Jan P. Amend

Group additivity equations of state for calculating the standard molal thermodynamic properties of aqueous organic species at elevated temperatures and pressures

Abstract Group additivity equations of state for aqueous organic molecules have been generated by combining the revised Helgeson-Kirkham-Flowers (HKF) equations of state ( Shock and Helgeson, 1988, 1990 ; Tanger and Helgeson, 1988 ; Shock et al., 1989, 1992 ) with experimental values of the standard molal properties of aqueous alkanes, alkanols, alkylbenzenes, car☐ylic acids, amides, and amines. Equations of state parameters for the groups represented by -CH 2 −, -CH 3 , -CHCH 3 −, -C 6 H 5 , -CH 2 OH, -COOH, -CONH 2 , and -CH 2 NH 2 were determined by regression of the experimental data. This procedure permits calculation of the standard molal thermodynamic properties of these groups at elevated temperatures and pressures. Although curves representing the apparent standard molal Gibbs free energies (Δ G °) and enthalpies (Δ H °) of formation, and the standard molal entropies ( S °) of the groups as a function of temperature and pressure are respectively similar for each of them, the temperature dependence of the standard molal heat capacities ( C p °) and volumes ( V °) of a number of the groups are quite different from one another. For example, the standard molal heat capacities of the hydrocarbon groups minimize with increasing temperature, but those of -CH 2 OH and -CH 2 NH 2 maximize. Computed values of Δ G °, Δ H °, S °, C p °, V °, and the equations of state parameters for the various groups were used together with group additivity relations to generate corresponding values of these properties for aqueous n -alkanes, 2-methylalkanes, n -alkylbenzenes, n -alkanols, n -car☐ylic acids, n -amides, and n -amines at temperatures ≤ 250°C and pressures ≤ 1 kbar. The validity and generality of the equations of state are supported by the fact that predicted equilibrium constants for liquid n -alkane solubility reactions in water compare favorably with experimental values reported in the literature for temperatures as high as 200°C. Furthermore, equilibrium constants for aqueous ethane coexisting with ethene at 325 and 350°C at 350 bars predicted from the equations of state are in close agreement with independently determined experimental values reported by Seewald (1994) . The standard molal thermodynamic properties and equations of state parameters reported below provide the means to characterize the thermodynamic behavior of a wide variety of aqueous organic species involved in hydrothermal reactions at elevated temperatures and pressures.

Calculation of the standard molal thermodynamic properties ofaqueous biomolecules at elevated temperatures and pressures Part1L-α-Amino acids

Experimental thermodynamic data for aqueous biomolecules reported in the literature have been combined with group additivity equations of state to generate parameters which can be used to calculate the apparent standard molal Gibbs energies and enthalpies of formation (ΔG° and ΔH°, respectively) and the standard molal third law entropies (S°), heat capacities (C P ° ), and volumes (V°) of the 20 common neutral and 5 charged L-α-amino acids as a function of temperature and pressure.‡ Values of C P ° and V° for neutral and charged L-α-amino acids minimize, maximize, or exhibit a reverse sigmoid configuration with increasing temperature at P SAT .§ For example, curves depicting C P ° of Val, Leu, and Ile minimize with increasing temperature, but those corresponding to C P ° and V° of most of the other neutral L-α-amino acids show reverse sigmoid configurations.¶ In contrast, curves representing C P ° and V° of the ionized amino acids maximize with increasing temperature. As a consequence, the temperature and pressure dependence of the relative stabilities of the various neutral and charged L-α-amino acids for which C P ° and V° exhibit different configurations also differ substantially from one another. Equilibrium calculations indicate that amino acids such as Lys and Arg, which are present almost entirely as Lys + and Arg + at 25°C and pH 7, are ca. 50% dissociated at ca. 125°C and pH 7, where neutrality occurs at ca. pH 6. Such changes in speciation with increasing temperature may have a profound effect on the relative stabilities of other biomolecules such as peptides and proteins at elevated temperatures and pressures.

Carbohydrates in thermophile metabolism: Calculation of the standard molal thermodynamic properties of aqueous pentoses and hexoses at elevated temperatures and pressures

Experimental thermodynamic data for aqueous organic compounds can be combined with the revised Helgeson-Kirkham-Flowers (HKF) equations of state to generate parameters that can be used to estimate standard molal properties as functions of temperature and pressure. In this study, we regressed thermodynamic data for aqueous carbohydrates at temperatures up to 393 K reported in the literature to permit the calculation of the apparent standard molal Gibbs free energies and enthalpies of formation (G o and H o , respectively) and the standard molal entropies (S2 ), heat capacities (CP,2 o ), and volumes (V 2 o )t o 423 Ka nd several hundred MPa of aqueous C5 aldoses (ribose, arabinose, xylose, lyxose) and C 5 ketoses (ribulose, xylulose) as well as C6 aldoses (glucose, mannose, galactose) and C6 ketoses (fructose, sorbose). Values of G o for these 11 aqueous carbohydrates are given as a function of temperature at the saturated water vapor pressure (PSAT) and at 50 MPa. Values of G o for aqueous glucose are then combined with those of other aqueous organic and inorganic compounds to calculate values of the standard molal Gibbs free energies of 13 fermentation and respiration reactions (Gr ) known or likely to be carried out by thermophilic microorgan- isms. Finally, values of the overall Gibbs free energies of these reactions (Gr) are calculated at the temperature, pressure, and chemical composition that obtain in the hydrothermal fluids of Vulcano Island, southern Italy, a site that is widely known for its tremendous diversity of organisms able to live at high temperatures. At likely activities of aqueous glucose, it is shown that thermophiles in the hot springs of Vulcano at 373 K and 0.1 MPa can gain between 400 and 3000 kJ per mole of glucose fermented or respired. Copyright

The energetics of organic synthesis inside and outside the cell

Thermodynamic modelling of organic synthesis has largely been focused on deep-sea hydrothermal systems. When seawater mixes with hydrothermal fluids, redox gradients are established that serve as potential energy sources for the formation of organic compounds and biomolecules from inorganic starting materials. This energetic drive, which varies substantially depending on the type of host rock, is present and available both for abiotic (outside the cell) and biotic (inside the cell) processes. Here, we review and interpret a library of theoretical studies that target organic synthesis energetics. The biogeochemical scenarios evaluated include those in present-day hydrothermal systems and in putative early Earth environments. It is consistently and repeatedly shown in these studies that the formation of relatively simple organic compounds and biomolecules can be energy-yielding (exergonic) at conditions that occur in hydrothermal systems. Expanding on our ability to calculate biomass synthesis energetics, we also present here a new approach for estimating the energetics of polymerization reactions, specifically those associated with polypeptide formation from the requisite amino acids.

Calculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures II. Unfolded proteins

Equations of state for completely unfolded proteins have been generated from group additivity algorithms and the revised Helgeson-Kirkham-Flowers (HKF) equations of state to compute the standard molal thermodynamic properties of these molecules at elevated temperatures and pressures. The requisite equations of state parameters were computed from those of groups retrieved by regression of experimental calorimetric and densimetric data reported in the literature. This approach permits calculation of the standard molal thermodynamic properties as a function of temperature and pressure for any completely unfolded protein for which the amino acid sequence is known. Calculations of this kind have been carried out for 11 thermophilic proteins. The thermodynamic properties reported below can be combined with those for protein unfolding to compute the corresponding properties of completely folded (i.e. native) proteins.

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA

The deep subsurface is an enormous repository of microbial life. However, the metabolic capabilities of these microorganisms and the degree to which they are dependent on surface processes are largely unknown. Due to the logistical difficulty of sampling and inherent heterogeneity, the microbial populations of the terrestrial subsurface are poorly characterized. In an effort to better understand the biogeochemistry of deep terrestrial habitats, we evaluate the energetic yield of chemolithotrophic metabolisms and microbial diversity in the Sanford Underground Research Facility (SURF) in the former Homestake Gold Mine, SD, USA. Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment. SURF provides access into an iron-rich Paleoproterozoic metasedimentary deposit that contains deeply circulating groundwater. Geochemical analyses of subsurface fluids reveal enormous geochemical diversity ranging widely in salinity, oxidation state (ORP 330 to −328 mV), and concentrations of redox sensitive species (e.g., Fe2+ from near 0 to 6.2 mg/L and Σ S2- from 7 to 2778μg/L). As a direct result of this compositional buffet, Gibbs energy calculations reveal an abundance of energy for microorganisms from the oxidation of sulfur, iron, nitrogen, methane, and manganese. Pyrotag DNA sequencing reveals diverse communities of chemolithoautotrophs, thermophiles, aerobic and anaerobic heterotrophs, and numerous uncultivated clades. Extrapolated across the mine footprint, these data suggest a complex spatial mosaic of subsurface primary productivity that is in good agreement with predicted energy yields. Notably, we report Gibbs energy normalized both per mole of reaction and per kg fluid (energy density) and find the later to be more consistent with observed physiologies and environmental conditions. Further application of this approach will significantly expand our understanding of the deep terrestrial biosphere.

Order-specific 16S rRNA-targeted oligonucleotide probes for (hyper)thermophilic archaea and bacteria

New oligonucleotide probes were designed and evaluated for application in fluorescence in situ hybridization (FISH) studies on (hyper)thermophilic microbial communities—Arglo32, Tcoc164, and Aqui1197 target the 16S rRNA of Archaeoglobales, Thermococcales, and Aquificales, respectively. Both sequence information and experimental evaluation showed high coverage and specificity of all three probes. The signal intensity of Aqui1197 was improved by addition of a newly designed, unlabeled “helper” oligonucleotide, hAqui1045. It was shown that in addition to its function as a probe for Aquificales, Aqui1197 is suitable as a supplementary probe to extend the coverage of the domain-specific bacterial probe EUB338. In sediments from two hydrothermal seeps on Vulcano Island, Italy, the microbial community structure was analyzed by FISH with both established and the new oligonucleotide probes, showing the applicability of Arglo32, Tcoc164, and Aqui1197/hAqui1045 to natural samples. At both sites, all major groups of (hyper)thermophiles, except for methanogens, were detected: Crenarchaeota (19%, 16%), Thermococcales (14%, 22%), Archaeoglobales (14%, 12%), Aquificales (5%, 8%), Thermotoga/Thermosipho spp. (12%, 9%), Thermus sp. (12%, none), and thermophilic Bacillus sp. (12%, 8%).

Catabolic rates, population sizes and doubling/replacement times of microorganisms in natural settings

Directly assessing the impact of subsurface microbial activity on global element cycles is complicated by the inaccessibility of most deep biospheres and the difficulty of growing representative cultivars in the laboratory. In order to constrain the rates of biogeochemical processes in such settings, a quantitative relationship between rates of microbial catalysis, energy supply and demand and population size has been developed that complements the limited biogeochemical data describing subsurface environments. Within this formulation, rates of biomass change are determined as a function of the proportion of catabolic power that is converted into anabolism—either new microorganisms or the replacement of existing cell components—and the amount of energy that is required to synthesize biomass. Catabolic power is related to biomass through an energy-based yield coefficient that takes into account the constraints that different environments impose on biomolecule synthesis; this method is compared to other approaches for determining yield coefficients. Furthermore, so-called microbial maintenance energies that have been reported in the literature, which span many orders of magnitude, are reviewed. The equations developed in this study are used to demonstrate the interrelatedness of catabolic reaction rates, Gibbs energy of reaction, maintenance energy, biomass yield coefficients, microbial population sizes and doubling/replacement times. The number of microorganisms that can be supported by particular combinations of energy supply and demand is illustrated as a function of the catabolic rates in marine environments. Replacement/doubling times for various population sizes are shown as well. Finally, cell count and geochemical data describing two marine sedimentary environments in the South Pacific Gyre and the Peru Margin are used to constrain in situ metabolic and catabolic rates. The formulations developed in this study can be used to better define the limits and extent of life because they are valid for any metabolism under any set of conditions.

Submarine Hydrothermal Vents of the Aeolian Islands: Relationship Between Microbial Communities and Thermal Fluids

The relationship between fluid geochemistry and microbial communities was investigated for shallow (< 25 m) submarine hydrothermal vents in the Aeolian Islands (Southern Italy). Thermal waters, gases, and deposits of white filamentous material were collected from 11 sites. The geochemical analyses showed a magmatic component was present in all sampled fluids. The total microbial abundances, evaluated as direct counts of picoplanktonic cells (ranging from 0.2 to 2 mu m in diameter), were between 1.55 107 and 4.18 108 cells per liter. Picophytoplankton (total autofluorescent cells) ranged from 9.6 105 to 7.88 106 cells per liter. Yellow-orange autofluorescent prokaryotes belonging to the cyanobacteria were more abundant than red autofluorescent eukaryotic cells. Chemolithoautotrophic, sulfur-oxidizing, rod-shaped Bacteria were isolated from venting water samples and identified as Thiobacillus -like. Microscopic examination of the white mat deposits showed the presence of filamentous microorganisms.

Prokaryotic Populations in Arsenic-Rich Shallow-Sea Hydrothermal Sediments of Ambitle Island, Papua New Guinea

This study is the first to investigate the microbial ecology of the Tutum Bay (Papua New Guinea) shallow-sea hydrothermal system. The subsurface environment was sampled by SCUBA using push cores, which allowed collection of sediments and pore fluids. Geochemical analysis of sediments and fluids along a transect emanating from a discrete venting environment, about 10 mbsl, revealed a complex fluid flow regime and mixing of hydrothermal fluid with seawater within the sediments, providing a continuously fluctuating redox gradient. Vent fluids are highly elevated in arsenic, up to ∼1 ppm, serving as a “point source” of arsenic to this marine environment. 16S rRNA gene and FISH (fluorescence in situ hybridization) analyses revealed distinct prokaryotic communities in different sediment horizons, numerically dominated by Bacteria. 16S rRNA gene diversity at the genus level is greater among the Bacteria than the Archaea. The majority of taxa were similar to uncultured Crenarchaea, Chloroflexus, and various heterotrophic Bacteria. The archaeal community did not appear to increase significantly in number or diversity with depth in these sediments. Further, the majority of sequences identifying with thermophilic bacteria were found in the shallower section of the sediment core. No 16S rRNA genes of marine Crenarchaeota or Euryarchaeota were identified, and none of the identified Crenarchaeota have been cultured. Both sediment horizons also hosted “Korarchaeota”, which represent 2–5% of the 16S rRNA gene clone libraries. Metabolic functions, especially among the Archaea, were difficult to constrain given the distant relationships of most of the community members from cultured representatives. Identification of phenotypes and key ecological processes will depend on future culturing, identification of arsenic cycling genes, and RNA-based analyses.