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Chapter 6. Geomicrobial Processes: Physiological and Biochemical Overview

Chapter 6. Geomicrobial Processes: Physiological and Biochemical Overview

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90



Geomicrobiology

Eukaryotes

Protozoa, fungi, animals, plants



Prokaryotes



Archaea

Bacteria



FIGURE 6.1 Phylogenetic relationships of the Prokaryotes, domains of the Bacteria and the Archaea,

and the Eukaryotes. (Based on Woese CR, Kandler O, Wheelis ML, Proc. Natl. Acad. Sci. USA, 87,

4576–4579, 1990.)



Examples of geomicrobially important Archaea include methanogens (methane-forming bacteria), oxidizers of reduced forms of sulfur, extreme halophiles, and thermoacidophiles. Examples

of geomicrobially important Bacteria include some aerobic and anaerobic hydrogen-metabolizing

bacteria, iron-oxidizing and iron-reducing bacteria, manganese-oxidizing and manganese-reducing

bacteria, nitrifying and denitrifying bacteria, sulfate-reducing bacteria, sulfur-oxidizing and sulfurreducing bacteria, anaerobic photosynthetic sulfur bacteria, oxygen-producing cyanobacteria, and

many others. Examples of geomicrobially important eukaryotes include fungi that can attack silicate, carbonate, and phosphate minerals, among others. They are also important in initiating degradation of somewhat recalcitrant natural organic polymers such as lignin, cellulose, and chitin, as in

the O and A horizons of soil (see Chapter 4), or on and in surface sediments. Other geomicrobially

important eukaryotes are algae, which together with cyanobacteria (prokaryotes), are a major source

of oxygen in the atmosphere. Some algae promote calcium carbonate precipitation or dissolution,

and others precipitate silica as frustules. Still other geomicrobially important eukaryotes include

protozoa, some of which lay down siliceous, calcium carbonate, strontium sulfate, or manganese

oxide tests, and others may accumulate preformed iron oxide on their cell surface.



6.2



GEOMICROBIALLY IMPORTANT PHYSIOLOGICAL

GROUPS OF PROKARYOTES



Prokaryotes can be divided into various physiological groups such as chemolithoautotrophs, photolithoautotrophs, mixotrophs, photoheterotrophs, and heterotrophs (Figure 6.2). Each of these groups

includes some geomicrobially important organisms. Chemolithoautotrophs (chemosynthetic autotrophs) include members of both the Bacteria and the Archaea. They are microorganisms that derive

energy for doing metabolic work from the oxidation of inorganic compounds and assimilate car2−

bon as CO2, HCO−

3 , or CO3 (see Wood, 1988). Photolithoautotrophs (photosynthetic autotrophs)

include various Bacteria but no known Archaea. They are microorganisms that derive energy for

doing metabolic work by converting radiant energy from the sun into chemical energy and use it, in

2−

part, in the assimilation of carbon as CO2, HCO−

3 , or CO3 as their carbon source (photosynthesis).

Some of these microbes are anoxygenic (do not produce oxygen from photosynthesis), whereas others are oxygenic (produce oxygen from photosynthesis). Mixotrophs include some members of the

Bacteria and the Archaea. They may derive energy simultaneously from the oxidation of reduced

carbon compounds and oxidizable inorganic compounds and their carbon simultaneously from

organic carbon and CO2; or they may derive their energy totally from the oxidation of an inorganic

compound but their carbon from organic compounds. Photoheterotrophs include mostly Bacteria

but also a few Archaea (extreme halophiles). They derive all or part of their energy from sunlight



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Chemolithotroph



Photolithotroph



Oxidation of

mineral



Oxidation of reduced

sulfur or water



(e−) reducing power



(e−) reducing power



CO2



Anabolic machinery

of the cell



(e−) reducing power

Energy



CO2



Oxygen, nitrate,

carbon dioxide,

ferric iron,

manganese oxide



Anabolic machinery

of the cell



Sunlight

Anaerobically

respiring

heterotroph



Mixotroph

or

photoheterotroph



Reduction of

mineral matter



Oxidation of

organic or

mineral matter

or sunlight



(e−) reducing power

Energy



(e−) reducing power



Oxidation of

organic carbon

Anabolic machinery

of the cell

Organic carbon



Oxygen, sulfate,

ferric iron,

manganese oxide, etc.

(mixotrophs only)



Energy



Anabolic machinery

of the cell



Organic carbon



FIGURE 6.2 Geomicrobially important physiological groups among prokaryotes.



but their carbon by assimilating organic compounds. Heterotrophs include members of both the

Bacteria and the Archaea. They derive all of their energy from the oxidation of organic compounds

and most or all of their carbon from the assimilation of organic compounds. They may respire (oxidize their energy source) aerobically or anaerobically, or they may ferment their energy source by

disproportionation (see Sections 6.5.1 through 6.5.4).



6.3



ROLE OF MICROBES IN INORGANIC CONVERSIONS

IN LITHOSPHERE AND HYDROSPHERE



A number of microbes in the biosphere can be considered to be geologic agents. They may serve as

agents of concentration, dispersion, or fractionation of geologically important matter. As agents of

concentration, they cause localized accumulation of inorganic matter by (1) depositing inorganic

products of metabolism in or on special parts of the cell, (2) passive accumulations involving surface

adsorption or ion exchange, or (3) promoting precipitation of insoluble compounds external to the

cell (Ehrlich, 1999). An example of mineral accumulation of an inorganic metabolic product inside



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a cell is the deposition of polyphosphate (volutin) in the cytoplasm of bacteria, such as Spirillum

volutans, lactobacilli, rhizobia, and some others. An example of metabolic product accumulation

in the bacterial cell envelope is the deposition of elemental sulfur granules in the periplasm (region

between the plasma membrane and the outer membrane of gram-negative bacteria) by Beggiatoa

and Thiothrixx (Strohl et al., 1981; Smith and Strohl, 1991). An example of metabolic product accumulation at the cell surface is the formation of silica frustules by diatoms (algae), the frustules being

their cell walls (de Vrind-de Jong and de Vrind, 1997) (see also Chapter 10).

Examples of passive accumulation of inorganic matter by adsorption or ion exchange are the

binding of specific metallic cations by carboxyl groups of peptidoglycan or phosphate groups of

teichoic or teichuronic acids in the cell wall of gram-positive bacteria (e.g., Bacillus subtilis),

s or

by the lipopolysaccharide phosphoryl groups of outer membranes of gram-negative bacteria (e.g.,

Escherichia coli). The bound cations may subsequently react with certain anions, such as sulfide,

carbonate, or phosphate, and form insoluble salts that may serve as nuclei in the formation of corresponding minerals (Beveridge et al., 1983; Beveridge, 1989; Beveridge and Doyle, 1989; Doyle,

1989; Ferris, 1989; Geesey and Jang, 1989; Macaskie et al., 1987, 1992).

An example of extracellular inorganic accumulation is the precipitation of metal cations in the

cellular surround (bulk phase) by sulfides produced in sulfate reduction by sulfate-reducing bacteria. Many such sulfides are insoluble and fairly stable in the absence of oxygen (anoxic condition)

(see Chapter 20).

As agents of dispersion, microbes promote dissolution of insoluble mineral matter as, for example, in the dissolution of CaCO3 by respiratory CO2 (see Chapter 9), or in the biochemical reduction of insoluble ferric oxide or manganese(IV) oxide to corresponding soluble compounds (see

Chapters 16 and 17).

As agents of fractionation, microbes may act on a mixture of insoluble inorganic compounds

(minerals) by promoting selective mobilization involving one or a few compounds in the mixture.

One example is the oxidation of arsenopyrite (FeAsS) in pyritic gold ore by Acidithiobacillus (formerly Thiobacillus)

s ferrooxidans (Ehrlich, 1964) (see also Chapter 14). In this process, some of

the iron solubilized by oxidation reacts with arsenic, which is simultaneously mobilized from the

mineral, to precipitate in the bulk phase as a new compound—ferric arsenate. Another example is

the preferential solubilization by reduction of Mn(IV) over Fe(III) contained in ferromanganese

nodules by bacteria (Ehrlich et al., 1973; Ehrlich, 2000) (see also Chapter 17).

Microbes may also cause fractionation by preferentially attacking the light isotope in a mixture of stable heavy and light isotopes of an element in a compound in preference to the heavier

isotope(s). Examples are the reduction of 32SO42− in preference to 34SO42− by some sulfate-reducing

bacteria and the assimilation of 12CO2 in preference to 13CO2 by some autotrophs, in either instance

under conditions of slow growth (see discussion by Doetsch and Cook, 1973). Other isotope mixtures that may be fractionated by microbes include hydrogen/deuterium (Estep and Hoering, 1980),

6

Li/7Li (Sakaguchi and Tomita, 2000), 14N/15N (Wada and Hattori, 1978), 16O/18O (Duplessy et al.,

1981), 28Si/30Si (De La Rocha et al., 1997), and 54Fe//56Fe (Beard et al., 1999). In the laboratory, the

magnitude of these fractionations may be relatively large and may involve significant changes in

isotopic ratios in a relatively short time. In some natural settings, corresponding microbial isotope

fractionations are also readily detectable but may be of somewhat smaller magnitude. Studies so far

lead to the impression that only a few mostly unrelated organisms have the capacity to fractionate

stable isotope mixtures.



6.4



TYPES OF MICROBIAL ACTIVITIES INFLUENCING

GEOLOGICAL PROCESSES



Microbes influence a number of geologic processes at the Earth’s surface and in the uppermost crust

(deep subsurface). Lithification is a type of geological process in which microbes may produce the

cementing substance that binds inorganic sedimentary particles together to form sedimentary rock.



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The microbially produced cementing substance may be calcium carbonate, iron- or aluminumoxide, or silicate.

Some types of mineral formation may be the result of microbial activity. Iron sulfides such as

pyrite (FeS2), iron oxides such as magnetite (Fe3O4) or goethite (FeOOH), manganese oxides such

as vernadite (MnO2) or psilomelane (Ba, Mn2+Mn4+O16(OH)4), calcium carbonates such as calcite

and aragonite (CaCO3), and silica (SiO2) may be generated authigenically by microbes (for a more

extensive survey, see Lowenstamm, 1981).

In some instances, microbes may be responsible for mineral diagenesis in which microbes may

cause alteration of rock structure and transformation of primary into secondary minerals, as in the

conversion of orthoclase to kaolinite (Chapter 4).

Rock weathering may be promoted by microbes through production and excretion of metabolic

products, which attack the rock and cause solubilization or diagenesis of some mineral constituents

of the rock. Rock weathering may also involve direct enzymatic attack of certain oxidizable or

reducible rock minerals by microbes, thereby causing their solubilization or their diagenesis.

Microbes may contribute to sediment accumulation in the form of calcium carbonate tests as

those from coccolithophores or foraminifera, silica frustules from diatoms, or silica tests from radiolaria or actinopods in oceans and lakes. The aging of lakes may be influenced by microbes through

their rock weathering activity or their generation of organic debris from incomplete decomposition

of organic matter (see Chapter 5).

Geologic processes that are not influenced by microbes include magmatic activity or volcanism,

rock metamorphism resulting from heat and pressure, tectonic activity related to crustal formation

and transformation, and the allied processes of orogeny or mountain building. Windd and water

erosion should also be included, although these processes may be facilitated by prior or concurrent microbial weathering activity. Although microbes do not influence these geologic processes,

microbes may be influenced by them because these processes may create new environments that

may be more or less favorable for microbial growth and activities than their previous occurrence.



6.5 MICROBES AS CATALYSTS OF GEOCHEMICAL PROCESSES

Most of the influence that microbes exert on geological processes is physiological. They may act as

catalysts in some geochemical processes or as producers or consumers of certain geochemically

active substances and thereby influence the rate of a geochemical reaction in which such substances

are reactants or products (see Ehrlich, 1996). In either case, the microbes act through their metabolism, which has two components. One of these components is catabolism, which provides the cell

with needed energy through energy conservation and may also yield to the cell some compounds

that can serve as building blocks for polymers. A key reaction in energy conservation is the oxidation of a suitable nutrient or metabolite (a compound metabolically derived from a nutrient). The

other component of metabolism is anabolism. It deals with assimilation (synthesis and polymerization) and leads to the formation of organic polymers such as nucleic acids, proteins, polysaccharides,

lipids, and others. It also deals with the synthesis of inorganic polymers such as the polysilicates

in diatom frustules and radiolarian tests and the polyphosphate granules that are formed by some

bacteria and yeasts as energy storage compounds within their cells. Anabolism, by contributing

to an increase in cellular mass and duplication of vital molecules, makes growth and reproduction possible. Catabolism and anabolism are linked to one another in such a way that catabolism

provides the energy and some or all of the building blocks that make anabolism, which overall is

an energy-consuming process, possible. Both catabolism and anabolism may play a geomicrobial

role. Catabolism is involved, for instance, in large-scale oxidation that brings about transformation

of inorganic substances and degradation of organic molecules, whereas anabolism is involved, for

instance, in the synthesis of organic compounds from which fossil fuels (peat, coal, and petroleum)

are generated. Anabolism is also the process by which the diatom frustules and radiolarian tests that

accumulate in siliceous oozes are formed.



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Catabolism may take the form of aerobic or anaerobic respiration, both of which are oxidation

processes, or fermentation. Catabolism may thus be carried on in the presence or absence of oxygen

in air. Oxygen is used as terminal electron acceptor. Indeed, microorganisms can be grouped as

aerobes (oxygen-requiring organisms), anaerobes (oxygen-shunning organisms), microaerophilic

organisms (requiring low concentrations of oxygen), or facultative organisms (can adapt their

catabolism to operate in the presence or absence of oxygen in air). Facultative organisms use oxygen

as terminal electron acceptor when it is available. When oxygen is not available, they use a reducible

inorganic (e.g., nitrate or ferric iron) or an organic (e.g., fumarate) compound as a substitute terminal

electron acceptor, or they ferment.



6.5.1



CATABOLIC REACTIONS: AEROBIC RESPIRATION



In aerobic respiration, hydrogen atoms or electrons are removed in the oxidation of organic compounds

and electrons in the oxidation of inorganic entities by various biochemical reactions and conveyed by

an electron transport system (ETS) to oxygen to form water. Among these biochemical reactions, an

important reaction sequence in which reducing power (hydrogen atoms, electrons) is generated as part

of aerobic respiration is the Krebs tricarboxylic acid cycle (Figure 6.3). By this reaction sequence,

organic substances are completely oxidized to CO2 and H2O (Stryer, 1995; Schaechter et al., 2006). The

reaction sequence is initiated when acetyl∼SCoA, produced enzymatically in the oxidative degradation

of a large variety of organic nutrients, is enzymatically combined with oxalacetate to form citrate with

the release of CoASH. Citrate is converted stepwise to isocitrate, α-ketoglutarate, succinate, fumarate,

malate, and back to oxalacetate. One turn of this cycle produces four hydrogen pairs and two CO2 as

well as one adenosine 5′-triphosphate (ATP) by substrate-level phosphorylation. The hydrogen pairs

are the source of reducing power that is fed into the ETS and transported to oxygen as part of aerobic

respiration to form water. In the transfer of the reducing power via the ETS, some of the energy that

is liberated is conserved in special phosphate anhydride bonds of ATP by a chemiosmotic process

called oxidative phosphorylation (see Section 6.5.5). Upon hydrolysis, these bonds (Figure 6.4)

yield 7.3 kcal mol−1 (30.5 kJ mol−1) of free energy at pH 7 and 25°C (Stryer, 1995), as opposed to

ordinary phosphate ester bonds, which release only ∼2 kcal mol−1 (8.4 kJ mol−1) of energy under these

conditions. The energy in high-energy bonds is used by cells for driving energy-consuming reactions

such as syntheses or polymerizations.

Acetyl~SCoA



Oxaloacetate

−2H



−CoASH



cis -Aconitate



Malate

+H2O



Isocitrate



Fumarate

−2H



−2H



Succinate

Oxalosuccinate



+ADP, +P, −CoASH, −ATP



Succinyl~SCoA

−CO2, −2H, +CoASH



−CO2



α-Ketoglutarate



FIGURE 6.3 Krebs tricarboxylic acid cycle. One turn of the cycle converts one molecule of acetate to two

molecules of CO2 and four hydrogen pairs (2H), with the formation of one molecule of ATP by substrate-level

phosphorylation. An additional 11 ATP can be formed when the four hydrogen pairs are oxidized to H2O with

oxygen as terminal electron acceptor.



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NH2

N



C



N

C

CH



HC



C

N



N

CH2 O



O

CH



CH



O



O



O



P



O ~P



O ~P



O

H



O

H



O

H



OH



H

C

O

H



H

C

O

H



Adenosine-5′-triphosphate (ATP)

O

CH3C ~ O



O

P



O

CH3C ~ SCoA



OH



OH

Acetyl phosphate



Acetyl-coenzyme A

O



CH2



O



OH



P

OH



HCOH

O

C ~O



O

P



OH



OH

1,3-diphosphoglyceric acid



FIGURE 6.4



Examples of compounds containing one or more high-energy phosphate bonds (∼).



Typical components of the ETS include nicotinamide adenine dinucleotide (NAD), flavoproteins

(FP), iron–sulfur protein (Fe–S), quinone (CoQ), cytochromes (cyt Fe), and cytochrome oxidase

(cyt oxid). They are arranged in complexes in the plasma membrane of aerobically respiring bacteria, as, for instance, in Paracoccus denitrificans (Payne et al., 1987; Onishi et al., 1987) and marine

bacterial strain SSW22 (Graham, 1987) (Figure 6.5), and in the inner mitochondrial membrane

eukaryotes. The types of electron carriers and enzymes and their arrangement in complexes, if

any, differ among different kinds of bacteria. Indeed, in the same bacterium, the carriers may vary

quantitatively and qualitatively, depending on growth conditions. Whatever may be the makeup of

the assemblage of electron carriers, they interact in a specific sequence such as the one shown in

Figure 6.6. Hydrogen or electrons enter the ETS where the Eh of the half-reaction by which they are

removed from a substrate is near or below the Eh of the half-reaction of the appropriate hydrogenor electron-accepting component of the system. For example, electrons from the oxidation of H2 or

pyruvate may enter the transport system at the level of complex I via NAD+ as carrier and are transferred to complex III via CoQ and thence to complex IV via cytochrome c. Complex IV transfers

the electrons that it receives to O2, which is then transformed to form H2O (Stryer, 1995; Schaechter

et al., 2006). Electrons from the oxidation of succinate enter the transport system via complex II

and are then transferred to complex III and so on to O2. Electrons from the oxidation of ferrous

iron enter the ETS at the level of complex IV. Table 6.1 lists the Eh values of some geomicrobially

important enzyme-catalyzed oxidations, the level at which their hydrogens or electrons are fed into

the ETS upon their oxidation, and also the estimated maximum number of high-energy phosphate

bonds (ATP) that may be generated in the transfer of hydrogen or electron pairs to oxygen.



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H+



H+



H+



H+

CoQ



III



Cyt c

IV



I



2H +



+



H>



D

NA



+1



/2



O



2



AD



N



+2



e−



=>



H



2O



ADP +



+P

H+



H+



H+



Cytosol



P



ATPase



ADP



H+



ATP



ATP



Suc

fum cinate

ara

te >



Membrane



II



IV



CoQ

H+

H+



III



Cyt c

H+



Periplasm

(bulk phase)



FIGURE 6.5 Schematic display of the bioenergetic machinery in a prokaryotic (domain Bacteria) cell envelope. Structures labeled I, II, III, and IV represent specific electron transport complexes involved in some

prokaryotes. Complex I, reactive with NADH, includes a flavoprotein and an Fe–S protein; complex II, reactive with succinate, includes succinic dehydrogenase (another flavoprotein) and an Fe–S protein; complex III

includes cytochromes b and c1 and an Fe–S protein; and complex IV includes cytochrome oxidase (e.g., cytochrome a + a3). Coenzyme Q (CoQ) and cytochrome c (cyt cc) shuttle electrons between respective complexes.

Proton translocation from the cytosol to the periplasm involves complex I or II, CoQ and complex III, and

often complex IV. Oxygen reduction to water occurs on the inner surface of the plasma membrane. ATPase

(ATP synthase) is the site of ATP synthesis.



6.5.2 CATABOLIC REACTIONS: ANAEROBIC RESPIRATION

In aerobic respiration, oxygen is always the terminal electron acceptor, whereas in anaerobic respiration other reducible substrates species such as nitrate, Fe3+, sulfate, carbon dioxide, or an organic

compound such as fumarate serve as terminal electron acceptors. Anaerobic respiration is performed by some Bacteria and some Archaea. Microorganisms performing such respiration may be

facultative (e.g., nitrate reducers, some iron(III) and manganese(IV) reducers) or obligately respiring anaerobes (e.g., sulfate reducers, methanogens, homoacetogens, some other Fe(III) and Mn(IV)

reducers). Some fermenters (see Section 6.5.4), although not anaerobic respirers, may also be

facultative—that is, aerobically they respire (see Section 6.5.1) whereas anaerobically they ferment.

Certain facultative respirers may reduce O2 and concurrently another inorganic electron acceptor

(e.g., certain nitrate, chromate, and MnO2 reducers; see Chapters 13, 17, and 18, respectively). In

most cases of anaerobic respiration by facultative organisms, oxygen competes with the other possible terminal electron acceptors and thus must be absent or present at significantly lower concentration than in normal air for anaerobic respiration to occur. Anaerobic respiration usually employs



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Substrate

(oxidized)



Substrate

(reduced)



NADH + H+



NAD+



FP

(oxidized)



97



FP

(reduced)



CoQ

(reduced)



CoQ

(oxidized)



Cyt b Fe2+



Cyt b Fe3+



Cyt c1 Fe3+



2+



Cyt c1 Fe



Cyt c Fe3+



Cyt c Fe2+



Cyt oxidase

(reduced)



Cyt oxidase

(oxidized)



1/2O2 + 2H+



H2O



FIGURE 6.6 Schematic representation of the sequence of interactions of components of an ETS in a bacterial membrane by which reducing power is transferred from a substrate to oxygen.



TABLE 6.1

Microbially Catalyzed Oxidations of Geological Significance and Some

Characteristics of Their Interaction with the ETS

Reaction



Eh at pH 7 (V)



Fe → Fe + e

+



S0 + 4H2O → SO2−

4 + 8H + 6e

H2S → S0 + 2H+ + 2e−

H2 → 2H+ + 2e−

Mn2+ + 2H2O → MnO2 + 4H+ + 2e−

2+



a



3+







+0.77

−0.20

−0.27

−0.42

+0.46



Entrance Level

into ETS

Complex IV

Complex III or IV

Complex I or III

Complex I or III

Complex IV (?)



ATP/2e− or 2H

1

2 or 1a

3 or 2

3 or 2

1



Add 0.5 mol of ATP per mol of SO32− oxidized to SO42− if substrate-level phosphorylation is part of the oxidation

process.



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some of the hydrogen and electron carriers of aerobic respiration but usually substitutes a suitable

terminal reductase for cytochrome oxidase to convey electrons to the terminal electron acceptor that

replaces oxygen. If the organic substrate being consumed anaerobically is oxidized completely, the

tricarboxylic acid cycle may be involved; but other pathways may be used instead. Among the best

characterized pathways of these anaerobic respiratory systems are those in which sulfate and nitrate

are reduced as terminal electron acceptors.



6.5.3



CATABOLIC REACTIONS: RESPIRATION INVOLVING INSOLUBLE INORGANIC

SUBSTRATES AS ELECTRON DONORS OR ACCEPTORS



It is important to recognize that in prokaryotic cells the ETS is located in the plasma membrane

(Figure 6.7), and sometimes parts of it are located in the cell envelope (Figures 6.8A and 6.8B). By

contrast, in eukaryotic cells the ETS is located internally in special organelles called mitochondria (Figure 6.9). As a result, the prokaryotes that are endowed with appropriate oxidoreductases



FIGURE 6.7 Location of ETS in typical prokaryotes. Thin sections of (A) the gram-positive cell wall of

Bacillus subtilis and (B) the gram-negative cell wall of Escherichia coli. Both sections were prepared by

freeze substitution. OM, outer membrane; PM, plasma membrane; P, periplasmic gel containing peptidoglycan

located between the outer and plasma membranes. In both types of cells, the ETS is located in the plasma

membrane. The bars in (A) and (B) equal 25 nm. (From Beveridge TJ, Doyle RJ, Metal Ions and Bacteria,

Wiley, New York, 1989. With permission.)



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Oxidation

A



Bulk phase



Reduction



Bulk phase



+



X + e−



+



A + e−

Cyt



OM



99



X



OM



PP



PP



PM



ETS

0.5O2 + 2H+ + 2e−



(A)



ETS



PM

B



H2O

(B)



Cytosol



B+ + e−

Cytosol



FIGURE 6.8 Generalized diagrams of the ETS of gram-negative prokaryotes capable of oxidizing or reducing oxidizable or reducible constituents of insoluble minerals or dissolved electron donors or acceptors at their

cell surface–bulk phase interface by electron import or export, respectively. (A) Electron import (oxidation).

(B) Electron export (reduction). OM, outer membrane; PP, periplasm; PM, plasma membrane; ETS, electron

transport system in plasma membrane.



Mi



II



PM



Mi

M

PS



FIGURE 6.9 Location of ETS in eukaryotes. Cross section of a dormant conidium (spore) of Aspergillus

fumigatus, a fungus (×64,000). ETS is located in the mitochondria. Mi, mitochondria; PM, plasma membrane;

M, thin layer of electron-dense material; PS, polysaccharide storage material; II, membrane-bound storage

body. (Courtesy of Ghiorse WC, Department of Microbiology, Cornell University, Ithaca, NY, USA.)



(enzymes that transfer hydrogen atoms or electrons) in their cell surface are able to oxidize or reduce

insoluble inorganic substrates when these are in physical contact with the cell surface (Figures 6.8A

and 6.8B); in other words, these organisms can use insoluble, oxidizable or reducible inorganic substrates (e.g., minerals) as electron donors or terminal electron acceptors, respectively, in their respiration by importing or exporting electrons, respectively. In at least one instance, a bacterium known

as Geobacter sulfurreducens has been shown to facilitate electron transfer to the surface of Fe(III)

oxides via special pilli—protein filaments projecting from the cell surface (Reguera et al., 2005).



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Oxidoreductases in the cell envelope of some prokaryotes also enable these organisms to oxidize

dissolved electron donors or acceptors without first taking them into the cytosol. This avoids any

possible intracellular toxic effects from these dissolved electron donors or acceptors, or from the

intracellular accumulation of insoluble products resulting from the oxidation or reduction of these

electron donors or acceptors that cannot be readily expelled from the cell. Examples of insoluble inorganic substrates that can serve as electron donors or acceptors at the cell surface of some

prokaryotes are elemental sulfur, iron sulfide, iron(III) oxide, and manganese(IV) oxide.

In gram-negative bacteria, enzymes and electron carriers in the periplasmic space of the cell

envelope participate in the transfer of electrons in the appropriate direction between catalytic sites

in the outer membrane and the ETS in the plasma membrane. The details of the mechanism of electron transfer in gram-positive Bacteria and Archaea that oxidize or reduce electron donors or acceptors at their cell surface remain to be elucidated. Pham et al. (2008) found that the gram-positive

Brevibacillus sp. strain PTH1 in culture was able to export electrons to the anode of a microbial

fuel cell using acetate as electron donor in the presence of purified phenazine-1-carboxamide (PCN)

from Pseudomonas sp. CMR12a and rhamnolipids as biosurfactants. PCN appeared to serve as an

electron shuttle. Brevibacillus also appeared to be able to reduce goethite (FeOOH) under these

conditions, but only to a limited extent. The ability of phenazines to act as an electron shuttle

in electron export in gram-negative Pseudomonas chlororaphis PCL1391 and some other gramnegative bacteria was first shown by Hernandez et al. (2004).

Although most experimental evidence in support of electron transfer across the cell envelope

has so far been gathered from studies of gram-negative bacteria, such as Shewanella oneidensis

MR-1 and Geobacterr spp., which are able to respire anaerobically using ferric oxide or Mn(IV)

oxide as terminal electron acceptors (Myers and Myers, 1992; Lovley, 2000; review by Ehrlich,

2002), evidence for the presence of c-type cytochrome Cyc2 in the outer membrane of iron-grown

cells of A. ferrooxidans strain 33020 indicates that during Fe(II) oxidation by this organism, electrons are transferred from Fe(II) via this outer membrane cytochrome and rusticyanin and another

cytochrome in the periplasmic space to the ETS in the plasma membrane (Yarzábal et al., 2002 a,b,

2004; Appia-Ayme et al., 1999; see also Chapter 20). This electron transport mechanism probably

operates as well when these organisms oxidize insoluble metal sulfide minerals such as chalcocite

(Cu2S) and covellite (CuS) (see discussion in Chapter 20).

Eukaryotic cells are unable to enzymatically oxidize or reduce insoluble, oxidizable or reducible

substrates because their ETS is located on the inner membrane of the mitochondria (Figure 6.9), which

reside in the cytoplasm of these cells. Thus, the mitochondrial ETS, which is spatially removed from

the cell surface, lacks direct access to insoluble substrates (Ehrlich, 1978; Stryer, 1995; Schaechter

et al., 2006).



6.5.4



CATABOLIC REACTIONS: FERMENTATION



Fermentation is a catabolic process that involves energy conservation from a disproportionation

process in which part of the energy-yielding substrate is oxidized by the reduction of the remainder of the consumed substrate. No externally supplied terminal electron acceptor is involved in

the redox process. Glucose fermentation to lactic acid by the Embden–Meyerhoff pathway is a

typical example (Figure 6.10). Pairs of hydrogen atoms are removed in an oxidation step from an

intermediate metabolic product, glyceraldehyde 3-phosphate, resulting in the formation of 1,3diphosphoglycerate. The hydrogen pairs that are removed are transferred to pyruvate, thereby

reducing it to lactic acid. The source of pyruvate is the stepwise enzymatic transformation of the previously formed 1,3-diphosphoglycerate. A variant of this pathway leads to the formation of ethanol and

CO2. Other mechanisms of glucose fermentation that can lead to the formation of acetate include the

Entner–Doudoroff pathway, the pentose phosphate pathway, and the pentose phosphoketolase pathway

(Stryer, 1995; Schaechter et al., 2006). Recently, a new glycolytic pathway leading to the formation of

acetate and formate was discovered in the archeon Thermococcus zilligii (Xavier et al., 2000).



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