Ferrous iron oxidation by anoxygenic phototrophic bacteria

Outer membrane c-type cytochromes required for Fe(III) and Mn(IV) oxide reduction in Geobacter sulfurreducens

The potential role of outer membrane proteins in electron transfer to insoluble Fe(III) oxides by Geobacter sulfurreducens was investigated because this organism is closely related to the Fe(III) oxide-reducing organisms that are predominant in many Fe(III)-reducing environments. Two of the most abundant proteins that were easily sheared from the outer surfaces of intact cells were c-type cytochromes. One, designated OmcS, has a molecular mass of ca. 50 kDa and is predicted to be an outer membrane hexaheme c-type cytochrome. Transcripts for omcS could be detected during growth on Fe(III) oxide, but not on soluble Fe(III) citrate. The omcS mRNA consisted primarily of a monocistronic transcript, and to a lesser extent, a longer transcript that also contained the downstream gene omcT, which is predicted to encode a second hexaheme outer membrane cytochrome with 62.6% amino acid sequence identity to OmcS. The other abundant c-type cytochrome sheared from the outer surface of G. sulfurreducens, designated OmcE, has a molecular mass of ca. 30 kDa and is predicted to be an outer membrane tetraheme c-type cytochrome. When either omcS or omcE was deleted, G. sulfurreducens could no longer reduce Fe(III) oxide but could still reduce soluble electron acceptors, including Fe(III) citrate. The mutants could reduce Fe(III) in Fe(III) oxide medium only if the Fe(III) chelator, nitrilotriacetic acid, or the electron shuttle, anthraquinone 2,6-disulfonate, was added. Expressing omcS or omcE in trans restored the capacity for Fe(III) oxide reduction. OmcT was not detected among the sheared proteins, and genetic studies indicated that G. sulfurreducens could not reduce Fe(III) oxide when omcT was expressed but OmcS was absent. In contrast, Fe(III) oxide was reduced when omcS was expressed in the absence of OmcT. These results suggest that OmcS and OmcE are involved in electron transfer to Fe(III) oxides in G. sulfurreducens. They also emphasize the importance of evaluating mechanisms for Fe(III) reduction with environmentally relevant Fe(III) oxide, rather than the more commonly utilized Fe(III) citrate, because additional electron transfer components are required for Fe(III) oxide reduction that are not required for Fe(III) citrate reduction.

Anaerobic nitrate-dependent iron(II) bio-oxidation by a novel lithoautotrophic betaproteobacterium, strain 2002

Microbial nitrate-dependent Fe(II) oxidation is known to contribute to iron biogeochemical cycling; however, the microorganisms responsible are virtually unknown. In an effort to elucidate this microbial metabolic process in the context of an environmental system, a 14-cm sediment core was collected from a freshwater lake and geochemically characterized concurrently with the enumeration of the nitrate-dependent Fe(II)-oxidizing microbial community and subsequent isolation of a nitrate-dependent Fe(II)-oxidizing microorganism. Throughout the sediment core, ambient concentrations of Fe(II) and nitrate were observed to coexist. Concomitant most probable number enumeration revealed the presence of an abundant nitrate-dependent Fe(II)-oxidizing microbial community (2.4 x 10(3) to 1.5 x 10(4) cells g(-1) wet sediment) from which a novel anaerobic, lithoautotrophic, Fe(II)-oxidizing bacterium, strain 2002, was isolated. Analysis of the complete 16S rRNA gene sequence revealed that strain 2002 was a member of the beta subclass of the proteobacteria with 94.8% similarity to Chromobacterium violaceum, a bacterium not previously recognized for the ability to oxidize nitrate-dependent Fe(II). Under nongrowth conditions, both strain 2002 and C. violaceum incompletely reduced nitrate to nitrite with Fe(II) as the electron donor, while under growth conditions nitrate was reduced to gaseous end products (N2 and N2O). Lithoautotrophic metabolism under nitrate-dependent Fe(II)-oxidizing conditions was verified by the requirement of CO2 for growth as well as the assimilation of 14C-labeled CO2 into biomass. The isolation of strain 2002 represents the first example of an anaerobic, mesophilic, neutrophilic Fe(II)-oxidizing lithoautotroph isolated from freshwater samples. Our studies further demonstrate the abundance of nitrate-dependent Fe(II) oxidizers in freshwater lake sediments and provide further evidence for the potential of microbially mediated Fe(II) oxidation in anoxic environments.

The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis

Although biomarker, trace element, and isotopic evidence have been used to claim that oxygenic photosynthesis evolved by 2.8 giga-annum before present (Ga) and perhaps as early as 3.7 Ga, a skeptical examination raises considerable doubt about the presence of oxygen producers at these times. Geological features suggestive of oxygen, such as red beds, lateritic paleosols, and the return of sedimentary sulfate deposits after a approximately 900-million year hiatus, occur shortly before the approximately 2.3-2.2 Ga Makganyene "snowball Earth" (global glaciation). The massive deposition of Mn, which has a high redox potential, practically requires the presence of environmental oxygen after the snowball. New age constraints from the Transvaal Supergroup of South Africa suggest that all three glaciations in the Huronian Supergroup of Canada predate the Snowball event. A simple cyanobacterial growth model incorporating the range of C, Fe, and P fluxes expected during a partial glaciation in an anoxic world with high-Fe oceans indicates that oxygenic photosynthesis could have destroyed a methane greenhouse and triggered a snowball event on time-scales as short as 1 million years. As the geological evidence requiring oxygen does not appear during the Pongola glaciation at 2.9 Ga or during the Huronian glaciations, we argue that oxygenic cyanobacteria evolved and radiated shortly before the Makganyene snowball.

Isolation and characterization of a genetically tractable photoautotrophic Fe(II)-oxidizing bacterium, Rhodopseudomonas palustris strain TIE-1

We report the isolation and characterization of a phototrophic ferrous iron [Fe(II)]-oxidizing bacterium named TIE-1 that differs from other Fe(II)-oxidizing phototrophs in that it is genetically tractable. Under anaerobic conditions, TIE-1 grows photoautotrophically with Fe(II), H2, or thiosulfate as the electron donor and photoheterotrophically with a variety of organic carbon sources. TIE-1 also grows chemoheterotrophically in the dark. This isolate appears to be a new strain of the purple nonsulfur bacterial species Rhodopseudomonas palustris, based on physiological and phylogenetic analysis. Fe(II) oxidation is optimal at pH 6.5 to 6.9. The mineral products of Fe(II) oxidation are pH dependent: below pH 7.0 goethite (alpha-FeOOH) forms, and above pH 7.2 magnetite (Fe3O4) forms. TIE-1 forms colonies on agar plates and is sensitive to a variety of antibiotics. A hyperactive mariner transposon is capable of random insertion into the chromosome with a transposition frequency of approximately 10(-5). To identify components involved in phototrophic Fe(II) oxidation, mutants of TIE-1 were generated by transposon mutagenesis and screened for defects in Fe(II) oxidation in a cell suspension assay. Among approximately 12,000 mutants screened, 6 were identified that are specifically impaired in Fe(II) oxidation. Five of these mutants have independent disruptions in a gene that is predicted to encode an integral membrane protein that appears to be part of an ABC transport system; the sixth mutant has an insertion in a gene that is a homolog of CobS, an enzyme involved in cobalamin (vitamin B12) biosynthesis.

Iron isotope constraints on the Archean and Paleoproterozoic ocean redox state

The response of the ocean redox state to the rise of atmospheric oxygen about 2.3 billion years ago (Ga) is a matter of controversy. Here we provide iron isotope evidence that the change in the ocean iron cycle occurred at the same time as the change in the atmospheric redox state. Variable and negative iron isotope values in pyrites older than about 2.3 Ga suggest that an iron-rich global ocean was strongly affected by the deposition of iron oxides. Between 2.3 and 1.8 Ga, positive iron isotope values of pyrite likely reflect an increase in the precipitation of iron sulfides relative to iron oxides in a redox stratified ocean.

Energy problems in life evolution

Evolutionary aspects of bioenergetics are considered. These include the origin of the first organisms, UV-protection and the beginnings of anoxygenic photosynthesis, the electron donor problem of life and the appearance of oxygenic photosynthesis, oxygen danger and strategies of defense, and the role of oxygen in programmed cell death.

Clues from Fe isotope variations on the origin of early Archean BIFs from Greenland

Archean rocks may provide a record of early Earth environments. However, such rocks have often been metamorphosed by high pressure and temperature, which can overprint the signatures of their original formation. Here, we show that the early Archean banded rocks from Isua, Akilia, and Innersuartuut, Greenland, are enriched in heavy iron isotopes by 0.1 to 0.5 per mil per atomic mass unit relative to igneous rocks worldwide. The observed enrichments are compatible with the transport, oxidation, and subsequent precipitation of ferrous iron emanating from hydrothermal vents and thus suggest that the original rocks were banded iron formations (BIFs). These variations therefore support a sedimentary origin for the Akilia banded rocks, which represent one of the oldest known occurrences of water-laid deposits on Earth.

Biogeochemistry of an iron-rich hypersaline microbial mat (Camargue, France)

In situ microsensor measurements were combined with biogeochemical methods to determine oxygen, sulfur, and carbon cycling in microbial mats growing in a solar saltern (Salin-de-Giraud, France). Sulfate reduction rates closely followed the daily temperature changes and were highest during the day at 25 degrees C and lowest during the night at 11 degrees C, most probably fueled by direct substrate interactions between cyanobacteria and sulfate-reducing bacteria. Sulfate reduction was the major mineralization process during the night and the contribution of aerobic respiration to nighttime DIC production decreased. This decrease of aerobic respiration led to an increasing contribution of sulfide (and iron) oxidation to nighttime O2 consumption. A peak of elemental sulfur in a layer of high sulfate reduction at low sulfide concentration underneath the oxic zone indicated anoxygenic photosynthesis and/or sulfide oxidation by iron, which strongly contributed to sulfide consumption. We found a significant internal carbon cycling in the mat, and sulfate reduction directly supplied DIC for photosynthesis. The mats were characterized by a high iron content of 56 micromol Fe cm(-3), and iron cycling strongly controlled the sulfur cycle in the mat. This included sulfide precipitation resulting in high FeS contents with depth, and reactions of iron oxides with sulfide, especially after sunset, leading to a pronounced gap between oxygen and sulfide gradients and an unusual persistence of a pH peak in the uppermost mat layer until midnight.

Enrichment and isolation of iron-oxidizing bacteria at neutral pH

Methods are provided for the culture of neutrophilic Fe-oxidizing bacteria (FeOB) that grow under microaerobic and anaerobic conditions. For oxygen-requiring lithotrophic Fe oxidizers, it is essential that both O2 and Fe(II) concentrations are kept low, but that an adequate flux of both O2 and Fe(II) are provided to support growth. Techniques using opposing gradients of Fe(II) and O2 are discussed. Preparation of stock solutions of FeS and FeCl2 are described. Methods for the culture of anaerobic FeOB that utilize nitrate or light (anoxygenic photosynthesis) are discussed and presented briefly.

Enrichment and isolation of ferric-iron- and humic-acid-reducing bacteria

In anoxic habitats, ferric iron oxides and humic acids are widespread, and ferric-iron- and humic-acid-reducing microorganisms presumably play an important role in the oxidation of organic matter. Representative strains of ferric-iron- or humic-acid-reducing bacteria were isolated from a wide range of freshwater or marine environments. Most of them are strict anaerobes, and facultatively anaerobic microorganisms reduce ferric iron oxides or humic acids only after oxygen has been consumed. Hence, anaerobic techniques have to be used for the preparation of media as well as for the cultivation of microorganisms. Furthermore, special caution is needed in the preparation of ferric iron oxides and humic acids.

The Genetics of Geochemistry

Bacteria are remarkable in their metabolic diversity due to their ability to harvest energy from myriad oxidation and reduction reactions. In some cases, their metabolisms involve redox transformations of metal(loid)s, which lead to the precipitation, transformation, or dissolution of minerals. Microorganism/mineral interactions not only affect the geochemistry of modern environments, but may also have contributed to shaping the near-surface environment of the early Earth. For example, bacterial anaerobic respiration of ferric iron or the toxic metalloid arsenic is well known to affect water quality in many parts of the world today, whereas the utilization of ferrous iron as an electron donor in anoxygenic photosynthesis may help explain the origin of Banded Iron Formations, a class of ancient sedimentary deposits. Bacterial genetics holds the key to understanding how these metabolisms work. Once the genes and gene products that catalyze geochemically relevant reactions are understood, as well as the conditions that trigger their expression, we may begin to predict when and to what extent these metabolisms influence modern geochemical cycles, as well as develop a basis for deciphering their origins and how organisms that utilized them may have altered the chemical and physical features of our planet.

Tapping into microbial diversity

Even though significant advances have been made in understanding microbial diversity, most microorganisms are still only characterized by 'molecular fingerprints' and have resisted cultivation. Many different approaches have been developed to overcome the problems associated with cultivation of microorganisms because one obvious benefit would be the opportunity to investigate the previously inaccessible resources that these microorganisms potentially harbour.

Microbial ferric iron reductases

Almost all organisms require iron for enzymes involved in essential cellular reactions. Aerobic microbes living at neutral or alkaline pH encounter poor iron availability due to the insolubility of ferric iron. Assimilatory ferric reductases are essential components of the iron assimilatory pathway that generate the more soluble ferrous iron, which is then incorporated into cellular proteins. Dissimilatory ferric reductases are essential terminal reductases of the iron respiratory pathway in iron-reducing bacteria. While our understanding of dissimilatory ferric reductases is still limited, it is clear that these enzymes are distinct from the assimilatory-type ferric reductases. Research over the last 10 years has revealed that most bacterial assimilatory ferric reductases are flavin reductases, which can serve several physiological roles. This article reviews the physiological function and structure of assimilatory and dissimilatory ferric reductases present in the Bacteria, Archaea and Yeast. Ferric reductases do not form a single family, but appear to be distinct enzymes suggesting that several independent strategies for iron reduction may have evolved.

Immobilization of radionuclides and heavy metals through anaerobic bio-oxidation of Fe(II)

Adsorption of heavy metals and radionuclides (HMR) onto iron and manganese oxides has long been recognized as an important reaction for the immobilization of these compounds. However, in environments containing elevated concentrations of these HMR the adsorptive capacity of the iron and manganese oxides may well be exceeded, and the HMR can migrate as soluble compounds in aqueous systems. Here we demonstrate the potential of a bioremediative strategy for HMR stabilization in reducing environments based on the recently described anaerobic nitrate-dependent Fe(II) oxidation by Dechlorosoma species. Bio-oxidation of 10 mM Fe(II) and precipitation of Fe(III) oxides by these organisms resulted in rapid adsorption and removal of 55 microM uranium and 81 microM cobalt from solution. The adsorptive capacity of the biogenic Fe(III) oxides was lower than that of abiotically produced Fe(III) oxides (100 microM for both metals), which may have been a result of steric hindrance by the microbial cells on the iron oxide surfaces. The binding capacity of the biogenic oxides for different heavy metals was indirectly correlated to the atomic radius of the bound element. X-ray absorption spectroscopy indicated that the uranium was bound to the biogenically produced Fe(III) oxides as U(VI) and that the U(VI) formed bidentate and tridentate inner-sphere complexes with the Fe(III) oxide surfaces. Dechlorosoma suillum oxidation was specific for Fe(II), and the organism did not enzymatically oxidize U(IV) or Co(II). Small amounts (less than 2.5 microM) of Cr(III) were reoxidized by D. suillum; however, this appeared to be inversely dependent on the initial concentration of the Cr(III). The results of this study demonstrate the potential of this novel approach for stabilization and immobilization of HMR in the environment.

Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems

Microorganisms populate every habitable environment on Earth and, through their metabolic activity, affect the chemistry and physical properties of their surroundings. They have done this for billions of years. Over the past decade, genetic, biochemical, and genomic approaches have allowed us to document the diversity of microbial life in geologic systems without cultivation, as well as to begin to elucidate their function. With expansion of culture-independent analyses of microbial communities, it will be possible to quantify gene activity at the species level. Genome-enabled biogeochemical modeling may provide an opportunity to determine how communities function, and how they shape and are shaped by their environments.

Complex evolution of photosynthesis

The origin of photosynthesis is a fundamental biological question that has eluded researchers for decades. The complexity of the origin and evolution of photosynthesis is a result of multiple photosynthetic components having independent evolutionary pathways. Indeed, evolutionary scenarios have been established for only a few photosynthetic components. Phylogenetic analysis of Mg-tetrapyrrole biosynthesis genes indicates that most anoxygenic photosynthetic organisms are ancestral to oxygen-evolving cyanobacteria and that the purple bacterial lineage may contain the most ancestral form of this pigment biosynthesis pathway. The evolutionary path of type I and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits. However, evidence for a cytochrome b origin for the type II reaction center apoproteins is emerging. Based on the combined information for both photopigments and reaction centers, a unified theory for the evolution of reaction center holoproteins is provided. Further insight into the evolution of photosynthesis will have to rely on additional broader sampling of photosynthesis genes from divergent photosynthetic bacteria.

Biogenic magnetite formation through anaerobic biooxidation of Fe(II)

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.

Microbially catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds

The potential for microbially catalyzed NO3(-)-dependent oxidation of solid-phase Fe(II) compounds was examined using a previously described autotrophic, denitrifying, Fe(II)-oxidizing enrichment culture. The following solid-phase Fe(II)-bearing minerals were considered: microbially reduced synthetic goethite, two different end products of microbially hydrous ferric oxide (HFO) reduction (biogenic Fe3O4 and biogenic FeCO3), chemically precipitated FeCO3, and two microbially reduced iron(III) oxide-rich subsoils. The microbially reduced goethite, subsoils, and chemically precipitated FeCO3 were subject to rapid NO3(-)-dependent Fe(II) oxidation. Significant oxidation of biogenic Fe3O4 was observed. Very little biogenic FeCO3 was oxidized. No reduction of NO3- or oxidation of Fe(II) occurred in pasteurized cultures. The molar ratio of NO3- reduced to Fe(II) oxidized in cultures containing chemically precipitated FeCO3, and one of the microbially reduced subsoils approximated the theoretical stoichiometry of 0.2:1. However, molar ratios obtained for oxidation of microbially reduced goethite, the other subsoil, and the HFO reduction end products did not agree with this theoretical value. These discrepancies may be related to heterotrophic NO3- reduction coupled to oxidation of dead Fe(III)-reducing bacterial biomass. Our findings demonstrate that microbally catalyzed NO3(-)-dependent Fe(II) oxidation has the potential to significantly accelerate the oxidation of solid-phase Fe(II) compounds by oxidized N species. This process could have an important influence on the migration of contaminant metals and radionuclides in subsurface environments.

Nitrate-dependent iron(II) oxidation in paddy soil

Iron(III) profiles of flooded paddy soil incubated in the greenhouse indicated oxidation of iron(II) in the upper 6 mm soil layer. Measurement of oxygen with a Clark-type microelectrode showed that oxygen was only responsible for the oxidation of iron(II) in the upper 3 mm. In the soil beneath, nitrate could be used as electron acceptor instead of oxygen for the oxidation of the iron(II). Nitrate was still available 3 mm below the soil surface, and denitrifying activity was indicated by higher concentrations of nitrite between 3 and 6 mm soil depth. Nitrate was generated by nitrification from ammonium. Ammonium concentrations increased beneath 6 mm soil depth, indicating ammonium release and diffusion from deeper soil layers. High concentrations of ammonium were also found at the surface, probably resulting from N2 fixation by cyanobacteria. Experimental adjustment of the nitrate concentration in the flooding water to 200 microM stimulated nitrate-dependent iron(II) oxidation, which was indicated by significantly lower iron(II) concentrations in soil layers in which nitrate-dependent iron(II) oxidation was proposed. Soil incubated in the dark showed high iron(III) concentrations only in the layer where oxygen was still available. In this soil, the nitrogen pool was depleted because of the lack of N2 fixation by cyanobacteria. In contrast, soil incubated in the dark with 500 microM nitrate in the flooding water showed significantly higher iron(II) and significantly lower iron(II) concentrations in the anoxic soil layers, indicating nitrate-dependent iron(II) oxidation. Anoxic incubations of soil with nitrate in the flooding water also showed high concentrations of iron(II) and low concentrations of iron(II) in the upper 3 mm. As oxygen was excluded in anoxic incubations, the high iron(III) concentrations are a sign of the activity of nitrate-dependent iron(II) oxidizers. The presence of these bacteria in non-amended soil was also indicated by the most probable number (MPN) counts of nitrate-dependent iron(II) oxidizers in the layer of 3-4 mm soil depth, which revealed 1.6 x 10(6) bacteria g(-1) dry weight.

Iron metabolism in anoxic environments at near neutral pH

Anaerobic dissimilatory ferric iron-reducing and ferrous iron-oxidizing bacteria gain energy through reduction or oxidation of iron minerals and presumably play an important role in catalyzing iron transformations in anoxic environments. Numerous ferric iron-reducing bacteria have been isolated from a great diversity of anoxic environments, including sediments, soils, deep terrestrial subsurfaces, and hot springs. In contrast, only few ferrous iron-oxidizing bacteria are known so far. At neutral pH, iron minerals are barely soluble, and the mechanisms of electron transfer to or from iron minerals are still only poorly understood. In natural habitats, humic substances may act as electron carriers for ferric iron-reducing bacteria. Also fermenting bacteria were shown to channel electrons to ferric iron via humic acids. Whether quinones or cytochromes released from cells act as electron transfer components in ferric iron reduction is still a matter of debate. Anaerobic ferrous iron-oxidizing phototrophic bacteria, on the other hand, appear to excrete complexing agents to prevent precipitation of ferric iron oxides at their cell surfaces. The present review evaluates recent findings on the physiology of ferric iron-reducing and ferrous iron-oxidizing bacteria with respect to their relevance to microbial iron transformations in nature.

Mineralogical biosignatures and the search for life on Mars

If life ever existed, or still exists, on Mars, its record is likely to be found in minerals formed by, or in association with, microorganisms. An important concept regarding interpretation of the mineralogical record for evidence of life is that, broadly defined, life perturbs disequilibria that arise due to kinetic barriers and can impart unexpected structure to an abiotic system. Many features of minerals and mineral assemblages may serve as biosignatures even if life does not have a familiar terrestrial chemical basis. Biological impacts on minerals and mineral assemblages may be direct or indirect. Crystalline or amorphous biominerals, an important category of mineralogical biosignatures, precipitate under direct cellular control as part of the life cycle of the organism (shells, tests, phytoliths) or indirectly when cell surface layers provide sites for heterogeneous nucleation. Biominerals also form indirectly as by-products of metabolism due to changing mineral solubility. Mineralogical biosignatures include distinctive mineral surface structures or chemistry that arise when dissolution and/or crystal growth kinetics are influenced by metabolic by-products. Mineral assemblages themselves may be diagnostic of the prior activity of organisms where barriers to precipitation or dissolution of specific phases have been overcome. Critical to resolving the question of whether life exists, or existed, on Mars is knowing how to distinguish biologically induced structure and organization patterns from inorganic phenomena and inorganic self-organization. This task assumes special significance when it is acknowledged that the majority of, and perhaps the only, material to be returned from Mars will be mineralogical.

Microbial interactions involving sulfur bacteria: implications for the ecology and evolution of bacterial communities

A major goal of microbial ecology is the identification and characterization of those microorganisms which govern transformations in natural ecosystems. This review summarizes our present knowledge of microbial interactions in the natural sulfur cycle. Central to the discussion is the recent progress made in understanding the co-occurrence in natural ecosystems of sulfur bacteria with contrasting nutritional requirements and of the spatially very close associations of bacteria, the so-called phototrophic consortia (e.g. 'Chlorochromatium aggregatum' or 'Pelochromatium roseum'). In a similar way, microbial interactions may also be significant during microbial transformations other than the sulfur cycle in natural ecosystems, and could also explain the low culturability of bacteria from natural samples.

Phototrophs in high iron microbial mats: microstructure of mats in iron-depositing hot springs

Chocolate Pots Hot Springs in Yellowstone National Park are high in ferrous iron, silica and bicarbonate. The springs are contributing to the active development of an iron formation. The microstructure of photosynthetic microbial mats in these springs was studied with conventional optical microscopy, confocal laser scanning microscopy and transmission electron microscopy. The dominant mats at the highest temperatures (48-54 degrees C) were composed of Synechococcus and Chloroflexus or Pseudanabaena and Mastigocladus. At lower temperatures (36-45 degrees C), a narrow Oscillatoria dominated olive green cyanobacterial mats covering most of the iron deposit. Vertically oriented cyanobacterial filaments were abundant in the top 0.5 mm of the mats. Mineral deposits accumulated beneath this surface layer. The filamentous microstructure and gliding motility may contribute to binding the iron minerals. These activities and heavy mineral encrustation of cyanobacteria may contribute to the growth of the iron deposit. Chocolate Pots Hot Springs provide a model for studying the potential role of photosynthetic prokaryotes in the origin of Precambrian iron formations.

Life: past, present and future

Molecular methods of taxonomy and phylogeny have changed the way in which life on earth is viewed; they have allowed us to transition from a eukaryote-centric (five-kingdoms) view of the planet to one that is peculiarly prokarote-centric, containing three kingdoms, two of which are prokaryotic unicells. These prokaryotes are distinguished from their eukaryotic counterparts by their toughness, tenacity and metabolic diversity. Realization of these features has, in many ways, changed the way we feel about life on earth, about the nature of life past and about the possibility of finding life elsewhere. In essence, the limits of life on this planet have expanded to such a degree that our thoughts of both past and future life have been altered. The abilities of prokaryotes to withstand many extreme conditions has led to the term extremophiles, used to describe the organisms that thrive under conditions thought just a few years ago, to be inconsistent with life. Perhaps the most extensive adaptation to extreme conditions, however, is represented by the ability of many bacteria to survive nutrient conditions not compatible with eukaryotic life. Prokaryotes have evolved to use nearly every redox couple that is in abundance on earth, filling the metabolic niches left behind by the oxygen-using, carbon-eating eukaryotes. This metabolic plasticity leads to a common feature in physically stratified environments of layered microbial communities, chemical indicators of the metabolic diversity of the prokaryotes. Such 'metabolic extremophily' forms a backdrop by which we can view the energy flow of life on this planet, think about what the evolutionary past of the planet might have been, and plan ways to look for life elsewhere, using the knowledge of energy flow on earth.

Phototrophs in high-iron-concentration microbial mats: physiological ecology of phototrophs in an iron-depositing hot spring

At Chocolate Pots Hot Springs in Yellowstone National Park the source waters have a pH near neutral, contain high concentrations of reduced iron, and lack sulfide. An iron formation that is associated with cyanobacterial mats is actively deposited. The uptake of [(14)C]bicarbonate was used to assess the impact of ferrous iron on photosynthesis in this environment. Photoautotrophy in some of the mats was stimulated by ferrous iron (1.0 mM). Microelectrodes were used to determine the impact of photosynthetic activity on the oxygen content and the pH in the mat and sediment microenvironments. Photosynthesis increased the oxygen concentration to 200% of air saturation levels in the top millimeter of the mats. The oxygen concentration decreased with depth and in the dark. Light-dependent increases in pH were observed. The penetration of light in the mats and in the sediments was determined. Visible radiation was rapidly attenuated in the top 2 mm of the iron-rich mats. Near-infrared radiation penetrated deeper. Iron was totally oxidized in the top few millimeters, but reduced iron was detected at greater depths. By increasing the pH and the oxygen concentration in the surface sediments, the cyanobacteria could potentially increase the rate of iron oxidation in situ. This high-iron-content hot spring provides a suitable model for studying the interactions of microbial photosynthesis and iron deposition and the role of photosynthesis in microbial iron cycling. This model may help clarify the potential role of photosynthesis in the deposition of Precambrian banded iron formations.

Archean molecular fossils and the early rise of eukaryotes

Molecular fossils of biological lipids are preserved in 2700-million-year-old shales from the Pilbara Craton, Australia. Sequential extraction of adjacent samples shows that these hydrocarbon biomarkers are indigenous and syngenetic to the Archean shales, greatly extending the known geological range of such molecules. The presence of abundant 2alpha-methylhopanes, which are characteristic of cyanobacteria, indicates that oxygenic photosynthesis evolved well before the atmosphere became oxidizing. The presence of steranes, particularly cholestane and its 28- to 30-carbon analogs, provides persuasive evidence for the existence of eukaryotes 500 million to 1 billion years before the extant fossil record indicates that the lineage arose.

Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse European sediments

Anaerobic, nitrate-dependent microbial oxidation of ferrous iron was recently recognized as a new type of metabolism. In order to study the occurrence of three novel groups of ferrous iron-oxidizing, nitrate-reducing bacteria (represented by strains BrG1, BrG2, and BrG3), 16S rRNA-targeted oligonucleotide probes were developed. In pure-culture experiments, these probes were shown to be suitable for fluorescent in situ hybridization, as well as for hybridization analysis of denaturing gradient gel electrophoresis (DGGE) patterns. However, neither enumeration by in situ hybridization nor detection by the DGGE-hybridization approach was feasible with sediment samples. Therefore, the DGGE-hybridization approach was combined with microbiological methods. Freshwater sediment samples from different European locations were used for enrichment cultures and most-probable-number (MPN) determinations. Bacteria with the ability to oxidize ferrous iron under nitrate-reducing conditions were detected in all of the sediment samples investigated. At least one of the previously described types of bacteria was detected in each enrichment culture. MPN studies showed that sediments contained from 1 x 10(5) to 5 x 10(8) ferrous iron-oxidizing, nitrate-reducing bacteria per g (dry weight) of sediment, which accounted for at most 0.8% of the nitrate-reducing bacteria growing with acetate. Type BrG1, BrG2, and BrG3 bacteria accounted for an even smaller fraction (0.2% or less) of the ferrous iron-oxidizing, nitrate-reducing community. The DGGE patterns of MPN cultures suggested that more organisms than those isolated thus far are able to oxidize ferrous iron with nitrate. A comparison showed that among the anoxygenic phototrophic bacteria, organisms that have the ability to oxidize ferrous iron also account for only a minor fraction of the population.

Photosynthetic reaction centers

The reaction center is the key component for the primary events in the photochemical conversion of light into chemical energy. After excitation by light, a charge separation that spans the cell membrane is formed in the reaction center in a few hundred picoseconds with a quantum yield of essentially one. A conserved pattern in the cofactors and core proteins of reaction centers from different organisms can be defined based on comparisons of the three dimensional structure of two types of reaction centers. Different functional aspects of the reaction center are discussed, including the properties of the bacteriochlorophyll or chlorophyll dimer that constitutes the primary electron donor, the pathway of electron transfer, and the different functional roles of the electron acceptors. The implication of these results on the evolution of the reaction center is presented.

Phototrophic oxidation of ferrous iron by a Rhodomicrobium vannielii strain

Oxidation of ferrous iron was studied with the anaerobic phototrophic bacterial strain BS-1. Based on morphology, substrate utilization patterns, arrangement of intracytoplasmic membranes and the in vivo absorption spectrum, this strain was assigned to the known species Rhodomicrobium vannielii. Also, the type strain of this species oxidized ferrous iron in the light. Phototrophic growth of strain BS-1 with ferrous iron as electron donor was stimulated by the presence of acetate or succinate as cosubstrates. The ferric iron hydroxides produced precipitated on the cell surfaces as solid crusts which impeded further iron oxidation after two to three generations. The complexing agent nitrilotriacetate stimulated iron oxidation but the yield of cell mass did not increase stoichiometrically under these conditions. Other complexing agents inhibited cell growth. Ferric iron was not reduced in the dark, and manganese salts were neither oxidized nor reduced. It is concluded that ferrous iron oxidation by strain BS-1 is only a side activity of this bacterium that cannot support growth exclusively with this electron source over prolonged periods of time.

The use of biologically produced ferrihydrite for the isolation of novel iron-reducing bacteria

Ferric iron was produced anaerobically from ferrous iron through the metabolic activity of recently described ferrous iron-oxidizing, nitrate-reducing bacteria. It was identified as poorly crystallized 2-line ferrihydrite with a particle size of 1-2 nm. This biologically produced ferrihydrite was shown to be a suitable electron acceptor for dissimilatory ferric iron-reducing bacteria in freshwater enrichment cultures, and was completely reduced to the ferrous state; no magnetite formation occurred. Geobacter metallireducens was also able to completely reduce the biologically produced ferrihydrite. These results indicate the possibility of an anaerobic, microbial cycling of iron. Using the biologically produced ferric iron, two isolates of obligately anaerobic, dissimilatory ferric iron-reducing bacteria, strains Dfr1 and Dfr2, were obtained from freshwater enrichment cultures. Analysis of 16S rRNA gene sequences revealed an affiliation with the Geobacter cluster within the family Geobacteraceae. The sequence similarity between strains Dfr1 and Dfr2 is 92.5%. The closest relative of strain Dfr1 is Geobacter sulfurreducens with 92.9%, and of strain Dfr2 Geobacter chapelleii with 93.7% sequence similarity. In addition, strains Dfr1 and Dfr2 are both able to grow by dissimilatory reduction of Mn(IV), S degree, and fumarate. Furthermore, strain Dfr2 is able to reduce akaganeite (beta-FeOOH), a more crystallized type of ferric iron oxide.

A periplasmic and extracellular c-type cytochrome of Geobacter sulfurreducens acts as a ferric iron reductase and as an electron carrier to other acceptors or to partner bacteria

An extracellular electron carrier excreted into the growth medium by cells of Geobacter sulfurreducens was identified as a c-type cytochrome. The cytochrome was found to be distributed in about equal amounts in the membrane fraction, the periplasmic space, and the surrounding medium during all phases of growth with acetate plus fumarate. It was isolated from periplasmic preparations and purified to homogeneity by cation-exchange chromatography, gel filtration, and hydrophobic interaction chromatography. The electrophoretically homogeneous cytochrome had a molecular mass of 9.57 +/- 0.02 kDa and exhibited in its reduced state absorption maxima at wavelengths of 552, 522, and 419 nm. The midpoint redox potential determined by redox titration was -0.167 V. With respect to molecular mass, redox properties, and molecular features, this cytochrome exhibited its highest similarity to the cytochromes c of Desulfovibrio salexigens and Desulfuromonas acetoxidans. The G. sulfurreducens cytochrome c reduced ferrihydrite (Fe(OH)3), Fe(III) nitrilotriacetic acid, Fe(III) citrate, and manganese dioxide at high rates. Elemental sulfur, anthraquinone disulfonate, and humic acids were reduced more slowly. G. sulfurreducens reduced the cytochrome with acetate as an electron donor and oxidized it with fumarate. Wolinella succinogenes was able to reduce externally provided cytochrome c of G. sulfurreducens with molecular hydrogen or formate as an electron donor and oxidized it with fumarate or nitrate as an electron acceptor. A coculture could be established in which G. sulfurreducens reduced the cytochrome with acetate, and the reduced cytochrome was reoxidized by W. succinogenes in the presence of nitrate. We conclude that this cytochrome can act as iron(III) reductase for electron transfer to insoluble iron hydroxides or to sulfur, manganese dioxide, or other oxidized compounds, and it can transfer electrons to partner bacteria.

The origin and evolution of oxygenic photosynthesis

The evolutionary developments that led to the ability of photosynthetic organisms to oxidize water to molecular oxygen are discussed. Two major changes from a more primitive non-oxygen-evolving reaction center are required: a charge-accumulating system and a reaction center pigment with a greater oxidizing potential. Intermediate stages are proposed in which hydrogen peroxide was oxidized by the reaction center, and an intermediate pigment, similar to chlorophyll d, was present.

Evolution of the atmosphere

Planetary atmospheres depend fundamentally upon their geochemical inventory, temperature and the ability of their gravitational field to retain gases. In the case of Earth and other inner planets, early outgassing released mainly carbon dioxide and water vapour. The secondary veneer of comets and meteorites added further volatiles. Photodissociation caused secondary changes, including the production of traces of oxygen from water. Earth's gravity cannot retain light gases, including hydrogen. but retains oxygen. Water vapour generally does not pass the cold trap at the stratopause. In the archaean, early evolution of life, probably in hydrothermal vents, and the subsequent development of photosynthesis in surface waters, produced oxygen, at 3500 Ma or even earlier, becoming a significant component of the atmosphere from about 2000 Ma. Thereafter banded iron formations became rare, and iron was deposited in oxidized red beds. Atmospheric levels of carbon dioxide and oxygen have varied during the Phanerozoic: major changes may have caused extinctions. particularly the Permian/Triassic. The declining greenhouse effect due to the long-term decrease in carbon dioxide has largely offset increasing solar luminosity, and changes in carbon dioxide levels relate strongly to cycles of glaciation.

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

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.

Anaerobic, nitrate-dependent microbial oxidation of ferrous iron

Enrichment and pure cultures of nitrate-reducing bacteria were shown to grow anaerobically with ferrous iron as the only electron donor or as the additional electron donor in the presence of acetate. The newly observed bacterial process may significantly contribute to ferric iron formation in the suboxic zone of aquatic sediments.

Physiological ecology of cyanobacteria in microbial mats and other communities

In this review some aspects of the physiological ecology of cyanobacteria are discussed by taking a microbial mat as an example. The majority of microbial mats are built and dominated by cyarsobacteria which are primary producers at the basis of the microbial foodweb in microbial mats. These micro-scale ecosystems are characterized by steep and fluctuating physico-chemical gradients of which those of light, oxygen and sulphide are the most conspicuous. Light is strongly attenuated in the sediment, and owing to constant sedimentation, the mat-forming cyanobacteria have to move upwards towards the light. However, at the sediment surface, light intensity, particularly in the u.v. part of the spectrum, is often deleterious. The gliding movement of the cyanobacteria, with photo- and chemotaxis, allows the organism to position itself in a thin layer at optimal conditions. The organic matter produced by cyanobacterial photosynthesis is decomposed by the ruicrobial community. Sulphate-reducing bacteria are important in the end-oxidation of the organic matter. These organisms are obligate anaerobes and produce sulphide. Gradients of sulphide and oxygen move up and down in the sediment as a response to diurnal variations of light intensity. Cyanobacteria, therefore, are sometimes exposed to large concentrations of the extremely toxic sulphide. Some species are capable of sulphide-dependent anoxygenic photosynthesis. Other cyanobacteria show increased rates of oxygenic photosynthesis in the presence of sulphide and have mechanisms to oxidize sulphide while avoiding sulphide toxicity. Iron might play an important role in this process. Under anoxic conditions in the dark, mat-forming cyanobacteria switch to fermentative metabolism. Many species are also capable of fermentative reduction of elemental sulphur to sulphide. The gradients of sulphide and oxygen are of particular importance for nitrogen fixation. Very few microbial mats are formed by heterocystous cyanobacteria, which are best adapted to diazntrophic growth. However, these organisms probably cannot tolerate greater concentrations of sulphide or anoxic conditions or both. Under such conditions non-heterocystous cyanobacteria become dominant as diazotrophs. These organisms avoid conditions of oxygen supersaturation. In the ecosystem, nitrogen fixation and photosynthesis might be separated temporally as well as spatially. In addition, non-heterocystous diazotrophic cyanobacteria have mechanisms at the subcellular level to protect the oxygen-sensitive nitrogenase from inaction. CONTENTS Summary 1 I. Introduction 2 II. Microbial mats 3 III. Cyanobacteria in light gradients 7 IV. Dark metabolism 10 V. Interactions with sulphide 13 VI. Nitrogen fixation 16 VII. References 28.

Anaerobic oxidation of ferrous iron by purple bacteria, a new type of phototrophic metabolism

Anoxic iron-rich sediment samples that had been stored in the light showed development of brown, rusty patches. Subcultures in defined mineral media with ferrous iron (10 mmol/liter, mostly precipitated as FeCO3) yielded enrichments of anoxygenic phototrophic bacteria which used ferrous iron as the sole electron donor for photosynthesis. Two different types of purple bacteria, represented by strains L7 and SW2, were isolated which oxidized colorless ferrous iron under anoxic conditions in the light to brown ferric iron. Strain L7 had rod-shaped, nonmotile cells (1.3 by 2 to 3 microns) which frequently formed gas vesicles. In addition to ferrous iron, strain L7 used H2 + CO2, acetate, pyruvate, and glucose as substrate for phototrophic growth. Strain SW2 had small rod-shaped, nonmotile cells (0.5 by 1 to 1.5 microns). Besides ferrous iron, strain SW2 utilized H2 + CO2, monocarboxylic acids, glucose, and fructose. Neither strain utilized free sulfide; however, both strains grew on black ferrous sulfide (FeS) which was converted to ferric iron and sulfate. Strains L7 and SW2 grown photoheterotrophically without ferrous iron were purple to brownish red and yellowish brown, respectively; absorption spectra revealed peaks characteristic of bacteriochlorophyll a. The closest phototrophic relatives of strains L7 and SW2 so far examined on the basis of 16S rRNA sequences were species of the genera Chromatium (gamma subclass of proteobacteria) and Rhodobacter (alpha subclass), respectively. In mineral medium, the new isolates formed 7.6 g of cell dry mass per mol of Fe(II) oxidized, which is in good agreement with a photoautotrophic utilization of ferrous iron as electron donor for CO2 fixation. Dependence of ferrous iron oxidation on light and CO2 was also demonstrated in dense cell suspensions. In media containing both ferrous iron and an organic substrate (e.g., acetate, glucose), strain L7 utilized ferrous iron and the organic compound simultaneously; in contrast, strain SW2 started to oxidize ferrous iron only after consumption of the organic electron donor. Ferrous iron oxidation by anoxygenic phototrophs is understandable in terms of energetics. In contrast to the Fe3+/Fe2+ pair (E0 = +0.77 V) existing in acidic solutions, the relevant redox pair at pH 7 in bicarbonate-containing environments, Fe(OH)3 + HCO3-/FeCO3, has an E0' of +0.2 V. Ferrous iron at pH 7 can therefore donate electrons to the photosystem of anoxygenic phototrophs, which in purple bacteria has a midpoint potential around +0.45 V. The existence of ferrous iron-oxidizing anoxygenic phototrophs may offer an explanation for the deposition of early banded-iron formations in an assumed anoxic biosphere in Archean times.