Rates and pathways of CH4 oxidation in ferruginous Lake Matano,Indonesia

This study evaluates rates and pathways of methane (CH₄) oxidation and uptake using ¹⁴C‐based tracer experiments throughout the oxic and anoxic waters of ferruginous Lake Matano. Methane oxidation rates in Lake Matano are moderate (0.36 nmol L^?1 day^?1 to 117 μmol L^?1 day^?1) compared to other lakes, but are sufficiently high to preclude strong CH₄ fluxes to the atmosphere. In addition to aerobic CH₄ oxidation, which takes place in Lake Matano's oxic mixolimnion, we also detected CH₄ oxidation in Lake Matano's anoxic ferruginous waters. Here, CH₄ oxidation proceeds in the apparent absence of oxygen (O₂) and instead appears to be coupled to some as yet uncertain combination of nitrate (), nitrite (), iron (Fe) or manganese (Mn), or sulfate () reduction. Throughout the lake, the fraction of CH₄ carbon that is assimilated vs. oxidized to carbon dioxide (CO₂) is high (up to 93%), indicating extensive CH₄ conversion to biomass and underscoring the importance of CH₄ as a carbon and energy source in Lake Matano and potentially other ferruginous or low productivity environments.     

Oxidation of Fe(II)‐EDTA by nitrite and by two nitrate‐reducing Fe(II)‐oxidizing Acidovorax strains

The enzymatic oxidation of Fe(II) by nitrate‐reducing bacteria was first suggested about two decades ago. It has since been found that most strains are mixotrophic and need an additional organic co‐substrate for complete and prolonged Fe(II) oxidation. Research during the last few years has tried to determine to what extent the observed Fe(II) oxidation is driven enzymatically, or abiotically by nitrite produced during heterotrophic denitrification. A recent study reported that nitrite was not able to oxidize Fe(II)‐EDTA abiotically, but the addition of the mixotrophic nitrate‐reducing Fe(II)‐oxidizer, Acidovorax sp. strain 2AN, led to Fe(II) oxidation (Chakraborty & Picardal, 2013). This, along with other results of that study, was used to argue that Fe(II) oxidation in strain 2AN was enzymatically catalyzed. However, the absence of abiotic Fe(II)‐EDTA oxidation by nitrite reported in that study contrasts with previously published data. We have repeated the abiotic and biotic experiments and observed rapid abiotic oxidation of Fe(II)‐EDTA by nitrite, resulting in the formation of Fe(III)‐EDTA and the green Fe(II)‐EDTA‐NO complex. Additionally, we found that cultivating the Acidovorax strains BoFeN1 and 2AN with 10 mm nitrate, 5 mm acetate, and approximately 10 mm Fe(II)‐EDTA resulted only in incomplete Fe(II)‐EDTA oxidation of 47–71%. Cultures of strain BoFeN1 turned green (due to the presence of Fe(II)‐EDTA‐NO) and the green color persisted over the course of the experiments, whereas strain 2AN was able to further oxidize the Fe(II)‐EDTA‐NO complex. Our work shows that the two used Acidovorax strains behave very differently in their ability to deal with toxic effects of Fe‐EDTA species and the further reduction of the Fe(II)‐EDTA‐NO nitrosyl complex. Although the enzymatic oxidation of Fe(II) cannot be ruled out, this study underlines the importance of nitrite in nitrate‐reducing Fe(II)‐ and Fe(II)‐EDTA‐oxidizing cultures and demonstrates that Fe(II)‐EDTA cannot be used to demonstrate unequivocally the enzymatic oxidation of Fe(II) by mixotrophic Fe(II)‐oxidizers.     

Oxygen isotope analysis of bacterial and fungal manganese oxidation

The ability of micro‐organisms to oxidize manganese (Mn) from Mn(II) to Mn(III/IV) oxides transcends boundaries of biological clade or domain. Many bacteria and fungi oxidize Mn(II) to Mn(III/IV) oxides directly through enzymatic activity or indirectly through the production of reactive oxygen species. Here, we determine the oxygen isotope fractionation factors associated with Mn(II) oxidation via various biotic (bacteria and fungi) and abiotic Mn(II) reaction pathways. As oxygen in Mn(III/IV) oxides may be derived from precursor water and molecular oxygen, we use a twofold approach to determine the isotope fractionation with respect to each oxygen source. Using both ¹⁸O‐labeled water and closed‐system Rayleigh distillation approaches, we constrain the kinetic isotope fractionation factors associated with O atom incorporation during Mn(II) oxidation to ?17.3‰ to ?25.9‰ for O₂ and ?1.9‰ to +1.8‰ for water. Results demonstrate that stable oxygen isotopes of Mn(III/IV) oxides have potential to distinguish between two main classes of biotic Mn(II) oxidation: direct enzymatic oxidation in which O₂ is the oxidant and indirect enzymatic oxidation in which superoxide is the oxidant. The fraction of Mn(III/IV) oxide‐associated oxygen derived from water varies significantly (38%–62%) among these bio‐oxides with only weak relationship to Mn oxidation state, suggesting Mn(III) disproportionation may account for differences in the fraction of mineral‐bound oxygen from water and O₂. Additionally, direct incorporation of molecular O₂ suggests that Mn(III/IV) oxides contain a yet untapped proxy of of environmental O₂, a parameter reflecting the integrated influence of global respiration, photorespiration, and several other biogeochemical reactions of global significance.     

Chemodenitrification in the cryoecosystem of Lake Vida,Victoria Valley,Antarctica

Lake Vida, in the Victoria Valley of East Antarctica, is frozen, yet harbors liquid brine (~20% salt, >6 times seawater) intercalated in the ice below 16 m. The brine has been isolated from the surface for several thousand years. The brine conditions (permanently dark, ?13.4 °C, lack of O₂, and pH of 6.2) and geochemistry are highly unusual. For example, nitrous oxide (N₂O) is present at a concentration among the highest reported for an aquatic environment. Only a minor ¹⁷O anomaly was observed in N₂O, indicating that this gas was predominantly formed in the lake. In contrast, the ¹⁷O anomaly in nitrate () in Lake Vida brine indicates that approximately half or more of the present is derived from atmospheric deposition. Lake Vida brine was incubated in the presence of ¹⁵N‐enriched substrates for 40 days. We did not detect microbial nitrification, dissimilatory reduction of to ammonium (), anaerobic ammonium oxidation, or denitrification of N₂O under the conditions tested. In the presence of ¹⁵N‐enriched nitrite (), both N₂ and N₂O exhibited substantial ¹⁵N enrichments; however, isotopic enrichment declined with time, which is unexpected. Additions of ¹⁵N– alone and in the presence of HgCl₂ and ZnCl₂ to aged brine at ?13 °C resulted in linear increases in the δ¹⁵N of N₂O with time. As HgCl₂ and ZnCl₂ are effective biocides, we interpret N₂O production in the aged brine to be the result of chemodenitrification. With this understanding, we interpret our results from the field incubations as the result of chemodenitrification stimulated by the addition of ¹⁵N‐enriched and ZnCl₂ and determined rates of N₂O and N₂ production of 4.11–41.18 and 0.55–1.75 nmol L^?1 day^?1, respectively. If these rates are representative of natural production, the current concentration of N₂O in Lake Vida could have been reached between 6 and 465 years. Thus, chemodenitrification alone is sufficient to explain the high levels of N₂O present in Lake Vida.     

Temperature response of denitrification rate and greenhouse gas production in agricultural river marginal wetland soils

Soils are predicted to exhibit significant feedback to global warming via the temperature response of greenhouse gas (GHG) production. However, the temperature response of hydromorphic wetland soils is complicated by confounding factors such as oxygen (O₂), nitrate () and soil carbon (C). We examined the effect of a temperature gradient (2–25 °C) on denitrification rates and net nitrous oxide (N₂O), methane (CH₄) production and heterotrophic respiration in mineral (Eutric cambisol and Fluvisol) and organic (Histosol) soil types in a river marginal landscape of the Tamar catchment, Devon, UK, under non‐flooded and flooded with enriched conditions. It was hypothesized that the temperature response is dependent on interactions with ‐enriched flooding, and the physicochemical conditions of these soil types. Denitrification rate (mean, 746 ± 97.3 μg m^?2 h^?1), net N₂O production (mean, 180 ± 26.6 μg m^?2 h^?1) and net CH₄ production (mean, 1065 ± 183 μg m^?2 h^?1) were highest in the organic Histosol, with higher organic matter, ammonium and moisture, and lower concentrations. Heterotrophic respiration (mean, 127 ± 4.6 mg m^?2 h^?1) was not significantly different between soil types and dominated total GHG (CO₂eq) production in all soil types. Generally, the temperature responses of denitrification rate and net N₂O production were exponential, whilst net CH₄ production was unresponsive, possibly due to substrate limitation, and heterotrophic respiration was exponential but limited in summer at higher temperatures. Flooding with increased denitrification rate, net N₂O production and heterotrophic respiration, but a reduction in net CH₄ production suggests inhibition of methanogenesis by or N₂O produced from denitrification. Implications for management and policy are that warming and flood events may promote microbial interactions in soil between distinct microbial communities and increase denitrification of excess with N₂O production contributing to no more than 50% of increases in total GHG production.     

The effect of O2 and pressure on thiosulfate oxidation by Thiomicrospira thermophila

Microbial sulfur cycling in marine sediments often occurs in environments characterized by transient chemical gradients that affect both the availability of nutrients and the activity of microbes. High turnover rates of intermediate valence sulfur compounds and the intermittent availability of oxygen in these systems greatly impact the activity of sulfur‐oxidizing micro‐organisms in particular. In this study, the thiosulfate‐oxidizing hydrothermal vent bacterium Thiomicrospira thermophila strain EPR85 was grown in continuous culture at a range of dissolved oxygen concentrations (0.04–1.9 mM) and high pressure (5–10 MPa) in medium buffered at pH 8. Thiosulfate oxidation under these conditions produced tetrathionate, sulfate, and elemental sulfur, in contrast to previous closed‐system experiments at ambient pressure during which thiosulfate was quantitatively oxidized to sulfate. The maximum observed specific growth rate at 5 MPa pressure under unlimited O₂ was 0.25 hr^?1. This is comparable to the μ_max (0.28 hr^?1) observed at low pH (<6) at ambient pressure when T. thermophila produces the same mix of sulfur species. The half‐saturation constant for O₂ () estimated from this study was 0.2 mM (at a cell density of 10⁵ cells/ml) and was robust at all pressures tested (0.4–10 MPa), consistent with piezotolerant behavior of this strain. The cell‐specific was determined to be 1.5 pmol O₂/cell. The concentrations of products formed were correlated with oxygen availability, with tetrathionate production in excess of sulfate production at all pressure conditions tested. This study provides evidence for transient sulfur storage during times when substrate concentration exceeds cell‐specific and subsequent consumption when oxygen dropped below that threshold. These results may be common among sulfur oxidizers in a variety of environments (e.g., deep marine sediments to photosynthetic microbial mats).     

The effect of rock composition on cyanobacterial weathering of crystalline basalt and rhyolite

The weathering of volcanic rocks contributes significantly to the global silicate weathering budget, effecting carbon dioxide drawdown and long‐term climate control. The rate of chemical weathering is influenced by the composition of the rock. Rock‐dwelling micro‐organisms are known to play a role in changing the rate of weathering reactions; however, the influence of rock composition on bio‐weathering is unknown. Cyanobacteria are known to be a ubiquitous surface taxon in volcanic rocks. In this study, we used a selection of fast and slow growing cyanobacterial species to compare microbial‐mediated weathering of bulk crystalline rocks of basaltic and rhyolitic composition, under batch conditions. Cyanobacterial growth caused an increase in the pH of the medium and an acceleration of rock dissolution compared to the abiotic controls. For example, Anabaena cylindrica increased the linear release rate () of Ca, Mg, Si and K from the basalt by more than fivefold (5.21–12.48) and increased the pH of the medium by 1.9 units. Although A. cylindrica enhanced rhyolite weathering, the increase in was less than threefold (2.04–2.97) and the pH increase was only 0.83 units. The values obtained with A. cylindrica were at least ninefold greater with the basalt than the rhyolite, whereas in the abiotic controls, the difference was less than fivefold. Factors accounting for the slower rate of rhyolite weathering and lower biomass achieved are likely to include the higher content of quartz, which has a low rate of weathering and lower concentrations of bio‐essential elements, such as, Ca, Fe and Mg, which are known to be important in controlling cyanobacterial growth. We show that at conditions where weathering is favoured, biota can enhance the difference between low and high Si‐rock weathering. Our data show that cyanobacteria can play a significant role in enhancing rock weathering and likely have done since they evolved on the early Earth.     

微生物介导硝酸盐还原耦合亚铁氧化过程的动力学及其影响因素

【目的】探究不同菌浓度和亚铁浓度条件下,Acidovorax sp. strain BoFeN1介导的厌氧亚铁氧化耦合硝酸盐还原过程的动力学和次生矿物。【方法】构建包含菌BoFeN1、硝酸盐、亚铁的厌氧培养体系,测试硝酸根、亚硝酸根、乙酸根、亚铁等浓度,并收集次生矿物,采用XRD、SEM进行矿物种类和形貌表征。【结果】在微生物介导硝酸盐还原耦合亚铁氧化的体系中,高菌浓度促进硝酸盐还原,对亚铁氧化也有一定促进作用;高浓度亚铁在低菌浓度下氧化反应速率和程度降低,但是在高菌浓度下无明显影响;亚铁浓度越高次生矿物结晶度越高,但对硝酸盐还原具有一定抑制作用。在微生物介导亚硝酸盐还原耦合亚铁氧化的体系中,高的菌浓度和亚铁浓度都会促进亚硝酸盐还原,但亚铁氧化的次生矿物会对亚硝酸盐的微生物还原产生较强的抑制作用,次生矿物的种类和结晶度主要受亚铁浓度影响。【结论】硝酸盐还原主要是生物反硝化作用,亚硝酸盐还原包含生物反硝化和化学反硝化两部分,在硝酸盐体系中亚铁氧化与次生矿物生成是受生物和化学反硝化作用的共同影响,但亚硝酸盐体系中亚铁氧化与次生矿物生成主要是受化学反硝化作用影响。该研究可为深入理解厌氧微生物介导铁氮耦合反应机制提供基础数据和理论支撑。     

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

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 10⁵ cells mL⁻¹ of the total heterotrophic nitrate-reducing bacteria, with about 1% (10³ cells mL⁻¹) 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 O₂, 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⁻¹ acetate) by about 1.4 g dry mass mol⁻¹ Fe(II). Also, pure cultures of Pseudomonas stutzeri and Paracoccus 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.     

Isotopically anomalous organic carbon in the aftermath of the Marinoan snowball Earth

Throughout most of the sedimentary record, the marine carbon cycle is interpreted as being in isotopic steady state. This is most commonly inferred via isotopic reconstructions, where two export fluxes (organic carbon and carbonate) are offset by a constant isotopic fractionation of ~25 (termed ). Sedimentary deposits immediately overlying the Marinoan snowball Earth diamictites, however, stray from this prediction. In stratigraphic sections from the Ol Formation (Mongolia) and Sheepbed Formation (Canada), we observe a temporary excursion where the organic matter has anomalously heavy C and is grossly decoupled from the carbonate C. This signal may reflect the unique biogeochemical conditions that persisted in the aftermath of snowball Earth. For example, physical oceanographic modeling suggests that a strong density gradient caused the ocean to remain stratified for about 50,000 years after termination of the Marinoan snowball event, during which time the surface ocean and continental weathering consumed the large atmospheric CO₂ reservoir. Further, we now better understand how C records of carbonate can be post‐depostionally altered and thus be misleading. In an attempt to explain the observed carbon isotope record, we developed a model that tracks the fluxes and isotopic values of carbon between the surface ocean, deep ocean, and atmosphere. By comparing the model output to the sedimentary data, stratification alone cannot generate the anomalous observed isotopic signal. Reproducing the heavy C in organic matter requires the progressively diminishing contribution of an additional anomalous source of organic matter. The exact source of this organic matter is unclear.     

Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico)

The microbial communities thriving in deep‐sea brines are sustained largely by energy rich substrates supplied through active seepage. Geochemical, microbial activity, and microbial community composition data from different habitats at a Gulf of Mexico brine lake in Alaminos Canyon revealed habitat‐linked variability in geochemistry that in turn drove patterns in microbial community composition and activity. The bottom of the brine lake was the most geochemically extreme (highest salinity and nutrient concentrations) habitat and its microbial community exhibited the highest diversity and richness indices. The habitat at the upper halocline of the lake hosted the highest rates of sulfate reduction and methane oxidation, and the largest inventories of dissolved inorganic carbon, particulate organic carbon, and hydrogen sulfide. Statistical analyses indicated a significant positive correlation between the bacterial and archaeal diversity in the bottom brine sample and inventories. Other environmental factors with positive correlation with microbial diversity indices were DOC, H₂S, and DIC concentrations. The geochemical regime of different sites within this deep seafloor extreme environment exerts a clear selective force on microbial communities and on patterns of microbial activity.     

Neutrophilic, nitrate-dependent, Fe(II) oxidation by a Dechloromonas species

A species of Dechloromonas, strain UWNR4, was isolated from a nitrate-reducing, enrichment culture obtained from Wisconsin River (USA) sediments. This strain was characterized for anaerobic oxidation of both aqueous and chelated Fe(II) coupled to nitrate reduction at circumneutral pH. Dechloromonas sp. UWNR4 was incubated in anoxic batch reactors in a defined medium containing 4.5–5 mM NO₃ ^?, 6 mM Fe²⁺ and 1–1.8 mM acetate. Strain UWNR4 efficiently oxidized Fe²⁺ with 90 % oxidation of Fe²⁺ after 3 days of incubation. However, oxidation of Fe²⁺ resulted in Fe(III)-hydroxide-encrusted cells and loss of metabolic activity, suggested by inability of the cells to utilize further additions of acetate. In similar experiments with chelated iron (Fe(II)-EDTA), encrusted cells were not produced and further additions of acetate and Fe(II)-EDTA could be oxidized. Although members of the genus Dechloromonas are primarily known as perchlorate and nitrate reducers, our findings suggest that some species could be members of microbial communities influencing iron redox cycling in anoxic, freshwater sediments. Our work using Fe(II)-EDTA also demonstrates that Fe(II) oxidation was microbially catalyzed rather than a result of abiotic oxidation by biogenic NO₂ ^?.     

Ordinary stoichiometry of extraordinary microorganisms

All life on Earth seems to be made of the same chemical elements in relatively conserved proportions (stoichiometry). Whether this stoichiometry is conserved in settings that differ radically in physicochemical conditions (extreme environments) from those commonly encountered elsewhere on the planet provides insight into possible stoichiometries for putative life beyond Earth. Here, we report measurements of elemental stoichiometry for extremophile microbes from hot springs of Yellowstone National Park (YNP). Phototrophic and chemotrophic microbes were collected in locations spanning large ranges of temperature (24 °C to boiling), pH (1.6–9.6), redox (0.1–7.2 mg L^?1 dissolved oxygen), and nutrient concentrations (0.01–0.25 mg L^?1 , 0.7–12.9 mg L^?1 , 0.01–42 mg L^?1 NH₄⁺, 0.003–1.1 mg L^?1 P mostly as phosphate). Despite these extreme conditions, the microbial cells sampled had a major and trace element stoichiometry within the ranges commonly encountered for microbes living in the more moderate environments of lakes and surface oceans. The cells did have somewhat high C:P and N:P ratios that are consistent with phosphorus (P) limitation. Furthermore, chemotrophs and phototrophs had similar compositions with the exception of Mo content, which was enriched in cells derived from chemotrophic sites. Thus, despite the extraordinary physicochemical and biological diversity of YNP environments, life in these settings, in a stoichiometric sense, remains much the same as we know it elsewhere.     

A sluggish mid‐Proterozoic biosphere and its effect on Earth's redox balance

The possibility of low but nontrivial atmospheric oxygen (O₂) levels during the mid‐Proterozoic (between 1.8 and 0.8 billion years ago, Ga) has important ramifications for understanding Earth's O₂ cycle, the evolution of complex life and evolving climate stability. However, the regulatory mechanisms and redox fluxes required to stabilize these O₂ levels in the face of continued biological oxygen production remain uncertain. Here, we develop a biogeochemical model of the C‐N‐P‐O₂‐S cycles and use it to constrain global redox balance in the mid‐Proterozoic ocean–atmosphere system. By employing a Monte Carlo approach bounded by observations from the geologic record, we infer that the rate of net biospheric O₂ production was Tmol year^?1 (1σ), or ~25% of today's value, owing largely to phosphorus scarcity in the ocean interior. Pyrite burial in marine sediments would have represented a comparable or more significant O₂ source than organic carbon burial, implying a potentially important role for Earth's sulphur cycle in balancing the oxygen cycle and regulating atmospheric O₂ levels. Our statistical approach provides a uniquely comprehensive view of Earth system biogeochemistry and global O₂ cycling during mid‐Proterozoic time and implicates severe P biolimitation as the backdrop for Precambrian geochemical and biological evolution.     

Fe(III) mineral formation and cell encrustation by the nitrate-dependent Fe(II)-oxidizer strain BoFeN1

Understanding the mechanisms of anaerobic microbial iron cycling is necessary for a full appreciation of present‐day biogeochemical cycling of iron and carbon and for drawing conclusions about these cycles on the ancient Earth. Towards that end, we isolated and characterized an anaerobic nitrate‐dependent Fe(II)‐oxidizing bacterium from a freshwater sediment. The 16SrRNA gene sequence of the isolated bacterium (strain BoFeN1) places it within the β‐Proteobacteria, with Acidovorax sp. strain G8B1 as the closest known relative. During mixotrophic growth with acetate plus Fe(II) and nitrate as electron acceptor, strain BoFeN1 forms Fe(III) mineral crusts around the cells. The amount of the organic cosubstrate acetate present seems to control the rate and extent of Fe(II) oxidation and the viability of the cells. The crystallinity of the mineral products is influenced by nucleation by Fe minerals that are already present in the inoculum.     

Composition and Activity of an Autotrophic Fe(II)-Oxidizing,Nitrate-Reducing Enrichment Culture

16S rRNA gene libraries from the lithoautotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458-1460, 1996) were dominated by a phylotype related (95% 16S rRNA gene homology) to the autotrophic Fe(II) oxidizer Sideroxydans lithotrophicus. The libraries also contained phylotypes related to known heterotrophic nitrate reducers Comamonas badia, Parvibaculum lavamentivorans, and Rhodanobacter thiooxidans. The three heterotrophs were isolated and found to be capable of only partial (12 to 24%) Fe(II) oxidation, suggesting that the Sideroxydans species has primary responsibility for Fe(II) oxidation in the enrichment culture.A variety of microorganisms oxidize Fe(II) with nitrate under anaerobic, circumneutral pH conditions (29) and may contribute to an active microbially driven anoxic Fe redox cycle (1, 27-29, 31, 32). Straub et al. (28) obtained the first Fe(II)-oxidizing, nitrate-reducing (enrichment) culture capable of fully autotrophic growth by a reaction such as 5Fe²⁺ + NO₃⁻ + 12H₂O → 5Fe(OH)₃ + 0.5N₂ + 9H⁺. This process has since been demonstrated in detail with the hyperthermophilic archaeon Ferroglobus placidus (9) and with the mesophilic Proteobacteria Chromobacterium violacens strain 2002 (34) and Paracoccus ferrooxidans strain BDN-1 (16). Nitrate-dependent Fe(II) oxidation in the presence of fixed carbon has been documented for Dechlorosoma suillum strain PS (4), Geobacter metallireducens (7), Desulfitobacterium frappieri (23), and Acidovorax strain BoFeN1 (15). In addition to oxidizing insoluble Fe(II)-bearing minerals (33), the enrichment culture described by Straub et al. (28) is the only autotrophic Fe(II)-oxidizing, nitrate-reducing culture capable of near-complete oxidation of uncomplexed Fe(II) with reduction of nitrate to N₂. During Fe(II) oxidation, F. placidus reduces nitrate to nitrite, which may play a significant role in overall Fe(II) oxidation. Although both C. violacens and Paracoccus ferrooxidans reduce nitrate to N₂, C. violacens oxidizes only 20 to 30% of the initial Fe(II), and P. ferrooxidans uses FeEDTA²⁻ but not free (uncomplexed) Fe(II) in medium analogous to that used for cultivation of the enrichment culture described by Straub et al. (28). The enrichment culture described by Straub et al. (28) is thus the most robust culture capable of autotrophic growth coupled to nitrate-dependent Fe(II) oxidation available at present. The composition and activity of this culture was investigated with molecular and cultivation techniques. The culture examined is one provided by K. L. Straub to E. E. Roden in 1998 for use in studies of nitrate-dependent oxidation of solid-phase Fe(II) compounds (33) and has been maintained in our laboratory since that time.     

Efficient aerobic oxidation of hydrocarbons promoted by high-spin nonheme Fe(II) complexes without any reductant

Fe(II)-tris(2-pyridylmethyl)amine complexes, Fe(II)-tpa, having different co-existing anions, [Fe(tpa)(MeCN)₂](ClO₄)₂ (1), [Fe(tpa)(MeCN)₂](CF₃SO₃)₂ (2) and [Fe(tpa)Cl₂] (3), were prepared. Effective magnetic moments (evaluated by the Evans method) revealed that while 1-3 in acetone and 3 in acetonitrile (MeCN) have a high-spin Fe(II) ion at 298 K, the Fe(II) ions of 1 and 2 are in the low-spin state in MeCN. The aerobic oxidation of 1-3 was monitored by UV-Vis spectral changes in acetone or MeCN under air at 298 K. Only the high-spin Fe(II)-tpa complexes were oxidized with rate constants of k_obs = 0.1-1.3 h⁻¹, while 1 and 2 were stable in MeCN. The aerobic oxidation of 1 or 2 in acetone was greatly accelerated in the presence of pure, peroxide-free cyclohexene (1000 equiv.) and yielded a large amount of oxidized products; 2-cyclohexe-1-ol (A) and 2-cyclohexene-1-one (K) (A + K: 23 940% yield based on Fe; A/K = 0.3), and cyclohexene oxide (810%). Besides cyclohexene, aerobic oxidation of norbornene, cyclooctene, ethylbenzene, and cumene proceeded in the presence of 1 in acetone at 348 K without any reductant. Essential factors in the reaction are high-spin Fe(II) ion and labile coordination sites, both of which are required to generate Fe(II)-superoxo species as active species for the H-atom abstraction of hydrocarbons.     

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

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.     

Pigment production and isotopic fractionations in continuous culture: okenone producing purple sulfur bacteria Part II

Okenone is a carotenoid pigment unique to certain members of Chromatiaceae, the dominant family of purple sulfur bacteria (PSB) found in euxinic photic zones. Diagenetic alteration of okenone produces okenane, the only recognized molecular fossil unique to PSB. The in vivo concentrations of okenone and bacteriochlorophyll a (Bchl a) on a per cell basis were monitored and quantified as a function of light intensity in continuous cultures of the purple sulfur bacterium Marichromatium purpuratum (Mpurp1591). We show that okenone‐producing PSB have constant bacteriochlorophyll to carotenoid ratios in light‐harvesting antenna complexes. The in vivo concentrations of Bchl a, 0.151 ± 0.012 fmol cell^?1, and okenone, 0.103 ± 0.012 fmol cell^?1, were not dependent on average light intensity (10–225 Lux) at both steady and non‐steady states. This observation revealed that in autotrophic continuous cultures of Mpurp1591, there was a constant ratio for okenone to Bchl a of 1:1.5. Okenone was therefore constitutively produced in planktonic cultures of PSB, regardless of light intensity. This confirms the legitimacy of okenone as a signature for autotrophic planktonic PSB and by extrapolation water column euxinia. We measured the δ¹³C, δ¹⁵N, and δ³⁴S bulk biomass values from cells collected daily and determined the isotopic fractionations of Mpurp1591. There was no statistical relationship in the bulk isotope measurements or stable isotope fractionations to light intensity or cell density under steady and non‐steady‐state conditions. The carbon isotope fractionation between okenone and Bchl a with respect to overall bulk biomass (¹³ε_{pigment – biomass}) was 2.2 ± 0.4‰ and ?4.1 ± 0.9‰, respectively. The carbon isotopic fractionation () for the production of pigments in PSB is more variable than previously thought with our reported values for okenone at ?15.5 ± 1.2‰ and ?21.8 ± 1.7‰ for Bchl a.     

Oxygen Dependency of Neutrophilic Fe(II) Oxidation by Leptothrix Differs from Abiotic Reaction

Neutrophilic Fe(II) oxidizing microorganisms are found in many natural environments. It has been hypothesized that, at low oxygen concentrations, microbial iron oxidation is favored over abiotic oxidation. Here, we compare the kinetics of abiotic Fe(II) oxidation to oxidation in the presence of the bacterium Leptothrix cholodnii Appels isolated from a wetland sediment. Rates of Fe(II) oxidation were determined in batch experiments at 20°C, pH 7 and oxygen concentrations between 3 and 120 μmol/l. The reaction progress in experiments with and without cells exhibited two distinct phases. During the initial phase, the oxygen dependency of microbial Fe(II) oxidation followed a Michaelis-Menten rate expression (K_M = 24.5 ± 10 μmol O₂/l, v_max = 1.8 ± 0.2 μmol Fe(II)/(l min) for 10⁸ cells/ml). In contrast, abiotic rates increased linearly with increasing oxygen concentrations. At similar oxygen concentrations, initial Fe(II) oxidation rates were faster in the experiments with bacteria. During the second phase, the accumulated iron oxides catalyzed further oxidative iron precipitation in both abiotic and microbial reaction systems. That is, abiotic oxidation also dominated the reaction progress in the presence of bacteria. In fact, in some experiments with bacteria, iron oxidation during the second phase proceeded slower than in the absence of bacteria, possibly due to an inhibitory effect of extracellular polymeric substances on the growth of Fe(III) oxides. Thus, our results suggest that the competitive advantage of microbial iron oxidation in low oxygen environments may be limited by the autocatalytic nature of abiotic Fe(III) oxide precipitation, unless the accumulation of Fe(III) oxides is prevented, for example, through a close coupling of Fe(II) oxidation and Fe(III) reduction.