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.

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 (ΔH_inc ) of microbial activity, and chemical changes in growth media were measured to calculate Gibbs energy change (ΔG_inc ) 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 ΔG_inc and ΔH_inc . ΔG_inc 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 ΔH_inc 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 ΔG_inc to -1.71 × 10⁴  kJ/C-mol, and more exothermic ΔH_inc 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.

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.

Thermodynamic characterization of proton-ionizable functional groups on the cell surfaces of ammonia-oxidizing bacteria and archaea

The ammonia-oxidizing archaeon Nitrosopumilus maritimus strain SCM1 (strain SCM1), a representative of the Thaumarchaeota archaeal phylum, can sustain high specific rates of ammonia oxidation at ammonia concentrations too low to sustain metabolism by ammonia-oxidizing bacteria (AOB). One structural and biochemical difference between N. maritimus and AOB that might be related to the oligotrophic adaptation of strain SCM1 is the cell surface. A proteinaceous surface layer (S-layer) comprises the outermost boundary of the strain SCM1 cell envelope, as opposed to the lipopolysaccharide coat of Gram-negative AOB. In this work, we compared the surface reactivities of two archaea having an S-layer (strain SCM1 and Sulfolobus acidocaldarius) with those of four representative AOB (Nitrosospira briensis, Nitrosomonas europaea, Nitrosolobus multiformis, and Nitrosococcus oceani) using potentiometric and calorimetric titrations to evaluate differences in proton-ionizable surface sites. Strain SCM1 and S. acidocaldarius have a wider range of proton buffering (approximately pH 10-3.5) than the AOB (approximately pH 10-4), under the conditions investigated. Thermodynamic parameters describing proton-ionizable sites (acidity constants, enthalpies, and entropies of protonation) are consistent with these archaea having proton-ionizable amino acid side chains containing carboxyl, imidazole, thiol, hydroxyl, and amine functional groups. Phosphorous-bearing acidic functional groups, which might also be present, could be masked by imidazole and thiol functional groups. Parameters for the AOB are consistent with surface structures containing anionic oxygen ligands (carboxyl- and phosphorous-bearing acidic functional groups), thiols, and amines. In addition, our results showed that strain SCM1 has more reactive surface sites than the AOB and a high concentration of sites consistent with aspartic and/or glutamic acid. Because these alternative boundary layers mediate interaction with the local external environment, these data provide the basis for further comparisons of the thermodynamic behavior of surface reactivity toward essential nutrients.

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.

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.

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.