David A. Fowle

X-ray absorption fine-structure determination of pH-dependent U-bacterial cell wall interactions.

X-ray absorption fine structure (XAFS) measurements was used at the U L3-edge to directly determine the pH dependence of the cell wall functional groups responsible for the absorption of aqueous UO22+ to Bacillus subtilis from pH 1.67 to 4.80. Surface complexation modeling can be used to predict metal distributions in water–rock systems, and it has been used to quantify bacterial adsorption of metal cations. However, successful application of these models requires a detailed knowledge not only of the type of bacterial surface site involved in metal adsorption/desorption, but also of the binding geometry. Previous acid-base titrations of B. subtilis cells suggested that three surface functional group types are important on the cell wall; these groups have been postulated to correspond to carboxyl, phosphoryl, and hydroxyl sites. When the U(VI) adsorption to B. subtilis is measured, observed is a significant pH-independent absorption at low pH values (<3.0), ascribed to an interaction between the uranyl cation and a neutrally charged phosphoryl group on the cell wall. The present study provides independent quantitative constraints on the types of sites involved in uranyl binding to B. subtilis from pH 1.67 to 4.80. The XAFS results indicate that at extremely low pH (pH 1.67) UO22+ binds exclusively to phosphoryl functional groups on the cell wall, with an average distance between the U atom and the P atom of 3.64 ± 0.01 A. This U-P distance indicates an inner-sphere complex with an oxygen atom shared between the UO22+ and the phosphoryl ligand. The P signal at extremely low pH value is consistent with the UO22+ binding to a protonated phosphoryl group, as previously ascribed. With increasing pH (3.22 and 4.80), UO22+ binds increasingly to bacterial surface carboxyl functional groups, with an average distance between the U atom and the C atom of 2.89 ± 0.02 A. This U-C distance indicates an inner-sphere complex with two oxygen atoms shared between the UO22+ and the carboxyl ligand. The results of this XAFS study confirm the uranyl-bacterial surface speciation model.

Adsorption of cadmium to Bacillus subtilis bacterial cell walls: A pH-dependent X-ray absorption fine structure spectroscopy study

The local atomic environment of Cd bound to the cell wall of the gram-positive bacterium Bacillus subtilis was determined by X-ray absorption fine structure (XAFS) spectroscopy. Samples were prepared at six pH values in the range 3.4 to 7.8, and the bacterial functional groups responsible for the adsorption were identified under each condition. Under the experimental Cd and bacterial concentrations, the spectroscopy results indicate that Cd binds predominantly to phosphoryl ligands below pH 4.4, whereas at higher pH, adsorption to carboxyl groups becomes increasingly important. At pH 7.8, we observe the activation of an additional binding site, which we tentatively ascribe to a phosphoryl site with smaller Cd-P distance than the one that is active at lower pH conditions. XAFS spectra of several cadmium acetate, phosphate, and perchlorate solutions were measured and used as standards for fingerprinting, as well as to assess the ability of FEFF8 and FEFFIT to model carboxyl, phosphoryl, and hydration environments, respectively. The results of this XAFS study in general corroborate existing surface complexation models; however, some binding mechanism details could only be detected with the XAFS technique.

Photoferrotrophs thrive in an Archean Ocean analogue

Considerable discussion surrounds the potential role of anoxygenic phototrophic Fe(II)-oxidizing bacteria in both the genesis of Banded Iron Formations (BIFs) and early marine productivity. However, anoxygenic phototrophs have yet to be identified in modern environments with comparable chemistry and physical structure to the ancient Fe(II)-rich (ferruginous) oceans from which BIFs deposited. Lake Matano, Indonesia, the eighth deepest lake in the world, is such an environment. Here, sulfate is scarce (<20 μmol·liter−1), and it is completely removed by sulfate reduction within the deep, Fe(II)-rich chemocline. The sulfide produced is efficiently scavenged by the formation and precipitation of FeS, thereby maintaining very low sulfide concentrations within the chemocline and the deep ferruginous bottom waters. Low productivity in the surface water allows sunlight to penetrate to the >100-m-deep chemocline. Within this sulfide-poor, Fe(II)-rich, illuminated chemocline, we find a populous assemblage of anoxygenic phototrophic green sulfur bacteria (GSB). These GSB represent a large component of the Lake Matano phototrophic community, and bacteriochlorophyll e, a pigment produced by low-light-adapted GSB, is nearly as abundant as chlorophyll a in the lakes euphotic surface waters. The dearth of sulfide in the chemocline requires that the GSB are sustained by phototrophic oxidation of Fe(II), which is in abundant supply. By analogy, we propose that similar microbial communities, including populations of sulfate reducers and photoferrotrophic GSB, likely populated the chemoclines of ancient ferruginous oceans, driving the genesis of BIFs and fueling early marine productivity.

The effect of growth phase on proton and metal adsorption by Bacillus subtilis

Several recent studies have applied surface complexation models to quantify metal adsorption by bacterial surfaces. Although these models can account for the effects of many abiotic variables (such as pH and ionic strength), to date, the effects of biotic variables (such as growth phase) have not been investigated. In this study, we quantify the effect of growth phase on surface site concentrations, deprotonation constants, and metal-binding constants by performing acid-base titrations and Cd and Fe(III) batch adsorption experi- ments using suspensions containing Bacillus subtilis cultured to exponential, stationary, and sporulated phase. For each type of surface site, concentrations and pKa values describing deprotonation decrease as the cells move from exponential to stationary phase, but remain constant from stationary to sporulated phase. Due to the variations in site concentrations and deprotonation constants, Cd and Fe(III) binding constants are largest for stationary-phase cells and smallest for sporulated cells, even though cells in stationary phase adsorb roughly 5% to 10% less metal (per unit weight) than exponential-phase cells, and roughly 10% to 20% more metal than sporulated cells. These variations in surface complexation model parameters indicate that any attempt to predict proton or metal adsorption by bacteria must consider the growth phase of the population. Copyright

Experimental measurements of the reversibility of metal–bacteria adsorption reactions

Abstract This study tests the reversibility of metal–bacteria interactions by comparing estimated extents of desorption based on surface complexation modeling, to those we observed in the experimental adsorption/desorption systems. The experiments also determine if extended adsorption contact time affects desorption kinetics. The experiments involved Ca and Cd adsorption/desorption onto the surface of a gram positive bacterium: Bacillus subtilis. Three types of experiments were performed: (1) Ca and Cd desorption from the cell wall of B. subtilis after 1 h of adsorption contact; (2) Cd and Ca desorption from the cell wall of B. subtilis after >15 h of adsorption contact; and (3) Ca and Cd desorption as a function of pH after 1 h of adsorption contact. Both the adsorption and desorption reactions are rapid, and the desorption kinetics are independent of adsorption contact time. Steady-state conditions are attained within 2 h for all adsorption reactions studied, and within 1 h for all desorption reactions studied. Furthermore, the extent of adsorption or desorption remains constant for at least 24 h (and up to 80 h for Cd). The observed extent of desorption in the experimental systems is in excellent agreement with the amount estimated from a surface complexation model based on independently conducted adsorption experiments. Therefore, this study indicates that the adsorption of Cd and Ca on B. subtilis is a rapid, fully reversible, and hence an equilibrium process. Therefore the use of surface complexation modeling of aqueous metal adsorption onto bacterial surfaces yields accurate estimates of the distribution of metals in bacteria-bearing solutions.

Competitive adsorption of metal cations onto two gram positive bacteria: testing the chemical equilibrium model

In order to test the ability of a surface complexation approach to account for metal-bacteria interactions in near surface fluid-rock systems, we have conducted experiments that measure the extent of adsorption in mixed metal, mixed bacteria systems. This study tests the surface complexation approach by comparing estimated extents of adsorption based on surface complexation modeling to those we observed in the experimental systems. The batch adsorption experiments involved Ca, Cd, Cu, and Pb adsorption onto the surfaces of 2 g positive bacteria: Bacillus subtilis and Bacillus licheniformis. Three types of experiments were performed: 1. Single metal (Ca, Cu, Pb) adsorption onto a mixture of B. licheniformis and B. subtilis; 2. mixed metal (Cd, Cu, and Pb; Ca and Cd) adsorption onto either B. subtilis or B. licheniformis; and 3. mixed or single metal adsorption onto B. subtilis and B. licheniformis. %Independent of the experimental results, and based on the site specific stability constants for Ca, Cd, Cu, and Pb interactions with the carboxyl and phosphate sites on B. licheniformis and B. subtilis determined by Fein et al. (1997), by Daughney et al. (1998) and in this study, we estimate the extent of adsorption that is expected in the above experimental systems. Competitive cation adsorption experiments in both single and double bacteria systems exhibit little adsorption at pH values less than 4. With increasing pH above 4.0, the extent of Ca, Cu, Pb and Cd adsorption also increases due to the increased deprotonation of bacterial surface functional groups. In all cases studied, the estimated adsorption behavior is in excellent agreement with the observations, with only slight differences that were within the uncertainties of the estimation and experimental procedures. Therefore, the results indicate that the use of chemical equilibrium modeling of aqueous metal adsorption onto bacterial surfaces yields accurate predictions of the distribution of metals in complex multicomponent systems.

The methane cycle in ferruginous Lake Matano

In Lake Matano, Indonesia, the worlds largest known ferruginous basin, more than 50% of authigenic organic matter is degraded through methanogenesis, despite high abundances of Fe (hydr)oxides in the lake sediments. Biogenic CH₄ accumulates to high concentrations (up to 1.4 mmol L⁻¹) in the anoxic bottom waters, which contain a total of 7.4 × 10⁵ tons of CH₄. Profiles of dissolved inorganic carbon (ΣCO₂) and carbon isotopes (δ¹³C) show that CH₄ is oxidized in the vicinity of the persistent pycnocline and that some of this CH₄ is likely oxidized anaerobically. The dearth of NO₃⁻ and SO₄²⁻ in Lake Matano waters suggests that anaerobic methane oxidation may be coupled to the reduction of Fe (and/or Mn) (hydr)oxides. Thermodynamic considerations reveal that CH₄ oxidation coupled to Fe(III) or Mn(III/IV) reduction would yield sufficient free energy to support microbial growth at the substrate levels present in Lake Matano. Flux calculations imply that Fe and Mn must be recycled several times directly within the water column to balance the upward flux of CH₄. 16S gene cloning identified methanogens in the anoxic water column, and these methanogens belong to groups capable of both acetoclastic and hydrogenotrophic methanogenesis. We find that methane is important in C cycling, even in this very Fe-rich environment. Such Fe-rich environments are rare on Earth today, but they are analogous to conditions in the ferruginous oceans thought to prevail during much of the Archean Eon. By analogy, methanogens and methanotrophs could have formed an important part of the Archean Ocean ecosystem.

Sulfate was a trace constituent of Archean seawater

Dissecting ancient microbial sulfur cycling Before the rise of oxygen, life on Earth depended on the marine sulfur cycle. The fractionation of different sulfur isotopes provides clues to which biogeochemical cycles were active long ago (see the Perspective by Ueno). Zhelezinskaia et al. found negative isotope anomalies in Archean rocks from Brazil and posit that metabolic fluxes from sulfate-reducing microorganisms influenced the global sulfur cycle, including sulfur in the atmosphere. In contrast, Paris et al. found positive isotope anomalies in Archean sediments from South Africa, implying that the marine sulfate pool was more disconnected from atmospheric sulfur. As an analog for the Archean ocean, Crowe et al. measured sulfur isotope signatures in modern Lake Matano, Indonesia, and suggest that low seawater sulfate concentrations restricted early microbial activity. Science, this issue p. 703, p. 742, p. 739; see also p. 735 Low levels of sulfate allowed for the preservation of mass-independent isotope signatures in the Archean. [Also see Perspective by Ueno] In the low-oxygen Archean world (>2400 million years ago), seawater sulfate concentrations were much lower than today, yet open questions frustrate the translation of modern measurements of sulfur isotope fractionations into estimates of Archean seawater sulfate concentrations. In the water column of Lake Matano, Indonesia, a low-sulfate analog for the Archean ocean, we find large (>20 per mil) sulfur isotope fractionations between sulfate and sulfide, but the underlying sediment sulfides preserve a muted range of δ34S values. Using models informed by sulfur cycling in Lake Matano, we infer Archean seawater sulfate concentrations of less than 2.5 micromolar. At these low concentrations, marine sulfate residence times were likely 103 to 104 years, and sulfate scarcity would have shaped early global biogeochemical cycles, possibly restricting biological productivity in Archean oceans.

Methane monooxygenase gene expression mediated by methanobactin in the presence of mineral copper sources

Methane is a major greenhouse gas linked to global warming; however, patterns of in situ methane oxidation by methane-oxidizing bacteria (methanotrophs), natures main biological mechanism for methane suppression, are often inconsistent with laboratory predictions. For example, one would expect a strong relationship between methanotroph ecology and Cu level because methanotrophs require Cu to sustain particulate methane monooxygenase (pMMO), the most efficient enzyme for methane oxidation. However, no correlation has been observed in nature, which is surprising because methane monooxygenase (MMO) gene expression has been unequivocally linked to Cu availability. Here we provide a fundamental explanation for this lack of correlation. We propose that MMO expression in nature is largely controlled by solid-phase Cu geochemistry and the relative ability of Cu acquisition systems in methanotrophs, such as methanobactins (mb), to obtain Cu from mineral sources. To test this hypothesis, RT-PCR expression assays were developed for Methylosinus trichosporium OB3b (which produces mb) to quantify pMMO, soluble MMO (the alternate MMO expressed when Cu is “unavailable”), and 16S-rRNA gene expression under progressively more stringent Cu supply conditions. When Cu was provided as CuCl2, pMMO transcript levels increased significantly consistent with laboratory work. However, when Cu was provided as Cu-doped iron oxide, pMMO transcript levels increased only when mb was also present. Finally, when Cu was provided as Cu-doped borosilicate glass, pMMO transcription patterns varied depending on the ambient mb:Cu supply ratio. Cu geochemistry clearly influences MMO expression in terrestrial systems, and, as such, local Cu mineralogy might provide an explanation for methane oxidation patterns in the natural environment.

Surface chemistry allows for abiotic precipitation of dolomite at low temperature

Significance Abundant in the geologic record, but scarce in modern environments below 50 °C, the mineral dolomite is used to interpret ancient fluid chemistry, paleotemperature, and is a major hydrocarbon reservoir rock. Because laboratory synthesis of abiotic dolomite had been unsuccessful, chemical mechanisms for precipitation are poorly constrained, and limit interpretations of its occurrence. Here we report the abiotic synthesis of dolomite at 25 °C, and demonstrate that carboxylated surfaces on organic matter catalyze precipitation through complexation between carboxyl groups and Mg2+, removing water to make Mg2+ available for dolomite precipitation. This mechanism is consistent with dolomite formation in depositional environments rich in organic matter. Our experimental protocol provides opportunities for calibrating conditions of low-temperature dolomite formation throughout the geologic record. Although the mineral dolomite is abundant in ancient low-temperature sedimentary systems, it is scarce in modern systems below 50 °C. Chemical mechanism(s) enhancing its formation remain an enigma because abiotic dolomite has been challenging to synthesize at low temperature in laboratory settings. Microbial enhancement of dolomite precipitation at low temperature has been reported; however, it is still unclear exactly how microorganisms influence reaction kinetics. Here we document the abiotic synthesis of low-temperature dolomite in laboratory experiments and constrain possible mechanisms for dolomite formation. Ancient and modern seawater solution compositions, with identical pH and pCO2, were used to precipitate an ordered, stoichiometric dolomite phase at 30 °C in as few as 20 d. Mg-rich phases nucleate exclusively on carboxylated polystyrene spheres along with calcite, whereas aragonite forms in solution via homogeneous nucleation. We infer that Mg ions are complexed and dewatered by surface-bound carboxyl groups, thus decreasing the energy required for carbonation. These results indicate that natural surfaces, including organic matter and microbial biomass, possessing a high density of carboxyl groups may be a mechanism by which ordered dolomite nuclei form. Although environments rich in organic matter may be of interest, our data suggest that sharp biogeochemical interfaces that promote microbial death, as well as those with high salinity may, in part, control carboxyl-group density on organic carbon surfaces, consistent with origin of dolomites from microbial biofilms, as well as hypersaline and mixing zone environments.