Bioenergetics of aerobic and anaerobic growth of Shewanella putrefaciens CN32.

Shewanella putrefaciens is a model dissimilatory iron-reducing bacterium that can use Fe(III) and O2 as terminal electron acceptors. Consequently, it has the ability to influence both aerobic and anaerobic groundwater systems, making it an ideal microorganism for improving our understanding of facultative anaerobes with iron-based metabolism. In this work, we examine the bioenergetics of O2 and Fe(III) reduction coupled to lactate oxidation in Shewanella putrefaciens CN32. Bioenergetics were measured directly via isothermal calorimetry and by changes to the chemically defined growth medium. We performed these measurements from 25 to 36°C. Modeling metabolism with macrochemical equations allowed us to define a theoretical growth stoichiometry for the catabolic reaction of 1.00 O2:lactate and 1.33 Fe(III):lactate that was consistent with the observed ratios of O2:lactate (1.20 ± 0.23) and Fe(III):lactate (1.46 ± 0.15) consumption. Aerobic growth showed minimal variation with temperature and minimal variation in thermodynamic potentials of incubation. Fe(III)-based growth showed a strong temperature dependence. The Gibbs energy and enthalpy of incubation was minimized at ≥30°C. Energy partitioning modeling of Fe(III)-based calorimetric incubation data predicted that energy consumption for non-growth associate maintenance increases substantially above 30°C. This prediction agrees with the data at 33 and 35°C. These results suggest that the effects of temperature on Shewanella putrefaciens CN32 are metabolism dependent. Gibbs energy of incubation above 30°C was 3-5 times more exergonic with Fe(III)-based growth than with aerobic growth. We compared data gathered in this study with predictions of microbial growth based on standard-state conditions and based on the thermodynamic efficiency of microbial growth. Quantifying the growth requirements of Shewanella putrefaciens CN32 has advanced our understanding of the thermodynamic constraints of this dissimilatory iron-reducing bacterium.

Mineralogy, morphology, and reaction kinetics of ureolytic bio-cementation in the presence of seawater ions and varying soil materials.

Microbially-induced calcium carbonate precipitation (MICP) is a bio-cementation process that can improve the engineering properties of granular soils through the precipitation of calcium carbonate (CaCO3) minerals on soil particle surfaces and contacts. The technology has advanced rapidly as an environmentally conscious soil improvement method, however, our understanding of the effect of changes in field-representative environmental conditions on the physical and chemical properties of resulting precipitates has remained limited. An improved understanding of the effect of subsurface geochemical and soil conditions on process reaction kinetics and the morphology and mineralogy of bio-cementation may be critical towards enabling successful field-scale deployment of the technology and improving our understanding of the long-term chemical permanence of bio-cemented soils in different environments. In this study, thirty-five batch experiments were performed to specifically investigate the influence of seawater ions and varying soil materials on the mineralogy, morphology, and reaction kinetics of ureolytic bio-cementation. During experiments, differences in reaction kinetics were quantified to identify conditions inhibiting CaCO3 precipitation and ureolysis. Following experiments, scanning electron microscopy, x-ray diffraction, and chemical composition analyses were employed to quantify differences in mineralogical compositions and material morphology. Ions present in seawater and variations in soil materials were shown to significantly influence ureolytic activity and precipitate mineralogy and morphology, however, calcite remained the predominant CaCO3 polymorph in all experiments with relative percentages exceeding 80% by mass in all precipitates.

Microbial maintenance energy quantified and modeled with microcalorimetry.

Refining the energetic costs of cellular maintenance is essential for predicting microbial growth and survival in the environment. Here, we evaluate a simple batch culture method to quantify energy partitioning between growth and maintenance using microcalorimetry and thermodynamic modeling. The constants derived from the batch culture system were comparable to those that have been reported from meta-analyses of data derived from chemostat studies. The model accurately predicted temperature-dependent biomass yield and the upper temperature limit of growth for Desulfovibrio alaskensis G20, suggesting the method may have broad application. An Arrhenius temperature dependence for the specific energy consumption rate, inferred from substrate consumption and heat evolution, was observed over the entire viable temperature range. By combining this relationship for specific energy consumption rates and observed specific growth rates, the model describes an increase in nongrowth associated maintenance at higher temperatures and the corresponding decrease in energy available for growth. This analytical and thermodynamic formulation suggests that simply monitoring heat evolution in batch culture could be a useful complement to the recognized limitations of estimating maintenance using extrapolation to zero growth in chemostats.

Energetics of Acidianus ambivalens growth in response to oxygen availability.

All life requires energy to drive metabolic reactions such as growth and cell maintenance; therefore, fluctuations in energy availability can alter microbial activity. There is a gap in our knowledge concerning how energy availability affects the growth of extreme chemolithoautotrophs. Toward this end, we investigated the growth of thermoacidophile Acidianus ambivalens during sulfur oxidation under aerobic to microaerophilic conditions. Calorimetry was used to measure enthalpy (ΔHinc ) of microbial activity, and chemical changes in growth media were measured to calculate Gibbs energy change (ΔGinc ) during incubation. In all experiments, Gibbs energy was primarily dissipated through the release of heat, which suggests enthalpy-driven growth. In microaerophilic conditions, growth was significantly more efficient in terms of biomass yield (defined as C-mol biomass per mole sulfur consumed) and resulted in lower ΔGinc and ΔHinc . ΔGinc in oxygen-limited (OL) and oxygen- and CO2 -limited (OCL) microaerophilic growth conditions resulted in averages of -1.44 × 103  kJ/C-mol and -7.56 × 102  kJ/C-mol, respectively, and average ΔHinc values of -1.11 × 105  kJ/C-mol and -4.43 × 104  kJ/C-mol, respectively. High-oxygen experiments resulted in lower biomass yield values, an increase in ΔGinc to -1.71 × 104  kJ/C-mol, and more exothermic ΔHinc values of -4.71 × 105  kJ/C-mol. The observed inefficiency in high-oxygen conditions may suggest larger maintenance energy demands due to oxidative stresses and a preference for growth in microaerophilic environments.

Magnesium isotope fractionation during microbially enhanced forsterite dissolution.

Bacillus subtilis endospore-mediated forsterite dissolution experiments were performed to assess the effects of cell surface reactivity on Mg isotope fractionation during chemical weathering. Endospores present a unique opportunity to study the isolated impact of cell surface reactivity because they exhibit extremely low metabolic activity. In abiotic control assays, 24 Mg was preferentially released into solution during forsterite dissolution, producing an isotopically light liquid phase (δ26 Mg = -0.39 ± 0.06 to -0.26 ± 0.09‰) relative to the initial mineral composition (δ26 Mg = -0.24 ± 0.03‰). The presence of endospores did not have an apparent effect on Mg isotope fractionation associated with the release of Mg from the solid into the aqueous phase. However, the endospore surfaces preferentially adsorbed 24 Mg from the dissolution products, which resulted in relatively heavy aqueous Mg isotope compositions. These aqueous Mg isotope compositions increased proportional to the fraction of dissolved Mg that was adsorbed, with the highest measured δ26 Mg (-0.08 ± 0.07‰) corresponding to the highest degree of adsorption (~76%). The Mg isotope composition of the adsorbed fraction was correspondingly light, at an average δ26 Mg of -0.49‰. Secondary mineral precipitation and Mg adsorption onto secondary minerals had a minimal effect on Mg isotopes at these experimental conditions. Results demonstrate the isolated effects of cell surface reactivity on Mg isotope fractionation separate from other common biological processes, such as metabolism and organic acid production. With further study, Mg isotopes could be used to elucidate the role of the biosphere on Mg cycling in the environment.

Mechanisms of the Removal of U(VI) from Aqueous Solution Using Biochar: A Combined Spectroscopic and Modeling Approach.

Biochar has been touted as a promising sorbent for the removal of inorganic contaminants, such as uranium (U), from water. However, the molecular-scale mechanisms of aqueous U(VI) species adsorption to biochar remain poorly understood. In this study, two approaches, grounded in equilibrium thermodynamics, were employed to investigate the U(VI) adsorption mechanisms: (1) batch U(VI) adsorption experiments coupled to surface complexation modeling (SCM) and (2) isothermal titration calorimetry (ITC), supported by synchrotron-based X-ray absorption spectroscopy (XAS) analyses. The biochars tested have considerable proton buffering capacity and most strongly adsorb U(VI) between approximately pH 4 and 6. FT-IR and XPS studies, along with XAS analyses, show that U(VI) adsorption occurs primarily at the proton-active carboxyl (-COOH) and phenolic hydroxyl (-OH) functional groups on the biochar surface. The SCM approach is able to predict U(VI) adsorption behavior across a wide range of pH and at varying initial U(VI) and biochar concentrations, and U adsorption is strongly influenced by aqueous U(VI) speciation. Supporting ITC measurements indicate that the calculated enthalpies of protonation reactions of the studied biochar, as well as the adsorption of U(VI), are consistent with anionic oxygen ligands and are indicative of both inner- and outer-sphere complexation. Our results provide new insights into the modes of U(VI) adsorption by biochar and more generally improve our understanding of its potential to remove radionuclides from contaminated waters.

Thermodynamic Analysis of Nickel(II) and Zinc(II) Adsorption to Biochar.

While numerous studies have investigated metal uptake from solution by biochar, few of these have developed a mechanistic understanding of the adsorption reactions that occur at the biochar surface. In this study, we explore a combined modeling and spectroscopic approach for the first time to describe the molecular level adsorption of Ni(II) and Zn(II) to five types of biochar. Following thorough characterization, potentiometric titrations were carried out to measure the proton (H+) reactivity of each biochar, and the data was used to develop protonation models. Surface complexation modeling (SCM) supported by synchrotron-based extended X-ray absorption fine structure (EXAFS) was then used to gain insights into the molecular scale metal-biochar surface reactions. The SCM approach was combined with isothermal titration calorimetry (ITC) data to determine the thermodynamic driving forces of metal adsorption. Our results show that the reactivity of biochar toward Ni(II) and Zn(II) directly relates to the site densities of biochar. EXAFS along with FT-IR analyses, suggest that Ni(II) and Zn(II) adsorption occurred primarily through proton-active carboxyl (-COOH) and hydroxyl (-OH) functional groups on the biochar surface. SCM-ITC analyses revealed that the enthalpies of protonation are exothermic and Ni(II) and Zn(II) complexes with biochar surface are slightly exothermic to slightly endothermic. The results obtained from these combined approaches contribute to the better understanding of molecular scale metal adsorption onto the biochar surface, and will facilitate the further development of thermodynamics-based, predictive approaches to biochar removal of metals from contaminated water.

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris.

Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance in D. vulgaris The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection.IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution.

Mechanism for microbial population collapse in a fluctuating resource environment.

Managing trade-offs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. To investigate this hypothesis, we imposed a fluctuating environment that required the sulfate-reducer Desulfovibrio vulgaris to undergo repeated ecologically relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen-consuming Methanococcus maripaludis Strikingly, the microbial community became progressively less proficient at restoring the environmentally relevant physiological state after each perturbation and most cultures collapsed within 3-7 shifts. Counterintuitively, the collapse phenomenon was prevented by a single regulatory mutation. We have characterized the mechanism for collapse by conducting RNA-seq analysis, proteomics, microcalorimetry, and single-cell transcriptome analysis. We demonstrate that the collapse was caused by conditional gene regulation, which drove precipitous decline in intracellular abundance of essential transcripts and proteins, imposing greater energetic burden of regulation to restore function in a fluctuating environment.

Submicron hard X-ray fluorescence imaging of synthetic elements.

Synchrotron-based X-ray fluorescence microscopy (XFM) using hard X-rays focused into sub-micron spots is a powerful technique for elemental quantification and mapping, as well as microspectroscopic measurements such as µ-XANES (X-ray absorption near edge structure). We have used XFM to image and simultaneously quantify the transuranic element plutonium at the L(3) or L(2)-edge as well as Th and lighter biologically essential elements in individual rat pheochromocytoma (PC12) cells after exposure to the long-lived plutonium isotope (242)Pu. Elemental maps demonstrate that plutonium localizes principally in the cytoplasm of the cells and avoids the cell nucleus, which is marked by the highest concentrations of phosphorus and zinc, under the conditions of our experiments. The minimum detection limit under typical acquisition conditions with an incident X-ray energy of 18 keV for an average 202 µm(2) cell is 1.4 fg Pu or 2.9×10(-20) moles Pu µm(-2), which is similar to the detection limit of K-edge XFM of transition metals at 10 keV. Copper electron microscopy grids were used to avoid interference from gold X-ray emissions, but traces of strontium present in naturally occurring calcium can still interfere with plutonium detection using its L(α) X-ray emission.

Optimizing Bacillus subtilis spore isolation and quantifying spore harvest purity.

Investigating the biochemistry, resilience and environmental interactions of bacterial endospores often requires a pure endospore biomass free of vegetative cells. Numerous endospore isolation methods, however, neglect to quantify the purity of the final endospore biomass. To ensure low vegetative cell contamination we developed a quality control technique that enables rapid quantification of endospore harvest purity. This method quantifies spore purity using bright-field and fluorescence microscopy imaging in conjunction with automated cell counting software. We applied this method to Bacillus subtilis endospore harvests isolated using a two-phase separation method that utilizes mild chemicals. The average spore purity of twenty-two harvests was 88±11% (error is 1σ) with a median value of 93%. A spearman coefficient of 0.97 correlating automated and manual bacterial counts confirms the accuracy of software generated data.

Direct determination of the intracellular oxidation state of plutonium.

Microprobe X-ray absorption near edge structure (µ-XANES) measurements were used to determine directly, for the first time, the oxidation state of intracellular plutonium in individual 0.1-µm(2) areas within single rat pheochromocytoma cells (PC12). The living cells were incubated in vitro for 3 h in the presence of Pu added to the media in different oxidation states (Pu(III), Pu(IV), and Pu(VI)) and in different chemical forms. Regardless of the initial oxidation state or chemical form of Pu presented to the cells, the XANES spectra of the intracellular Pu deposits were always consistent with tetravalent Pu even though the intracellular milieu is generally reducing.

Plutonium uptake and distribution in mammalian cells: molecular vs. polymeric plutonium.

PURPOSE: To study the cellular responses to molecular and polymeric forms of plutonium using PC12 cells derived from a rat pheochromocytoma. MATERIALS AND METHODS: Serum starved PC12 cells were exposed to polymeric and molecular forms of plutonium for 3 h. Cells were washed with 10 mM ethylene glycol tetraacetic acid (EGTA), 100 mM NaCl at pH 7.4 to remove surface sorbed plutonium. Localization of plutonium in individual cell was quantitatively analyzed by synchrotron X-ray fluorescence (XRF) microscopy. RESULTS: Molecular plutonium complexes introduced to cell growth media in the form of nitrilotriacetic acid (NTA), citrate, or transferrin complexes were taken up by PC12 cells, and mostly colocalized with iron within the cells. Aged polymeric plutonium prepared separately was not internalized by PC12 cells but it was always found on the cell surface as big agglomerates; however, polymeric plutonium formed in situ was mostly found within the cells as agglomerates. CONCLUSIONS: PC12 cells can differentiate molecular and polymeric forms of plutonium. Molecular plutonium is taken up by PC12 cells and mostly co-localizes with iron but aged polymeric plutonium is not internalized by the cells.

An iron-dependent and transferrin-mediated cellular uptake pathway for plutonium.

Plutonium is a toxic synthetic element with no natural biological function, but it is strongly retained by humans when ingested. Using small-angle X-ray scattering, receptor binding assays and synchrotron X-ray fluorescence microscopy, we find that rat adrenal gland (PC12) cells can acquire plutonium in vitro through the major iron acquisition pathway--receptor-mediated endocytosis of the iron transport protein serum transferrin; however, only one form of the plutonium-transferrin complex is active. Low-resolution solution models of plutonium-loaded transferrins derived from small-angle scattering show that only transferrin with plutonium bound in the protein's C-terminal lobe (C-lobe) and iron bound in the N-terminal lobe (N-lobe) (Pu(C)Fe(N)Tf) adopts the proper conformation for recognition by the transferrin receptor protein. Although the metal-binding site in each lobe contains the same donors in the same configuration and both lobes are similar, the differences between transferrin's two lobes act to restrict, but not eliminate, cellular Pu uptake.

Thermodynamic properties of autunite, uranyl hydrogen phosphate, and uranyl orthophosphate from solubility and calorimetric measurements.

In this study, we use solubility and drop-solution calorimetry measurements to determine the thermodynamic properties of the uranyl phosphate phases autunite, uranyl hydrogen phosphate, and uranyl orthophosphate. Conducting the solubility measurements from both supersaturated and undersaturated conditions and under different pH conditions rigorously demonstrates attainment of equilibrium and yields well-constrained solubility product values. We use the solubility data and the calorimetry data, respectively, to calculate standard-state Gibbs free energies of formation and standard-state enthalpies of formation for these uranyl phosphate phases. Combining these results allows us also to calculate the standard-state entropy of formation for each mineral phase. The results from this study are part of a combined effort to develop reliable and internally consistent thermodynamic data for environmentally relevant uranyl minerals. Data such as these are required to optimize and quantitatively assess the effect of phosphate amendment remediation technologies for uranium contaminated systems.

Calorimetric measurements of proton adsorption onto Pseudomonas putida.

Having an understanding of the reactive nature of the bacterial surface is enhanced when its reactivity is considered in a thermodynamic framework. Towards this end, isothermal titration calorimetry was used to measure heats of proton adsorption onto Pseudomonas putida, a common gram negative soil bacterium. Proton adsorption generated large exothermic heats and proton uptake continued down to pH 2.5. Applying a surface complexation model to the calorimetric data allowed for the derivation of site-specific enthalpies and entropies of proton adsorption. The 4-site non-electrostatic model of Borrok et al. [D.M. Borrok, J.B. Fein, J. Colloid Interface Sci. 286 (2005) 110] was chosen to describe proton adsorption and enabled derivation of site-specific enthalpies of -2.4+/-0.3, -3.7+/-0.2, -9.0+/-0.6, and -36.0+/-1.2 kJ/mol for Sites 1-4, respectively. Entropies of proton adsorption were calculated to be 51+/-3, 75+/-1, 91+/-2, and 55+/-4 J/mol K, for Sites 1-4, respectively. Enthalpies and entropies of Sites 1 and 3 are consistent with that of multifunctional organophosphonic acids, Site 2 is consistent with multifunctional carboxylic acids, and Site 4 is consistent with an amine. Temperature dependence of the acidity constants for Sites 1-3 is predicted to be minimal; however, Site 4 is predicted to more substantially affected by temperature.

Adsorption of aqueous uranyl complexes onto Bacillus subtilis cells.

In oxygenated, CO2-rich systems, negatively charged uranyl complexes dominate the aqueous uranium speciation, and it is commonly assumed that these complexes exhibit negligible adsorption onto negatively charged surfaces such as bacteria. We measured the adsorption of 4.2 x 10(-6) M aqueous uranium onto Bacillus subtilis from pH 1.5 to 9 and with wet weight bacterial concentrations from 0.125 to 0.5 g/L. Experiments were performed in the presence and absence of dissolved CO2, and additional experiments were performed in the presence of dissolved CO2 and Ca. We observed extensive uranium adsorption onto the bacterial surface under all conditions. Thermodynamic modeling of the data suggests that uranylhydroxide, uranyl-carbonate, and calcium-uranylcarbonate species each can form stable surface complexes on the bacterial cell wall. These results could dramatically alter predictions of uranium mobility in near-surface environments.

Experimental study of the adsorption of an ionic liquid onto bacterial and mineral surfaces.

Ionic liquids are being developed as a replacement for volatile organic solvents in a range of industrial applications. These liquids have a vanishingly small vapor pressure, making them an attractive alternative to the volatile organic solvents. However, a thorough assessment of the environmental impact of the use of ionic liquids requires a more complete understanding of their fate and transport in environmental systems. Toward this end, we measured the adsorption of the ionic liquid 1-butyl, 3-methylimidazolium chloride (Bmim CI) onto a range of surfaces meant to represent those commonly found in the near-surface environment. We measured adsorption onto the Gram-positive soil bacterial species Bacillus subtilis, onto gibbsite, onto quartz, and onto Na-montmorillonite. We conducted experiments as a function of pH, solid:solute ratio, time, and ionic strength. The experimental results reveal that Bmim CI is unstable in water below pH 6 and above pH 10 and that it exhibits pH independent and ionic strength dependent adsorption onto Na-montmorillonite with 0.4, 0.8, 1.0, 1.2, and 2.0 g/L of clay. We observed no adsorption of the Bmim CI onto B. subtilis (3.95 or 7.91 g (dry weight) bacteria/L) at pH 5.5-8.5 or onto gibbsite (500 or 1285 g/L) or quartz (1000 and 2000 g/L) over the pH range 6-10. Calculated distribution coefficient (KD) values for Bmim CI onto the Na-montmorillonite change as a function of ionic strength; the 10(-4) M ionic strength KD value is 1735 +/- 269 L/Kg, and the 10(-1) M ionic strength KD is 1133 +/- 291 L/Kg. Our results suggest that the geologic retardation of this class of ionic liquid, if present as a dissolved contaminant in the subsurface, would be significant when a significant fraction of interlayer clays are present. However, adsorption onto other common geologic and biological surfaces is likely to be minimal, and the ionic liquids may travel unimpeded in groundwater systems in which these types of surfaces dominate.