the sequence data. All three probes specifically bound to the morphologically distinctive clusters of PAOs in the A sludge, exactly coinciding with the beta-2 Proteobacteria probe. Sequential FISH and polyphosphate staining of EBPR sludges clearly demonstrated that PAO probe-binding cells contained polyphosphate. Subsequent PAO probe analyses of a number of sludges with various P removal capacities indicated a strong positive correlation between P removal from the wastewater as determined by sludge P content and number of PAO probe-binding cells. We conclude therefore that an important group of PAOs in EBPR sludges are bacteria closely related to Rhodocyclus and Propionibacter.

Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov

Article

Full-text available

Apr 2000

The species of the genus 'Thiobacillus' fall into the alpha-, beta- and gamma-subclasses of the Proteobacteria, the type species Thiobacillus thioparus being located in the beta-subclass. 'Thiobacillus' species exhibit almost as much diversity in DNA composition and physiology as is found collectively in all other proteobacterial groups. On the basis of physiological characters and 16S rRNA gene sequence comparisons, eight of the existing Thiobacillus species are proposed for reassignment to three newly designated genera within the gamma-subclass of the Proteobacteria, namely Acidithiobacillus, Halothiobacillus and Thermithiobacillus.

Suboxic Deposition of Ferric Iron by Bacteria in Opposing Gradients of Fe(II) and Oxygen at Circumneutral pH

Article

Full-text available

Mar 2001
APPL ENVIRON MICROB

The influence of lithotrophic Fe(II)-oxidizing bacteria on patterns of ferric oxide deposition in opposing gradients of Fe(II) and O2 was examined at submillimeter resolution by use of an O2 microelectrode and diffusion microprobes for iron. In cultures inoculated with lithotrophic Fe(II)-oxidizing bacteria, the majority of Fe(III) deposition occurred below the depth of O2 penetration. In contrast, Fe(III) deposition in abiotic control cultures occurred entirely within the aerobic zone. The diffusion microprobes revealed the formation of soluble or colloidal Fe(III) compounds during biological Fe(II) oxidation. The presence of mobile Fe(III) in diffusion probes from live cultures was verified by washing the probes in anoxic water, which removed ca. 70% of the Fe(III) content of probes from live cultures but did not alter the Fe(III) content of probes from abiotic controls. Measurements of the amount of Fe(III) oxide deposited in the medium versus the probes indicated that ca. 90% of the Fe(III) deposited in live cultures was formed biologically. Our findings show that bacterial Fe(II) oxidation is likely to generate reactive Fe(III) compounds that can be immediately available for use as electron acceptors for anaerobic respiration and that biological Fe(II) oxidation may thereby promote rapid microscale Fe redox cycling at aerobic-anaerobic interfaces.

Dechloromonas agitata gen. nov., sp. nov. and Dechlorosoma suillum gen. nov., sp. nov., two novel environmentally dominant (per)chlorate-reducing bacteria and their phylogenetic position

Article

Full-text available

Apr 2001

Previous studies on the ubiquity and diversity of microbial (per)chlorate reduction resulted in the isolation of 20 new strains of dissimilatory (per)chlorate-reducing bacteria. Phylogenetic analysis revealed that all of the isolates were members of the Proteobacteria with representatives in the alpha-, beta- and gamma-subclasses. The majority of the new isolates were located in the beta-subclass and were closely related to each other and to the phototrophic Rhodocyclus species. Here an in-depth analysis of these organisms which form two distinct monophyletic groups within the Rhodocyclus assemblage is presented. Two new genera, Dechloromonas and Dechlorosoma, are proposed for these beta-subclass lineages which represent the predominant (per)chlorate-reducing bacteria in the environment. The type species and strains for these new genera are Dechloromonas agitata strain CKBT and Dechlorosoma suillum strain PST, respectively.

Biogenic Magnetite Formation through Anaerobic Biooxidation of Fe(II)

Article

Full-text available

Jun 2001
APPL ENVIRON MICROB

The presence of isotopically light carbonates in association with fine-grained magnetite is considered to be primarily due to the reduction of Fe(III) by Fe(III)-reducing bacteria in the environment. Here, we report on magnetite formation by biooxidation of Fe(II) coupled to denitrification. This metabolism offers an alternative environmental source of biogenic magnetite.

Kinetics of Perchlorate- and Chlorate-Respiring Bacteria

Article

Full-text available

Jun 2001
APPL ENVIRON MICROB

Ten chlorate-respiring bacteria were isolated from wastewater and a perchlorate-degrading bioreactor. Eight of the isolates were able to degrade perchlorate, and all isolates used oxygen and chlorate as terminal electron acceptors. The growth kinetics of two perchlorate-degrading isolates, designated “Dechlorosoma” sp. strains KJ and PDX, were examined with acetate as the electron donor in batch tests. The maximum observed aerobic growth rates of KJ and PDX (0.27 and 0.28 h−1, respectively) were only slightly higher than the anoxic growth rates obtained by these isolates during growth with chlorate (0.26 and 0.21 h−1, respectively). The maximum observed growth rates of the two non-perchlorate-utilizing isolates (PDA and PDB) were much higher under aerobic conditions (0.64 and 0.41 h−1, respectively) than under anoxic (chlorate-reducing) conditions (0.18 and 0.21 h−1, respectively). The maximum growth rates of PDX on perchlorate and chlorate were identical (0.21 h−1) and exceeded that of strain KJ on perchlorate (0.14 h−1). Growth of one isolate (PDX) was more rapid on acetate than on lactate. There were substantial differences in the half-saturation constants measured for anoxic growth of isolates on acetate with excess perchlorate (470 mg/liter for KJ and 45 mg/liter for PDX). Biomass yields (grams of cells per gram of acetate) for strain KJ were not statistically different in the presence of the electron acceptors oxygen (0.46 ± 0.07 [n = 7]), chlorate (0.44 ± 0.05 [n = 7]), and perchlorate (0.50 ± 0.08 [n = 7]). These studies provide evidence that facultative microorganisms with the capability for perchlorate and chlorate respiration exist, that not all chlorate-respiring microorganisms are capable of anoxic growth on perchlorate, and that isolates have dissimilar growth kinetics using different electron donors and acceptors.

Characterisation of the microbial 16S rDNA diversity of an aerobic phosphorus-removal ecosystem and monitoring of its transition to nitrate respiration

Article

Full-text available

Jun 2001

The microbial community of a conventional anaerobic-aerobic sequencing batch reactor was investigated by cloning and sequencing bacterial 16S rDNA. The 92 16S rDNA sequences analysed ranged across 50 different operational taxonomic units (OTU). The majority of these sequences were not closely related to known species. They belonged to 12 different groups, but essentially to the Cytophagales and the Proteobacteria beta, which represented 38% and 17% of the retrieved sequences respectively. No OTU numerically outnumbered the others. However, similarities were observed with previous reports on molecular characterisation of phosphorus-accumulating ecosystems, suggesting an enrichment in microorganisms belonging to the Rhodocyclus group. Thereafter, the ability of this anaerobic-aerobic microbial community to accumulate phosphorus with nitrate as its energy source was investigated. The reactor was shifted from anaerobic-aerobic running conditions to anaerobic-anoxic conditions by injection of nitrate; and its microbial community was monitored by PCR-single strand conformation polymorphism (SSCP). The reactor maintained a good phosphorus accumulation and similar SSCP microbial community patterns for a period of 17 days, suggesting that the same microbial community was able to respire both oxygen and nitrate. However, this situation was unstable, since a breakdown in phosphorus accumulation occurred thereafter.

Growth Pattern and Yield of a Chemoautotrophic Beggiatoa sp. in Oxygen-Sulfide Microgradients

Article

Full-text available

Sep 1986

Recently developed techniques involving opposed, gel-stabilized gradients of O(2) and H(2)S permit cultivation of a marine Beggiatoa strain as a chemolithoautotroph which uses gliding motility to precisely track the interface between H(2)S and O(2). In the current study with microelectrodes, vertical profiles of H(2), O(2), and pH were measured in replicate cultures grown for various intervals. After an initial period of exponential biomass increase (doubling time, 11 h), linear growth prevailed throughout much of the time course. This H(2)S-limited growth was followed by a transition to stationary phase when the declining H(2)S flux was sufficient only to supply maintenance energy. During late-exponential and linear growth phases, the Beggiatoa sp. consumed a constant 0.6 mol of H(2)S for each 1.0 mol of O(2), the ratio anticipated for balanced lithoautotrophic growth at the expense of complete oxidation of H(2)S to SO(4). Over the entire range of conditions studied, this consumption ratio varied by approximately twofold. By measuring the extent to which the presence of the bacterial plate diminished the overlap of O(2) and H(2)S, we demonstrated that oxidation of H(2)S by Beggiatoa sp. is approximately 3 orders of magnitude faster than spontaneous chemical oxidation. By integrating sulfide profiles and comparing sulfide consumed with biomass produced, a growth yield of 8.4 g (dry weight) mol of H(2)S was computed. This is higher than that found for sulfide-grown thiobacilli, indicating very efficient growth of Beggiatoa sp. as a chemoautotroph. The methods used here offer a unique opportunity to determine the yield of H(2)S-oxidizing chemolithoautotrophs while avoiding several problems inherent in the use of homogeneous liquid culture. Finally, by monitoring time-dependent formation of H(2)S profiles under anoxic conditions, we demonstrate a method for calculating the molecular diffusion coefficient of soluble substrates in gel-stabilized media.

Microbial Oxidation of Fe(II) and Mn(II) at Circumneutral pH

Chapter

Apr 2014

David Emerson

An oxygen microelectrode with a guard cathode

Article

Jan 1989

Niels Peter Revsbech

Physiology and Ecology of Acidophilic Microorganisms

Article

Jan 2007

David Barrie Johnson

Acidophilic microorganisms are distributed throughout the three domains of living organisms. Within the archaeal domain, both extremely acidophilic Euryarchaeota and Crenarchaeota are known, and a number of different bacterial phyla (Firmicutes, Actinobacteria, and Proteobacteria [α, β, and γ subphyla], Nitrospira, and Aquifex) also contain extreme acidophiles. Acidophilic microorganisms exhibit a range of energy-transforming reactions and means of assimilating carbon as neutrophiles. Entire genomes have been sequenced of the iron/sulfur-oxidizing bacterium Acidithiobacillus ferrooxidans and of the archaea Thermoplasma acidophilum, Picrophilus torridus, Sulfolobus tokodaii, and Ferroplasma acidarmanus, and more genome sequences of acidophiles are due to be completed in the near future. Currently, there are four recognized species of this genus that grow autotrophically on sulfur, sulfide, and reduced inorganic sulfur compounds (RISCs). Acidithiobacillus ferrooxidans is the most well studied of all acidophilic microorganisms and has often, though erroneously, been regarded as an obligate aerobe. In both natural and anthropogenic environments, acidophilic microorganisms live in communities that range from relatively simple (two to three dominant members) to highly complex, and within these, acidophiles interact positively or negatively with each other. In a study which examined slime biofilms and snotites that had developed on the exposed surface of a pyrite ore within the abandoned Richmond mine at Iron Mountain, the major microorganisms identified were Leptospirillum spp. (L. ferriphilum and smaller numbers of L. ferrodiazotrophum) and Fp. acidarmanus, Sulfobacillus, and Acidimicrobium/Ferrimicrobium-related species. Using a modified plating technique, the uncharacterized β-proteobacterium can be isolated in pure culture and shown to be a novel iron-oxidizing acidophile.

Heterotrophic Acidophiles and Their Roles in the Bioleaching of Sulfide Minerals

Chapter

Jan 1997

The most familiar and well-studied microorganisms indigenous to acidic mineral leaching environments are autotrophic sulfur- and iron-oxidizing bacteria such as Thiobacillus ferrooxidans, Thiobacillus thiooxidans and Leptospirillum ferrooxidans. Some photoautotrophs, such as the thermophilic rhodophyte Cyanidium caldarium, may also be present in extremely acidic environments that receive light. Other microorganisms which require pre-fixed (organic) carbon have been isolated from mineral leach dumps and acid mine drainage (AMD) waters. These heterotrophic microorganisms include eukaryotes, such as some fungi and yeasts1 and protozoa,2 as well as prokaryotic bacteria and archaea. It is somewhat paradoxical, given that heterotrophy is the most widespread form of metabolism among bacteria, that the first acidophilic heterotrophic bacterium which is indigenous and active in mineral leaching environments was isolated and characterized some 40 years after the iron/sulfur-oxidizing chemolithotroph T. ferrooxidans and 70 years after the sulfur-oxidizing acidophile T. thiooxidans.

Role of pure and mixed cultures of Gram-positive eubacteria in mineral leaching

Article

Jan 2001

Molecular Cloning: A Laboratory Manual (2nd edn) Cold Spring Harbor, New York

Article

Jan 1982

Aquatic chemistry: Chemical equilibria and rates in natural waters third edition

Article

Jan 1996

Disparity between bacterial phylogeny and physiology

Article

Jan 2000
Am Soc Microbiol News

Database resources of the National Center for Biotechnology Information

Article

Jan 2000
NUCLEIC ACIDS RES

David L Wheeler

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval and resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing pages, GeneMap’99, Davis Human–Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP) pages, Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP) pages, SAGEmap, Online Mendelian Inheritance in Man (OMIM) and the Molecular Modeling Database (MMDB). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov

PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10

Book

Jan 2002

David L. Swofford

— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.

Benefits associated with the stalk of Gallionella ferruginea, evaluated by comparison of a stalk-forming and a non-stalk-forming strain and biofilm studies in situ

Article

Nov 1995

Factors that regulate and induce stalk formation by the iron-oxidizing and stalk-forming bacterium Gallionella ferruginea were studied in laboratory cultures and in situ. A stalk-forming strain, Sta(+), and a non-stalk-forming strain, Sta(-), were used for comparative studies of the benefits associated with the stalk. Two different growth media were used: a ferrous sulfide medium (FS-medium), with slow oxidation of iron giving high concentrations of toxic oxygen radicals and a ferrous carbonate medium (FC-medium), with fast iron oxidation giving low concentration of the toxic oxygen radicals. It was found that Sta(+) cells grown in the FS-medium survived 3 weeks longer than Sta(-) cells grown in the FS-medium. When each strain was grown in the FC-medium, the Sta(-) cells had an advantage and survived 8 weeks longer than the Sta(+) cells. No difference in survival was found for Sta(+) cells grown in FS-medium compared to growth in FC-medium. In laboratory cultures, the average stalk length per cell values were 7-2.5 times higher (92 h and 150-300 h growth, respectively) in a medium with 620 μM iron than in a medium with 290 μM iron. Gallionella ferruginea Sta(+) outcompeted Sta(-) cells when inoculated as mixed populations in FC-medium. It has previously been suggested that stalk formation in vitro is induced by oxygen. To confirm this observation, biofilm development in natural waters was studied in two wells, one with trace amounts of oxygen (LH) and one without (TH). A dense biofilm developed on surfaces exposed to flowing well LH water, but no biofilm developed in well TH. Stalks were formed in water samples from both wells when allowed to make contact with air. This work demonstrates for the first time that the stalk has a protecting function against the toxic oxygen radicals formed during the chemical iron oxidation. It also shows that it is the oxidation rate of the ferrous iron and not its concentration that is harmful to the cells. The stalk gives G. ferruginea a unique possibility to colonize and survive in habitats with high contents of iron, inaccessible for bacteria without a defense system against the oxidation of iron.

In situ identification of polyphosphate‐ and polyhydroxyalkanoate‐accumulating traits for microbial populations in a biological phosphorus removal process

Article

Dec 2001
ENVIRON MICROBIOL

Polyphosphate- and polyhydroxyalkanoate (PHA)-accumulating traits of predominant microorganisms in an efficient enhanced biological phosphorus removal (EBPR) process were investigated systematically using a suite of non-culture-dependent methods. Results of 16S rDNA clone library and fluorescence in situ hybridization (FISH) with rRNA-targeted, group-specific oligonucleotide probes indicated that the microbial community consisted mostly of the α- (9.5% of total cells), β- (41.3%) and γ- (6.8%) subclasses of the class Proteobacteria, Flexibacter–Cytophaga (4.5%) and the Gram-positive high G+C (HGC) group (17.9%). With individual phylogenetic groups or subgroups, members of Candidatus Accumulibacter phosphatis in the β-2 subclass, a novel HGC group closely related to Tetrasphaera spp., and a novel γ-proteobacterial group were the predominant populations. Furthermore, electron microscopy with energy-dispersive X-ray analysis was used to validate the staining specificity of 4,6-diamino-2-phenylindole (DAPI) for intracellular polyphosphate and revealed the composition of polyphosphate granules accumulated in predominant bacteria as mostly P, Ca and Na. As a result, DAPI and PHA staining procedures could be combined with FISH to identify directly the polyphosphate- and PHA-accumulating traits of different phylogenetic groups. Members of Accumulibacter phosphatis and the novel gamma-proteobacterial group were observed to accumulate both polyphosphate and PHA. In addition, one novel rod-shaped group, closely related to coccus-shaped Tetrasphaera, and one filamentous group resembling Candidatus Nostocoidia limicola in the HGC group were found to accumulate polyphosphate but not PHA. No cellular inclusions were detected in most members of the α-Proteobacteria and the Cytophaga–Flavobacterium group. The diversified functional traits observed suggested that different substrate metabolisms were used by predominant phylogenetic groups in EBPR processes.

Johnson DB.. Biodiversity and ecology of acidophilic microorganisms. FEMS Microbiol Ecol 27: 307-317

Article

Dec 1998
FEMS MICROBIOL ECOL

David Barrie Johnson

Microbial life in extremely low pH (<3) natural and man-made environments may be considerably diverse. Prokaryotic acidophiles (eubacteria and archaea) have been the focus of much of the research activity in this area, primarily because of the importance of these microorganisms in biotechnology (predominantly the commercial biological processing of metal ores) and in environmental pollution (genesis of ‘acid mine drainage’); however, obligately acidophilic eukaryotes (fungi, yeasts, algae and protozoa) are also known, and may form stable microbial communities with prokaryotes, particularly in lower temperature (<35°C) environments. Primary production in acidophilic environments is mediated by chemolitho-autotrophic prokaryotes (iron and sulfur oxidisers), and may be supplemented by phototrophic acidophiles (predominantly eukaryotic microalgae) in illuminated sites. The most thermophilic acidophiles are archaea (Crenarchaeota) whilst in moderately thermal (40–60°C) acidic environments archaea (Euryarchaeota) and bacteria (mostly Gram-positives) may co-exist. Lower temperature (mesophilic) extremely acidic environments tend to be dominated by Gram-negative bacteria, and there is recent evidence that mineral oxidation may be accelerated by acidophilic bacteria at very low (ca. 0°C) environments. Whilst most acidophiles have conventionally been considered to be obligately aerobic, there is increasing evidence that many isolates are facultative anaerobes, and are able to couple the oxidation of organic or inorganic electron donors to the reduction of ferric iron. A variety of interactions have been demonstrated to occur between acidophilic microorganisms, as in other environments; these include competition, predation, mutualism and synergy. Mixed cultures of acidophiles are frequently more robust and efficient (e.g. in oxidising sulfide minerals) than corresponding pure cultures. In view of the continuing expansion of microbial mineral processing (‘biomining’) as a cost-effective and environmentally sensitive method of metal extraction, and the ongoing concern of pollution from abandoned mine sites, acidophilic microbiology will continue to be of considerable research interest well into the new millennium.

Ferribacterium limneticum, gen. nov., sp. nov., an Fe(III)-reducing microorganism isolated from mining-impacted freshwater lake sediments

Article

Jan 1999

A dissimilatory Fe(III)-reducing bacterium was isolated from mining-impacted lake sediments and designated strain CdA-1. The strain was isolated from a 4-month enrichment culture with acetate and Fe(III)-oxyhydroxide. Strain CdA-1 is a motile, obligately anaerobic rod, capable of coupling the oxidation of acetate and other organic acids to the reduction of ferric iron. Fe(III) reduction was not observed using methanol, ethanol, isopropanol, propionate, succinate, fumarate, H2, citrate, glucose, or phenol as potential electron donors. With acetate as an electron donor, strain CdA-1 also grew by reducing nitrate or fumarate. Growth was not observed with acetate as electron donor and O2, sulfoxyanions, nitrite, trimethylamine N-oxide, Mn(IV), As(V), or Se(VI) as potential terminal electron acceptors. Comparative 16 S rRNA gene sequence analyses show strain CdA-1 to be most closely related (93.6% sequence similarity) to Rhodocyclus tenuis. However, R. tenuis did not grow heterotrophically by Fe(III) reduction, nor did strain CdA-1 grow photrophically. We propose that strain CdA-1 represents a new genus and species, Ferribacterium limneticum. Strain CdA-1 represents the first dissimilatory Fe(III) reducer in the β subclass of Proteobacteria, as well as the first Fe(III) reducer isolated from mine wastes.

The kinetics of the oxidation of ferrous iron in synthetic and natural waters

Article

Jan 1983
GEOCHIM COSMOCHIM AC

The rate of oxidation of ferrous iron in a seasonally anoxic lake was measured on 39 occasions with respect to both depth and time. Sample disturbance was minimal as only oxygen had to be introduced to initiate the reaction. The data were consistent with the simple rate law for homogeneous chemical kinetics previously established for synthetic solutions. The rate constant for the oxidation reaction in lake water was indistinguishable from that measured in synthetic samples. It did not appear to be influenced by changes in the microbial populations or by changes in any particulate or soluble components in the water, including iron and manganese. Analysis of the errors inherent in the kinetic measurements showed that the estimation of pH was the major source of inaccuracy and that values of the rate constant determined by different workers could easily differ by a factor of six.The present data, together with a comprehensive survey of the literature, are used to suggest a ‘universal’ rate constant of ca. 2 × 1013 M−2 atm−1 min−1 (range 1.5–3 × 1013) in the rate law for natural freshwaters in the pH range 6.5–7.4. Discrepancies in the effects of ionic strength and interfering substances reported in the literature are highlighted. Generally substances have only been found to interfere at concentrations which far exceed those in most natural waters.

The molecular genetics of Thiobacillus ferrooxidans and other mesophilic, acidophilic, chemolithotrophic, iron- or sulfur-oxidizing bacteria

Article

Feb 2001
HYDROMETALLURGY

Douglas E Rawlings

The bacteria primarily responsible for decomposing metal sulfide ores and concentrates at temperatures of 40°C or below have been identified as Thiobacillus ferrooxidans, Leptospirillum ferrooxidans (or related Leptospirillum spp.) T. thiooxidans and recently, T. caldus. These obligately acidophilic, autotrophic, usually aerobic, iron- or sulfur-oxidizing chemolithotrophic bacteria occupy an ecological niche that is largely inorganic and very different from that populated by the more commonly studied non-acidophilic heterotrophic bacteria. It has been of particular interest to discover how these ‘biomining’ bacteria are phylogenetically related to the rest of the microbial world. Based on 16S rRNA sequence data, the thiobacilli have been placed in the Proteobacteria division close to the junction between the β and γ sub-divisions. In contrast, the leptospirilli have been positioned within a relatively recently recognised division called the Nitrospira group. T. ferrooxidans is the only biomining bacterium whose molecular biology has been studied in some detail. Of the approximately 50 genes cloned or sequenced and published, by far the majority that can be tested are expressed and produce proteins which are functional in Escherichia coli (a member of the γ sub-division of Proteobacteria). These observations together with phylogenetic comparisons of most T. ferrooxidans protein sequences have confirmed the unexpectedly close relationship between T. ferrooxidans and E. coli. A special challenge has been the isolation of the various components of the iron-oxidation system and as a result of a global effort, this is almost complete. Several plasmids, transposons and insertion sequences have been isolated from T. ferrooxidans. These genetic elements are interesting because they may contain non-essential genes which are thought to improve the fitness of the bacterium and are frequently mobile. They have provided some fascinating insights into genetic exchanges that have occurred between T. ferrooxidans and other bacteria. There are clear indications that some of the other ‘biomining’ bacteria are even more important than T. ferrooxidans in many commercial biomining processes. The molecular biology of these bacteria is almost unstudied.

An Oxygen Microsensor with a Guard Cathode

Article

Mar 1989

Niels Peter Revsbech

This article is in Free Access Publication and may be downloaded using the “Download Full Text PDF” link at right.

[Functional significance of bivalent iron and manganese oxidation in Leptothrix pseudoochraceae]

Article

Sep 1978
Mikrobiologiya

G A Dubinina

The effect of oxidation of bivalent compounds of iron and manganese was studied on the growth of filamentous iron bacteria. The stimulating action of these metals could not be attributed to utilization of the energy of their oxidation in the assimilation of carbon dioxide or in lithoheterotrophic processes. The cells yield increased because the metal ions removed the toxic metabolite, hydrogen peroxide, which was formed in the respiratory chain upon oxidation of an organic substrate. This function of bivalent metals in detoxication of hydrogen peroxide accounts for the ecological confinement of iron bacteria to certain environment.

Evolutionary relationship among sulfur and iron oxidizing eubacteria

Article

Feb 1992

Some 37 reverse transcriptase, partial 16S rRNA sequences from sulfur- and/or iron-oxidizing eubacteria, including sequences from species of the genera Thiobacillus, Thiothrix, Thiomicrospira, Acidophilium, "Leptospirillum," Thiovulum, and Chlorobium, have been determined. In addition, 16S sequences from a number of unnamed sulfur- and/or iron-oxidizing bacteria from hydrothermal vent sites, from invertebrate-bacterial endosymbioses, and from various mineral recovery operations also have been determined. The majority of sequences place their bacterial donors in one or another of the subdivisions of the Proteobacteria. However, three unnamed facultatively thermophilic iron-oxidizing isolates, Alv, BC, and TH3, are affiliated with the gram-positive division. One H2S-oxidizer, from the genus Thiovulum, is affiliated with Campylobacter, Wolinella, and other genera in what appears to be a new subdivision of the Proteobacteria. Three "Leptospirillum"-helical vibrioid isolates, BU-1, LfLa, and Z-2, exhibit no clear phylum level affiliation at all, other than their strong relationship to each other. A picture is emerging of an evolutionary widespread capacity for sulfur and/or iron oxidation among the eubacteria.

16S Ribosomal DNA Amplification for Phylogenetic Study

Article

Feb 1991

A set of oligonucleotide primers capable of initiating enzymatic amplification (polymerase chain reaction) on a phylogenetically and taxonomically wide range of bacteria is described along with methods for their use and examples. One pair of primers is capable of amplifying nearly full-length 16S ribosomal DNA (rDNA) from many bacterial genera; the additional primers are useful for various exceptional sequences. Methods for purification of amplified material, direct sequencing, cloning, sequencing, and transcription are outlined. An obligate intracellular parasite of bovine erythrocytes, Anaplasma marginale, is used as an example; its 16S rDNA was amplified, cloned, sequenced, and phylogenetically placed. Anaplasmas are related to the genera Rickettsia and Ehrlichia. In addition, 16S rDNAs from several species were readily amplified from material found in lyophilized ampoules from the American Type Culture Collection. By use of this method, the phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the need to culture them. In theory, any gene segment for which polymerase chain reaction primer design is possible can be derived from a readily obtainable lyophilized bacterial culture.

Biology of Iron-and Manganese-Depositing Bacteria

Article

Feb 1984

W. C. Ghiorse

Identification of N2-fixing plant- and fungus-associated Azoarcus species by PCR-based genomic fingerprints

Article

Dec 1997

Most species of the diazotrophic Proteobacteria Azoarcus spp. occur in association with grass roots, while A. tolulyticus and A. evansii are soil bacteria not associated with a plant host. To facilitate species identification and strain comparison, we developed a protocol for PCR-generated genomic fingerprints, using an automated sequencer for fragment analysis. Commonly used primers targeted to REP (repetitive extragenic palindromic) and ERIC (enterobacterial repetitive intergenic consensus) sequence elements failed to amplify fragments from the two species tested. In contrast, the BOX-PCR assay (targeted to repetitive intergenic sequence elements of Streptococcus) yielded species-specific genomic fingerprints with some strain-specific differences. PCR profiles of an additional PCR assay using primers targeted to tRNA genes (tDNA-PCR, for tRNA(IIe)) were more discriminative, allowing differentiation at species-specific (for two species) or infraspecies-specific level. Our protocol of several consecutive PCR assays consisted of 16S ribosomal DNA (rDNA)-targeted, genus-specific PCR followed by BOX- and tDNA-PCR; it enabled us to assign new diazotrophic isolates originating from fungal resting stages (sclerotia) to known species of Azoarcus. The assignment was confirmed by phylogenetic analysis of 16S rDNA sequences. Additionally, the phylogenetic distances and the lack of monophyly suggested emendment of the genus Azoarcus: the unnamed species Azoarcus groups C and D and a new group (E) of Azoarcus, which was detected in association with fungi, are likely to have the taxonomic rank of three different genera. According to its small subunit rRNA, the sclerotium-forming basidiomycete was related to the Ustilagomycetes, facultatively biotrophic parasites of plants. Since they occurred in a field which was under cultivation with rice and wheat, these fungi might serve as a niche for survival for Azoarcus in the soil and as a source for reinfection of plants.

Phylogenetic Analysis of an Anaerobic, Trichlorobenzene-Transforming Microbial Consortium

Article

Feb 1999

A culture-independent phylogenetic survey for an anaerobic trichlorobenzene-transforming microbial community was carried out. Small-subunit rRNA genes were PCR amplified from community DNA by using primers specific for Bacteria or Euryarchaeota and were subsequently cloned. Application of a new hybridization-based screening approach revealed 51 bacterial clone families, one of which was closely related to dechlorinating Dehalobacter species. Several clone sequences clustered to rDNA sequences obtained from a molecular study of an anaerobic aquifer contaminated with hydrocarbons and chlorinated solvents (Dojka et al., Appl. Env. Microbiol. 64:3869-3877, 1998).

Enrichment, Phylogenetic Analysis and Detection of a Bacterium That Performs Enhanced Biological Phosphate Removal in Activated Sludge

Article

Oct 1999
SYST APPL MICROBIOL

Activated sludge communities which performed enhanced biological phosphate removal (EBPR) were phylogenetically analyzed by 16S rRNA-targeted molecular methods. Two anaerobic-aerobic sequencing batch reactors were operated with two different carbon sources (acetate vs. a complex mixture) for three years and showed anaerobic-aerobic cycles of polyhydroxybutyrate- (PHB) and phosphate-accumulation characteristic for EBPR-systems. In situ hybridization showed that the reactor fed with the acetate medium was dominated by bacteria phylogenetically related to the Rhodocyclus-group within the beta-Proteobacteria (81% of DAPI-stained cells). The reactor with the complex medium was also predominated by this phylogenetic group albeit at a lesser extent (23% of DAPI-stained cells). More detailed taxonomic information on the dominant bacteria in the acetate-reactor was obtained by constructing clone libraries of 16S rDNA fragments. Two different types of Rhodocyclus-like clones (R1 and R6) were retrieved. Type-specific in situ hybridization and direct rRNA-sequencing revealed that R6 was the type of the dominant bacteria. Staining of intracellular polyphosphate- and PHB-granules confirmed that the R6-type bacterium accumulates PHB and polyphosphate just as predicted by the metabolic models for EBPR. High similarities to 16S rDNA fragments from other EBPR-sludges suggest that R6-type organisms were present and may play an important role in EBPR in general. Although the R6-type bacterium is closely related to the genus Rhodocyclus, it did not grow phototrophically. Therefore, we propose a provisional new genus and species Candidatus Accumulibacter phosphatis.

Detection of lateral gene transfer among microbial genomes

Article

Jan 2002
CURR OPIN GENET DEV

Mark A. Ragan

An increasingly comprehensive assessment is being developed of the extent and potential significance of lateral gene transfer among microbial genomes. Genomic sequences can be identified as being of putatively lateral origin by their unexpected phyletic distribution, atypical sequence composition, differential presence or absence in closely related genomes, or incongruent phylogenetic trees. These complementary approaches sometimes yield inconsistent results. Not only more data but also quantitative models and simulations are needed urgently.

Propionivibrio limicola sp. nov., a fermentative bacterium specialized in the degradation of hydroaromatic compounds, reclassification of Propionibacter pelophilus as Propionivibrio pelophilus comb. nov. and amended description of the genus Propionivibrio

Article

Mar 2002
INT J SYST EVOL MICR

Strain GolChi1T, a mesophilic, anaerobic bacterium, was isolated with quinic acid (1,3,4,5-tetrahydroxy-cyclohexane-1-carboxylic acid) as the sole source of carbon and energy. Of more than 30 substrates tested, only the hydroaromatic compounds quinic acid and shikimic acid (3,4,5-trihydroxy-1-cyclohexene-1-carboxylic acid) were utilized, yielding acetate and propionate as the only fermentation products. Sugars, alcohols, (di-)carboxylic acids, amino acids and aromatic compounds were not fermented and no external electron acceptors were used. Strain GolChi1T is a gram-negative, rod-shaped, aerotolerant anaerobe that possesses superoxide dismutase; it does not employ the classical hydroaromatic pathway of aerobic bacteria for the degradation of hydroaromatic compounds (no aromatic intermediates involved). 16S-rRNA-based phylogenetic analyses revealed a common origin of this isolate and Rhodocyclus, Propionibacter and Propionivibrio species. High sequence similarity (> 96%) and phenotypic traits indicated a closer relationship between strain GolChi1T and the type species of the monospecific genera Propionivibrio and Propionibacter but, due to its phenotypic properties, strain GolChi1T could not be assigned conclusively to either of these taxa. We propose (i) the amended description of the genus Propionivibrio, (ii) the reclassification of Propionibacter pelophilus Meijer et al. 1999 as Propionivibrio pelophilus comb. nov. and (iii) designation of Propionivibrio limicola sp. nov., with the type strain GolChi1T (= DSM 6832T = ATCC BAA-290T).

The Microbial Community Composition of a Nitrifying-Denitrifying Activated Sludge from an Industrial Sewage Treatment Plant Analyzed by the Full-Cycle rRNA Approach

Article

May 2002
SYST APPL MICROBIOL

The composition of the microbial community present in the nitrifying-denitrifying activated sludge of an industrial wastewater treatment plant connected to a rendering facility was investigated by the full-cycle rRNA approach. After DNA extraction using three different methods, 94 almost full-length 16S rRNA gene clones were retrieved and analyzed phylogenetically. 59% of the clones were affiliated with the Proteobacteria and clustered with the β- (29 clones), α- (24), and δ-class (2 clones), respectively. 15 clones grouped within the green nonsulfur (GNS) bacteria and 11 clones belonged to the Planctomycetes. The Verrucomicrobia, Acidobacteria, Nitrospira, Bacteroidetes, Firmicutes and Actinobacteria were each represented by one to five clones. Interestingly, the highest "species richness" [measured as number of operational taxonomic units (OTUs)] was found within the α-class of Proteobacteria, followed by the Planctomycetes, the β-class of Proteobacteria, and the GNS-bacteria. The microbial community composition of the activated sludge was determined quantitatively by using 36 group-, subgroup-, and OTU-specific rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization (FISH), confocal laser scanning microscopy and digital image analysis. 89% of all bacteria detectable by FISH with a bacterial probe set could be assigned to specific divisions. Consistent with the 16S rRNA gene library data, members of the β-class of Proteobacteria dominated the microbial community and represented almost half of the biovolume of all bacteria detectable by FISH. Within the β-class, 98% of the cells could be identified by the application of genus- or OTU-specific probes demonstrating a high in situ abundance of bacteria related to Zoogloea and Azoarcus sensu lato. Taken together, this study provides the first encompassing, high-resolution insight into the in situ composition of the microbial community present in a full-scale, industrial wastewater treatment plant.

Evidence for rapid microscale bacterial redox cycling of iron in circumneutral environments

Article

Sep 2002

The potential for microscale bacterial Fe redox cycling was investigated in microcosms containing ferrihydrite-coated sand and a coculture of a lithotrophic Fe(II)-oxidizing bacterium (strain TW2) and a dissimilatory Fe(III)-reducing bacterium (Shewanella alga strain BrY). The Fe(II)-oxidizing organism was isolated from freshwater wetland surface sediments which are characterized by steep gradients of dissolved 02 and high concentrations of dissolved and solid-phase Fe(II) within mm of the sediment-water interface, and which support comparable numbers (10(5)-10(6) mL(-1)) of culturable Fe(II)-oxidizing and Fe(III)-reducing reducing. The coculture systems showed minimal Fe(III) oxide accumulation at the sand-water interface, despite intensive O2 input from the atmosphere and measurable dissolved O2 to a depth of 2 mm below the sand-water interface. In contrast, a distinct layer of oxide precipitates formed in systems containing Fe(IllI)-reducing bacteria alone. Examination of materials from the cocultures by fluorescence in situ hybridization indicated close physical juxtapositioning of Fe(II)-oxidizing and Fe(III)-reducing bacteria in the upper few mm of sand. Our results indicate that Fe(II)-oxidizing bacteria have the potential to enhance the coupling of Fe(II) oxidation and Fe(III) reduction at redox interfaces, thereby promoting rapid microscale cycling of Fe.

A ferrous-ion-oxidizing bacterium. I. Isolation and some general physiological characteristics

Article

May 1960

Jay V. Beck

Studies on the chemoautotrophic iron bacterium Ferrobacillus

Article

Oct 1959

The autotrophic Oxidation of iron by a new bacterium: Thiobacillus ferrooxidans

Article

Dec 1951

Lovley DR, Phillips EP.. Availability of ferric iron for microbial reduction in bottom sediments of the freshwater tidal Potomac river USA. Appl Environ Microbiol 52: 751-757

Article

Nov 1986

The distribution of Fe(III), its availability for microbial reduction, and factors controlling Fe(III) availability were investigated in sediments from a freshwater site in the Potomac River Estuary. Fe(III) reduction in sediments incubated under anaerobic conditions and depth profiles of oxalate-extractable Fe(III) indicated that Fe(III) reduction was limited to depths of 4 cm or less, with the most intense Fe(III) reduction in the top 1 cm. In incubations of the upper 4 cm of the sediments, Fe(III) reduction was as important as methane production as a pathway for anaerobic electron flow because of the high rates of Fe(III) reduction in the 0- to 0.5-cm interval. Most of the oxalate-extractable Fe(III) in the sediments was not reduced and persisted to a depth of at least 20 cm. The incomplete reduction was not the result of a lack of suitable electron donors. The oxalate-extractable Fe(III) that was preserved in the sediments was considered to be in a form other than amorphous Fe(III) oxyhydroxide, since synthetic amorphous Fe(III) oxyhydroxide, amorphous Fe(III) oxyhydroxide adsorbed onto clay, and amorphous Fe(III) oxyhydroxide saturated with adsorbed phosphate or fulvic acids were all readily reduced. Fe(3)O(4) and the mixed Fe(III)-Fe(II) compound(s) that were produced during the reduction of amorphous Fe(III) oxyhydroxide in an enrichment culture were oxalate extractable but were not reduced, suggesting that mixed Fe(III)-Fe(II) compounds might account for the persistence of oxalate-extractable Fe(III) in the sediments. The availability of microbially reducible Fe(III) in surficial sediments demonstrates that microbial Fe(III) reduction can be important to organic matter decomposition and iron geochemistry. However, the overall extent of microbial Fe(III) reduction is governed by the inability of microorganisms to reduce most of the Fe(III) in the sediment.

Characterization of a Neutrophilic, Chemolithoautotrophic Fe(II)Oxidizing ??-Proteobacterium from Freshwater Wetland Sediments

Abstract

No full-text available

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