Qusheng Jin

Bacterial sulfate reduction limits natural arsenic contamination in groundwater

Natural arsenic contamination of groundwater, increasingly recognized as a threat to human health worldwide, is characterized by arsenic concentrations that vary sharply over short distances. Variation in arsenic levels in the Mahomet aquifer system, a regional glacial aquifer in central Illinois, appears to arise from variable rates of bacterial sulfate reduction in the subsurface, not differences in arsenic supply. Where sulfate-reducing bacteria are active, the sulfide produced reacts to precipitate arsenic, or coprecipitate it with iron, leaving little in solution. In the absence of sulfate reduction, methanogenesis is the dominant type of microbial metabolism, and arsenic accumulates to high levels.

Reconstructing Earth's surface oxidation across the Archean-Proterozoic transition

The Archean-Proterozoic transition is characterized by the widespread deposition of organic-rich shale, sedimentary iron formation, glacial diamictite, and marine carbonates recording profound carbon isotope anomalies, but notably lacks bedded evaporites. All deposits refl ect environmental changes in oceanic and atmospheric redox states, in part associated with Earth’s earliest ice ages. Time-series data for multiple sulfur isotopes from carbonateassociated sulfate as well as sulfi des in sediments of the Transvaal Supergroup, South Africa, capture the concomitant buildup of sulfate in the ocean and the loss of atmospheric massindependent sulfur isotope fractionation. In phase with sulfur is the earliest recorded positive carbon isotope anomaly, convincingly linking these environmental perturbations to the Great Oxidation Event (ca. 2.3 Ga).

THE THERMODYNAMIC LADDER IN GEOMICROBIOLOGY

A tenet of geomicrobiology is that anaerobic life in the subsurface arranges itself into zones, according to a thermodynamic ladder. Iron reducers, given access to ferric minerals, use their energetic advantage to preclude sulfate reduction. Sulfate reducers exclude methanogens in the same way, by this tenet, wherever the environment provides sulfate. Examining usable energy—the energy in excess of a cells internal stores—in subsurface environments, we find that in groundwater of near neutral pH the three functional groups see roughly equivalent amounts. Iron reducers hold a clear energetic advantage under acidic conditions, but may be unable to grow in alkaline environments. The calculations fail to identify a fixed thermodynamic hierarchy among the groups. In long-term bioreactor experiments, usable energy did not govern microbial activity. Iron reducers and sulfate reducers, instead of competing for energy, entered into a tightly balanced mutualistic relationship. Results of the study show thermodynamics does not invariably favor iron reducers relative to sulfate reducers, which in turn do not necessarily have an energetic advantage over methanogens. The distribution of microbial life in the subsurface is controlled by ecologic and physiologic factors, and cannot be understood in terms of thermodynamics alone.

Cyanobacteria associated with coral black band disease in Caribbean and Indo-Pacific Reefs.

ABSTRACT For 30 years it has been assumed that a single species of cyanobacteria, Phormidium corallyticum, is the volumetrically dominant component of all cases of black band disease (BBD) in coral. Cyanobacterium-specific 16S rRNA gene primers and terminal restriction fragment length polymorphism analyses were used to determine the phylogenetic diversity of these BBD cyanobacteria on coral reefs in the Caribbean and Indo-Pacific Seas. These analyses indicate that the cyanobacteria that inhabit BBD bacterial mats collected from the Caribbean and Indo-Pacific Seas belong to at least three different taxa, despite the fact that the corals in each case exhibit similar signs and patterns of BBD mat development.

A New Rate Law Describing Microbial Respiration

ABSTRACT The rate of microbial respiration can be described by a rate law that gives the respiration rate as the product of a rate constant, biomass concentration, and three terms: one describing the kinetics of the electron-donating reaction, one for the kinetics of the electron-accepting reaction, and a thermodynamic term accounting for the energy available in the microbes environment. The rate law, derived on the basis of chemiosmotic theory and nonlinear thermodynamics, is unique in that it accounts for both forward and reverse fluxes through the electron transport chain. Our analysis demonstrates how a microbes respiration rate depends on the thermodynamic driving force, i.e., the net difference between the energy available from the environment and energy conserved as ATP. The rate laws commonly applied in microbiology, such as the Monod equation, are specific simplifications of the general law presented. The new rate law is significant because it affords the possibility of extrapolating in a rigorous manner from laboratory experiment to a broad range of natural conditions, including microbial growth where only limited energy is available. The rate law also provides a new explanation of threshold phenomena, which may reflect a thermodynamic equilibrium where the energy released by electron transfer balances that conserved by ADP phosphorylation.

Kinetics of Electron Transfer through the Respiratory Chain

We show that the rate at which electrons pass through the respiratory chain in mitochondria and respiring prokaryotic cells is described by the product of three terms, one describing electron donation, one acceptance, and a third, the thermodynamic drive. We apply the theory of nonequilibrium thermodynamics in the context of the chemiosmotic model of proton translocation and energy conservation. This approach leads to a closed-form expression that predicts steady-state electron flux as a function of chemical conditions and the proton motive force across the mitochondrial inner membrane or prokaryotic cytoplasmic membrane. The rate expression, derived considering reverse and forward electron flow, is the first to account for both thermodynamic and kinetic controls on the respiration rate. The expression can be simplified under specific conditions to give rate laws of various forms familiar in cellular physiology and microbial ecology. The expression explains the nonlinear dependence of flux on electrical potential gradient, its hyperbolic dependence on substrate concentration, and the inhibiting effects of reaction products. It provides a theoretical basis for investigating life under unusual conditions, such as microbial respiration in alkaline waters.

THE THERMODYNAMICS AND KINETICS OF MICROBIAL METABOLISM

The various kinetic rate laws commonly used to describe microbial metabolism are derived considering only forward reaction progress and hence are inconsistent with the requirements of thermodynamics. These laws may be applied without significant error where abundant energy is available to drive the metabolic reaction, so the forward reaction overwhelms the reverse. The laws are, however, unsuitable where little energy may be available. In previous papers we derived a new rate law for microbial respiration considering that reaction progresses simultaneously in both the forward and reverse directions. In this paper, we demonstrate in a new and rigorous way how the rate law can account quantitatively for the thermodynamic driving force for reaction. We refine our previous work on microbial respiration to better account for details of the electron transfer process. We furthermore extend the theory to account for enzymatic reaction and microbial fermentation. We show that commonly used rate laws of simple form can be modified to honor thermodynamic consistency by including a thermodynamic potential factor. Finally, we consider how the rate of biomass synthesis can be determined from the rate of respiration or fermentation. We apply these results to describe (1) the enzymatic reaction by which benzoyl-CoA forms, (2) crotonate fermentation, and (3) glucose fermentation; for each process we demonstrate how the reaction rate is affected by the thermodynamic driving force. Results of the study improve our ability to predict microbial metabolic rates accurately over a spectrum of geochemical environments, including under eutrophic and oligotrophic conditions.

Origin of microbiological zoning in groundwater flows

Reactive transport modeling helps explain the origin of the microbiological zoning observed in pristine freshwater aquifers. Zoned aquifers have been described previously as either thermodynamic or kinetic phenomena, but neither interpretation has proved fully satisfactory. Drawing on concepts of population dynamics, the modeling reported here offers an alternative explanation of how certain microbes exclude others from zones: one functional group maintains conditions under which cells in another group die more rapidly than they can reproduce. The modeling also lends support to the idea that a group of microbes that appears to dominate a particular zone in an aquifer may in fact coexist with, or even be subordinate to, another group.

Thermodynamics of Microbial Growth Coupled to Metabolism of Glucose, Ethanol, Short-Chain Organic Acids, and Hydrogen

ABSTRACT A literature compilation demonstrated a linear relationship between microbial growth yield and the free energy of aerobic and anaerobic (respiratory and/or fermentative) metabolism of glucose, ethanol, formate, acetate, lactate, propionate, butyrate, and H2. This relationship provides a means to estimate growth yields for modeling microbial redox metabolism in soil and sedimentary environments.

Geomicrobial Kinetics: Extrapolating Laboratory Studies to Natural Environments

Predicting metabolic rates and population sizes of microorganisms in natural environments is a central problem in geomicrobiology. Such predictions can be made on the basis of a thermodynamically consistent rate law that accounts for both kinetic and thermodynamic controls on microbial metabolism. Application of the rate law requires kinetic and growth parameters, the values of which have been determined for pure and mixed cultures growing in laboratory reactors. However, not all parameter values derived from laboratory studies can be validly applied to the environment. This article illustrates a best-choice approach for extrapolating experimentally-derived parameter values to natural environments, using microbial sulfate reduction coupled to acetate oxidation as an example. We compiled kinetic and growth parameters determined by previous laboratory studies and evaluated their applicability to natural environments. Our results suggest that some parameters, such as rate constants and maximum growth yields, can be applied directly to the environment; others, such as half-saturation constants and specific maintenance rates, are best determined using samples recovered from the environment of interest. The best-choice parameter values were applied to simulation of acetotrophic sulfate reduction in the sediments of a freshwater lake. Our analysis shows that the best-choice approach reduces the tasks of parameter fitting and simplifies the modeling exercise. The proposed approach also ensures that parameters in use are consistent with the physiology of indigenous microorganisms, and relevant to the environment of interest.