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Microbial energetics applied to waste repositories

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Summary

Through their catalytic abilities microbes can increase rates of chemical reactions which would take a very long time to reach equilibrium under abiotic conditions. Microbes also alter the concentration and composition of chemicals in the environment, thereby creating new conditions for further biological and chemical reactions. Rates of degradation and possible indirect consequences on leaching rates in waste repositories are a function of the presence or absence of microbes and of the conditions which allow them to become catalytically active.

Microbially mediated reactions are no exception to the rule that all chemical processes are basically governed by thermodynamic laws. Naturally occurring processes proceed in the direction that leads to the minimal potential energy level attained when equilibrium is reached. A continuous supply of energy to an ecosystem in the form of biochemically unstable compounds maintains non-equilibrium conditions, a prerequisite for all chemotrophic life. Energy is released as a chemical reaction progresses towards equilibrium. Microbes scavenge that portion of the free energy of reaction (ΔGr) which can be converted into biochemically usable forms during the chemical oxidation processes. As ‘electrontransfer catalysts’, the microorganisms mediate reactions which are thermodynamically possible thereby stimulating reaction rates. Decomposition and mineralization in systems without a continuous supply of substrates and oxidants will lead to equilibria with minimal free energy levels at which point further microbial action would cease. The differences in the free energy levels of reactions (ΔGr), represent the maximal energy which is available to microorganisms for maintenance and growth. How much of the released free energy will be conserved in energy-rich bonds, compounds (e.g. ATP), and chemical potentials (e.g. emf) useful for biosynthesis and biological work is characteristic for the microbes involved and the processes and metabolic routes employed.

Materials whose elements are not present in the most oxidized form attainable in the oxic environment of our planet are potentially reactive. Microbial activities are associated only with chemical reactions whose free energy changes are exergonic. This should be kept in mind for all investigations related to the role of microbes in repositories or in the layout of proper waste storage conditions. Rigorous application of thermodynamic concepts to environmental microbiology allows one to develop models and design experiments which are often difficult to conceive of in complex natural systems from physiological information alone. Thermodynamic considerations also aid in selecting proper deposition conditions and in carrying out thoughtful experiments in areas related to microbial ecology of waste repositories.

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Abbreviations

a, b, c, d, e, f g, x, y, z:

stoichiometric coefficients

act:

actual conditions, e.g. Tact

aj :

ion size parameter in [10−8 cm]

(am):

amorphous state

(aq):

aqueous state

[atm]:

standard atmosphere: 1 [atm] ≙ 101325 [Pa] ≙ 760 [Torr] ≙ 1.01325 [bar]

aw :

water activity

bar:

1 [bar] ≙ 105 [Pa] ≙ 0.986923 [atm] ≙ 750.062 [Torr]

c:

denotescombustion, e.g. ΔH 0c

ci :

concentration of chemical species i

c 0i :

standard concentration of species j [1 mol/dm3]

e− :

electron

e:

base of natural logarithm=2.71828183

emf:

electromotive force

eq:

equilibrium

exp:

exponential function to base e

f:

denotes thermochemical quantity associated with the formation of a substance from elements in their reference state, e.g. Gf, Hf, Sf

fj :

Debye-Hückel activity correction factor

(g):

gaseous state

h:

surplus charge of biomolecule

i, j:

chemical species designation

(l):

liquid state

[l]:

liter

ln:

natural logarithm=2.302585 ß10log

ln 10:

natural logarithm of 10=2.302585

m:

slope of a linear function

n:

number of electrons transferred

neq:

non-equilibrium

ox:

oxidized

p:

pressure

p0 :

standard state pressure 1 [atm] (earlier), 1 [bar0] (today)

pe:

−log {e−}; electron activity

pe0 :

electron activity reference state = 1/n · log Keq ≙ F·E0/2.3026·R·T

pK:

−log K

±q:

number of protons transferred, +if they are produced, — if they are consumed

r:

denotes thermodynamic quantity associated with areaction, e.g. ΔGr, ΔHr, ΔSr

ref:

reference state e.g. Tref=298.15 [K]

red:

reduced

(s):

solid state

vi, j :

stoichiometric coefficients of species i, j

x, y, z:

stoichiometric coefficients

y1 :

intercept on y-axes

zj :

charge of species j

[]:

designates concentration, or monomer unit

{}:

designates activity

<>:

designates hypothetical unit molecule, e.g. for biomass

[−CaHb−]:

designates repetitive molecular fragment e.g. monomer molecule

[C(H)2(C)(CO)]:

designates group increment

α0, α1, α2 γ0, γ1, γ2 ε0, ε1 ϑ0, ϑ1, ϑ2 :

acid-base pair distribution coefficients for mono- and diprotic acids

Σ:

sum of terms

Π:

product of terms

εT :

temperature-dependent dielectric coefficient of water

σ:

symmetry factor

I+, II−, V+ U, R, etc.:

designates oxidation states

+, −, 2−, 3+ h etc.:

designates ionic charges

o:

denotes standard state conditions with reactants in their pure state present at a pressure of 1 [atm] if the reactants are gases or 1-molal concentrations if the reactants are solutes

o:

denotes standard state except for 1 reactant (e.g. pH ≠ 0)

A, B, C, D, ... X, Y, Z:

chemical species

A, B:

Debye-Hückel-Onsager parameters A=1.82 · 106 (εT·T)−3/2 B=50.3 · (εT·T)−1/2

A−, A2− :

anions of mono and diprotic acids

[°C]:

temperature in degree Celsius=T/K −273.15

CT :

sum of inorganic carbonate species =[CO2(aq)]+[H2CO3(aq)]+[HCO −3(aq) ] +[CO 2−3 (aq) ]

C, H, O, N, P, S:

most common chemical elements in organic biomolecules

[Da]:

Dalton

E:

electrochemical potential in [V]=emf

E0 :

standard emf=electrochemical reference potential [V]=−G 0Γ /n·F ≙ 2.3026·RT·pe 0/F

E0′ :

standard emf at pH ≠ 0

F:

Faraday's constant=96.485309 [kJ · mol−1 · V−1]

Gf0 :

standard free energy of formation [kJ/mol]

ΔGf0 :

standard Gibbs free energy change of formation

ΔG 0r :

change of Gibbs free energy of reaction at standard conditions=−R · T · lnK0

ΔG 0′r :

change of Gibbs free energy of reaction at standard conditions except for one reactant (e.g. at pH ≠ 0)

ΔGr :

change of Gibbs free energy of reaction at actual conditions

H+ :

proton

Hf0 :

standard enthalpy of formation [kJ/mol]

ΔHf0 :

standard enthalpy change of formation

ΔH 0r :

change of enthalpy of reaction at standard conditions

ΔHr :

change of enthalpy of reaction at actual conditions

ΔH 0c :

change of standard heat of combustion

HA, H2A:

mono- and diprotic acids, protonated

I:

ionic strength\(\frac{1}{2}\sum\limits_j {c_j \cdot z_j ^2 [mol/1]}\)

IAP:

ion activity product

[J]:

Joule

[K]:

temperature in Kelvin degree

K:

dissociation, equilibrium or solubility coefficient

K ′1 , K ′2 :

temperature and/or ionic strength corrected dissociation coefficient

K 0a :

thermodynamic acid dissociation coefficient

KD :

Ostwald coefficient=KH · R · T [−]

Keq≙K0 :

thermodynamic equilibrium coefficient

log Keq:

=−ΔG 0r /2.3026 · R · T

KH :

Henry's law constant [mol · 1−1 · atm−1]

K 0s :

thermodynamic solubility product for standard conditions

K ′s :

actual solubility product for I ≠ 0

K 0′s :

operational solubility product for standard conditions at I=0

Kw :

dissociation coefficient of water

[kJ]:

kilojoule=103 Joule

LT :

sum of inorganic sulfate species =[H2SO4]+[HSO −4 ]+[SO 2−4 ]

M:

sum of minor elements in organic molecule

P:

reaction-product

[Pa]:

1 Pascal ≙ 9.86923·10−6[atm]≙7.50062·10−3 [Torr]

Q:

ratio of actual activity products of reactants

Q′:

ratio of actual activity products of reactants excluding protons (or/and electrons in half-reactions)

−R−:

rest of organic molecule, mostly C-entity

R+ :

average oxidation state of M

R:

gas constant=8.31451 · 10−3 [kJ · mol−1 · K−1] (concentration basis) =82.057844 · 10−3 [atm · l · mol−1 · K−1] (pressure basis)

RT :

sum of acetate and acetic acid =[CH3COO−]+[CH3COOH]

S:

substrate

Sf0 :

standard entropy of formation [J/K · mol]

ΔSf0 :

standard entropy change of formation

ΔS 0r :

change of entropy of reaction at standard conditions

ΔSr :

change of entropy of reaction at actual conditions

ST :

sum of inorganic sulfide species =[H2S]+[HS−]+[S2−]

T:

thermodynamic temperature in [K]

U:

oxidation state (number) of carbon in an organic molecule

[V]:

volt

V0 :

molar volume of ideal gas (at p0=1 bar, T=273.15K)=22.71108 [l · mol−1], ≙ 22.41409 [1·mol−1] for p0=1 [atm] and T=273.15 K; for p0=1 [atm] and T=298.15 K, V0=24.46554 [l · mol−1]

W:

number of possible structural configurations

X, Y:

chemical species

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  1. Institute of Plant Biology, Microbiology, University of Zürich, Zollikerstr. 107, CH-8008, Zürich, Switzerland

    K. W. Hanselmann

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Hanselmann, K.W. Microbial energetics applied to waste repositories. Experientia 47, 645–687 (1991). https://doi.org/10.1007/BF01958816

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