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CHAPTER 14
Metabolic
Diversity of
Microorganisms

© 2018 Pearson Education, Inc.

 I. Phototrophy

• 14.1 Photosynthesis and Chlorophylls

• 14.2 Carotenoids and Phycobilins

• 14.3 Anoxygenic Photosynthesis

• 14.4 Oxygenic Photosynthesis

© 2018 Pearson Education, Inc.

 14.1 Photosynthesis and Chlorophylls

• Photosynthesis is the conversion of light energy to

chemical energy.
• Phototrophs carry out photosynthesis.
• Most phototrophs are also autotrophs that use CO2 as
sole carbon source.
• Photoautotrophs use energy from light to reduce CO2 to
organic compounds.
• Photoheterotrophs are phototrophs that use organic
carbon as a carbon source.
• Photosynthesis originated in Bacteria.
• Photosynthesis also evolved in Eukarya.

© 2018 Pearson Education, Inc.

 14.1 Photosynthesis and Chlorophylls

• Photoautotrophy requires two sets of parallel

reactions.
• Light reactions produce ATP.
• Dark reactions reduce CO2 to cell material for growth.
• requires ATP and electrons (NADH or NADPH)
• NADH/NADPH requires an electron donor from the
environment (e.g., Water, H2S, H2).
• Oxygenic photosynthesis: Oxidation of H2O produces O2
(cyanobacteria).
• anoxygenic photosynthesis: all other phototrophic bacteria
(Figure 14.1)
• NADH/NADPH requires an electron donor from the
environment (e.g., Water, H2S, H2).

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.1
 14.1 Photosynthesis and Chlorophylls

• Photosynthesis requires light-sensitive pigments

called chlorophylls and bacteriochlorophylls that
absorb light energy.
• Chlorophyll and Bacteriochlorophyll
• tetrapyrroles with magnesium instead of iron in ring
• Several different types of chlorophyll exist, each with a
distinct absorption spectrum. (Figure 14.2)
• bacteriochlorophylls (Figure 14.3) found in anoxygenic
phototrophs
• Use of different pigments allows different phototrophs to
absorb different wavelengths and coexist in same
habitat.
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© 2018 Pearson Education, Inc. Figure 14.2
© 2018 Pearson Education, Inc. Figure 14.3
 14.1 Photosynthesis and Chlorophylls

• Reaction centers and antenna pigments

• Chlorophyll/bacteriochlorophyll is not free in the cell and
is found in photocomplexes containing proteins housed
within membranes.
• Reaction centers contain some pigments and participate
directly in energy conservation. (Figure 14.4)
• Antenna pigments surround and funnel light energy to
reaction centers.

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.4
 14.1 Photosynthesis and Chlorophylls

• Photosynthetic membranes, chloroplasts, and

chlorosomes
• Chlorophyll pigments and light-gathering apparatus are
located within special membranes.
• In eukaryotes, photosynthesis occurs in chloroplasts
(intracellular organelles containing thylakoids: sheet-like
membrane systems). (Figure 14.5)
• In prokaryotes, pigments are integrated into cytoplasmic
membrane: chromatophores or lamellae in purple bacteria,
thylakoids in cyanobacteria. (Figure 14.6)

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© 2018 Pearson Education, Inc. Figure 14.5
© 2018 Pearson Education, Inc. Figure 14.6
 14.1 Photosynthesis and Chlorophylls

• Photosynthetic membranes, chloroplasts, and

chlorosomes
• Chlorosomes capture low light intensities. (Figure 14.7)
• found in anoxygenic green sulfur bacteria, filamentous
green nonsulfur bacteria, and photosynthetic
Acidobacteria
• function as giant antenna systems
• contain bacteriochlorophyll in dense arrays
• transfers light energy through FMO protein
• Green bacteria grow at lowest light intensities.
• often found in deepest waters where light cannot support
other phototrophs
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© 2018 Pearson Education, Inc. Figure 14.7
 14.2 Carotenoids and Phycobilins

• Carotenoids
• most widespread accessory pigments
• hydrophobic, embedded in photosynthetic membrane
• example: β-carotene (Figure 14.8)
• typically yellow, red, brown, or green and absorb blue
light
• major carotenoids shown in Figure 14.9
• Some energy absorbed by carotenoids can be transferred
to a reaction center.
• function primarily as photoprotective agents, quenching
toxic oxygen species and preventing dangerous
photooxidation
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© 2018 Pearson Education, Inc. Figure 14.8
© 2018 Pearson Education, Inc. Figure 14.9
 14.2 Carotenoids and Phycobilins

• Phycobiliproteins and phycobilisomes

• Phycobiliproteins are main light-harvesting systems of
cyanobacteria and red algae chloroplasts.
• consist of red or blue-green tetrapyrroles called bilins bound
to proteins
• give characteristic colors (Figure 14.10)
• Phycoerythrin absorbs ~550 nm, phycocyanin absorbs
~620 nm, and allophycocyanin absorbs ~650 nm.
• Pigments are integrated into cytoplasmic membrane in
prokaryotes, into chromatophores or lamellae in purple
bacteria, and into thylakoids in cyanobacteria. (Figure 14.6)
• Phycobiliproteins assemble aggregates called
phycobilisomes that attach to thylakoids.
• allow cell to grow at lower light intensities
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© 2018 Pearson Education, Inc. Figure 14.10
 14.3 Anoxygenic Photosynthesis

• Electron flow in purple bacteria

• use a Q-type (quinone type) reaction center containing
three polypeptides (L, M, H) wound through photosynthetic
membrane several times with cytochrome c (Figure 14.11)
• L, M, and H bind the special pair of two bacteriochlorophyll
a molecules, two molecules of bacteriopheophytin a, two
quinones, and one carotenoid.
• Light energy is transferred to and excites special pair,
generating a strong electron donor.
• Electrons flow through a membrane from low E0' to high E0'
and generate proton motive force. (Figure 14.12)
• ATP synthesis called photophosphorylation
• Cyclic photophosphorylation: Electrons move within closed
loop; no net input or consumption.
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Figure 14.11
© 2018 Pearson Education, Inc. Figure 14.12
 14.3 Anoxygenic Photosynthesis

• Generation of reducing power

• For a purple bacterium to grow autotrophically, the
formation of ATP is not enough.
• Reducing power (NADH) is also necessary to reduce CO2
to cell material.
• Reducing power for purple bacteria comes from many
sources, especially sulfur compounds like H2S.
• requires reverse electron transport (against
electrochemical gradient) for NADH production in purple
phototrophs (Figure 14.13)
• also mechanism chemolithotrophs use to get reducing
power for CO2 fixation

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.13
 14.3 Anoxygenic Photosynthesis

• Photosynthetic electron flow in other anoxygenic

phototrophs
• Green sulfur bacteria, Acidobacteria, and Heliobacteria
use FeS-type reaction centers.
• Reverse electron flow is unnecessary in green sulfur
bacteria and Heliobacteria.
• Ferredoxin is critical for electron transfer.
• unclear whether electron transfer in green sulfur bacteria
and Heliobacteria is cyclic or noncyclic

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 14.4 Oxygenic Photosynthesis

• Oxygenic phototrophs use both FeS-type

(photosystem I, PS I, or P700) and Q-type reaction
centers (photosystem II, PSII, or P680).
• “Z scheme” of photosynthesis (Figure 14.14)
• Photosystem II transfers energy to photosystem I.
• In eukaryotes, occurs in chloroplast
• In cyanobacteria, occurs in stacked membranes in
cytoplasm

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© 2018 Pearson Education, Inc. Figure 14.14
 14.4 Oxygenic Photosynthesis
• Electron flow and ATP synthesis in oxygenic
photosynthesis
• PSII splits water into oxygen and electrons at water-
oxidizing complex. (Figure 14.15)
• Proton motive force generated by electron transport
through quinones and cytochromes (like aerobic
respiration).
• PSII transfers energy to PSI, terminating with reduction
of NADP+ to NADPH.
• 12 H+ translocated per O2 produced
• Noncyclic photophosphorylation: Electrons do not cycle
back and reduce NADP+ to NADPH.
• Cyclic photophosphorylation can occur if cell requires
less NADPH to produce more ATP.
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© 2018 Pearson Education, Inc. Figure 14.15
 14.4 Oxygenic Photosynthesis

• Anoxygenic photosynthesis in oxygenic

phototrophs
• If PSII is blocked, some oxygenic phototrophs can do
photosynthesis with just PSI.
• Cyclic photophosphorylation occurs exclusively.
• Reducing power for CO2 reduction comes from sources
other than water (H2S in cyanobacteria [Figure 14.16],
H2 in green algae).
• Anoxygenic photosynthesis must have been first on
Earth.
• Cyanobacteria evolved to connect PSI and PSII and use
H2O as an electron donor.
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Figure 14.16
 II. Autotrophy and N2 Fixation

• 14.5 Autotrophic Pathways

• 14.6 Nitrogen Fixation

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 14.5 Autotrophic Pathways
• Cells require carbon and nitrogen to form biomass.
• Atmospheric sources (CO2 and N2) must be
chemically reduced for assimilation (CO2 fixation
and N2 fixation).
• Requires ATP and reducing power
• Autotrophy: process by which CO2 is reduced and
assimilated into cells
• In phototrophs, autotrophy is often called the “dark
reactions.”
• In oxygenic photosynthesis, Calvin cycle reduces
CO2 to glyceraldehyde-3-phosphate.
• Many alternative pathways exist, reducing CO2 to
the central metabolite acetyl-CoA.
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 14.5 Autotrophic Pathways
• The Calvin cycle (Figure 14.17)
• found in purple bacteria, cyanobacteria, algae, green
plants, most chemolithotrophic Bacteria, few Archaea
• requires CO2, a CO2 acceptor, NADPH, ATP, ribulose
bisphophate carboxylase (RubisCO), and
phosphoribulokinase
• first step catalyzed by RubisCO, forming two molecules
3-phosphoglyceric acid (PGA) from ribulose bisphophate
and CO2
• PGA then phosphorylated and reduced to
glyceraldehyde-3-phosphate
• glucose formed by reversal of glycolysis
• easiest to consider cycle as six molecules of CO2
required to make one molecule of glucose (Figure 14.18);
12 NADPH and 18 ATP required
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© 2018 Pearson Education, Inc. Figure 14.17
© 2018 Pearson Education, Inc. Figure 14.18
 14.5 Autotrophic Pathways

• The Calvin cycle

• Carboxysomes: inclusions containing and improving
efficiency of RubisCO in many autotrophs (Figure 14.19)
• Inorganic carbon first incorporated as bicarbonate
(HCO3–), which is converted to CO2 by carbonic
anhydrase.
• CO2 cannot escape carboxysome.
• Carboxysome also protects RubisCO from O2, which
competes with CO2.

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.19
 14.5 Autotrophic Pathways

• The reverse citric acid cycle

• Also called reductive TCA cycle
• used by green sulfur bacteria (e.g., Chlorobium)
• CO2 reduced by reversal of steps in citric acid cycle
(Figure 14.20a)
• more efficient, requiring 4 NADH, 2 reduced
ferredoxins, 10 ATP
• requires some unique enzymes not found in citric acid
cycle (e.g., alpha-ketoglutarate synthase, pyruvate
synthase, citrate lyase, fumarate reductase)
• occurs in some chemoautotrophs (e.g., Thermoproteus,
Sulfolobus, Aquifex, Sulfurimonas)
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© 2018 Pearson Education, Inc. Figure 14.20
 14.5 Autotrophic Pathways
• Other pathways of CO2 fixation
• at least four other pathways known
• Chloroflexus uses the 3-hydroxypropionate bi-cycle to fix
CO2. (Figure 14.20b)
• may have been one of earliest mechanisms for autotrophy
• also found in several hyperthermophilic Archaea
• cyclic photophosphorylation: electrons move within closed
loop; no net input or consumption
• also 3-hydroxypropionate/4-hydroxybutyrate cycle and
dicarboxylate/4-hydroxybutyrate cycle (in Archaea)
• reductive acetyl-coenzyme A pathway found in obligate
anaerobes including methanogenic Archaea, acetogens,
Planctomyces
• most efficient: requires only six to eight ATP per
six CO2/1 glucose
• can be coupled directly to energy conservation
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 14.6 Nitrogen Fixation

• Nitrogen needed for proteins, nucleic acids, other

organics
• Only certain prokaryotes can form ammonia
(NH3) from gaseous dinitrogen (N2): nitrogen
fixation. (Table 14.1)
• Some nitrogen fixers are free-living, and others
are symbiotic (fixing only in association with
certain plants).
• No eukaryotes fix N2.

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© 2018 Pearson Education, Inc. Table 14.1
 14.6 Nitrogen Fixation

• Nitrogenase
• enzyme complex consisting of dinitrogenase and
dinitrogenase reductase
• Iron-molybdenum cofactor (FeMo-co) is where N2
reduction occurs. (Figure 14.21)
• Alternative nitrogenases lack molybdenum and contain
either vanadium (V) and iron or iron-only.
• inhibited by oxygen
• In obligate aerobes, nitrogenase is protected, for
example, by removal by respiration, oxygen-retarding
slime layers, anoxic heterocyst formation. (Figure 14.22)

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© 2018 Pearson Education, Inc. Figure 14.21
© 2018 Pearson Education, Inc. Figure 14.22
 14.6 Nitrogen Fixation

• Electron flow in nitrogen fixation (Figure 14.23)

• Triple bond stability makes activation and reduction very
energy demanding.
• Six electrons needed; eight actually consumed because
H2 must be produced.
• Electron donor → dinitrogenase reductase →
dinitrogenase →N2
• ATP required to lower reduction potential (total 16)

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© 2018 Pearson Education, Inc. Figure 14.23
 14.6 Nitrogen Fixation

• Assaying nitrogenase: Acetylene reduction

(Figure 14.24)
• Nitrogenases reduce other triply bonded compounds,
including acetylene, to form ethylene.
• Definitive proof requires 15N2 as tracer to form 15NH3.

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.24
 III. Respiratory Processes Defined by
Electron Donor
• 14.7 Principles of Respiration
• 14.8 Hydrogen (H2) Oxidation
• 14.9 Oxidation of Sulfur Compounds
• 14.10 Iron (Fe2+) Oxidation
• 14.11 Nitrification
• 14.12 Anaerobic Ammonia Oxidation (Anammox)

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 14.7 Principles of Respiration

• Energetics of respiration
• coupling of two redox half reactions
• The farther apart the half reactions are in terms of E0',
the greater the amount of energy released.
• Wide diversity of organic or inorganic electron donors
can be coupled to terminal electron acceptors.
(Figure 14.25 and Table 14.2)

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© 2018 Pearson Education, Inc. Figure 14.25
© 2018 Pearson Education, Inc. Table 14.2
 14.7 Principles of Respiration
• Aerobic and anaerobic respiration
• Anaerobic respirations use electron acceptors
other than O2.
• distinct from fermentation
• Fermentation does not require an external electron acceptor.
• ATP production in respiration is from proton motive force instead
of substrate-level phosphorylation.
• Anaerobic respiration yields less energy than aerobic
respiration because O2/H2O couple is most electropositive.
• Facultative aerobes can switch to alternative electron acceptors
if O2 is limiting (e.g., inorganic and organic compounds, Fe+3
and Mn+4).
• Anaerobes use electronegative electron acceptors (e.g., SO42-).
• Facultative aerobes can switch to alternative electron acceptors
if O2 is limiting (e.g., inorganic and organic compounds,
Fe+3 and Mn+4).
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 14.7 Principles of Respiration
• Assimilative and dissimilative reductions
• Biosynthetic reactions require ATP and reducing power.
• In cell, reducing power is typically NADH.
• Chemoorganotrophs readily generate NADH during
organic molecule oxidation.
• Reduction (assimilative reduction) of NO3–, SO42–, and
CO2 enables use as sources of N, S, and C for new cell
material (assimilation).
• consumes energy
• Most microbes do this.
• Reduction of these compounds during anaerobic
respiration is dissimilative reduction.
• conserves energy
• Product is a small molecule (e.g., N2, H2S, CH4) excreted.
• only found in microbes capable of anaerobic respiration
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 14.8 Hydrogen (H₂) Oxidation

• Chemolithotrophs conserve energy from the

oxidation of inorganic electron donors.
• Most are also autotrophs.
• Mixotrophs are chemolithotrophs that require
organic carbon as a carbon source.
• Hydrogenase and the energetics of H2 oxidation
• H2 + ½ O2 → H2O reaction is highly exergonic and can
be coupled to ATP synthesis.
• catalyzed by hydrogenase (Figure 14.26a)
• Some bacteria make two (cytoplasmic and membrane-
integrated) hydrogenases.
• Soluble hydrogenase binds H2 and reduces
NAD+ to NADH.
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© 2018 Pearson Education, Inc. Figure 14.26
 14.8 Hydrogen (H₂) Oxidation

• Autotrophy in H2 bacteria
• Most hydrogen bacteria can grow as chemoorganotrophs.
• In chemolithotrophic growth, CO2 fixed by Calvin cycle.
• Facultative chemolithotrophs: Repress synthesis of Calvin
cycle and hydrogenase enzymes when organics present
catalyzed by hydrogenase.
• H2-levels fleeting under oxic conditions
• Most H2 results from fermentation, which is anoxic.
• H2 is used up by anaerobic prokaryotes.

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 14.9 Oxidation of Sulfur Compounds

• Many reduced sulfur compounds are used as electron

donors by colorless (compared with green and purple) sulfur
bacteria.
• Chemolithotrophy discovered by Sergei Winogradsky
• Energetics of sulfur oxidation
• H2S, S0, S2O3– common; SO32– also possible (Table 14.2 and
Table 14.3)
• final oxidation product usually SO42–
• occurs in stages with first oxidation yielding S0, which can be
deposited inside cell as an energy reserve (Figure 14.27a)
• One product of sulfur oxidation is H+, which acidifies
surroundings, so many sulfur bacteria are acid tolerant or
acidophilic.
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© 2018 Pearson Education, Inc. Table 14.3
© 2018 Pearson Education, Inc. Figure 14.27
 14.9 Oxidation of Sulfur Compounds

• Biochemistry of sulfur oxidation: The Sox system

• Sox system oxidizes reduced sulfur compounds directly
to sulfate. (Figure 14.28)
• likely transferred by horizontal gene flow
• four key proteins: SoxXA, SoxYZ (carrier), SoxB, SoxCD
(sulfur dehydrogenase)
• Electrons are funneled into electron transport chain,
protons are released to and acidify environment.

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© 2018 Pearson Education, Inc. Figure 14.28
 14.9 Oxidation of Sulfur Compounds

• Other aspects of chemolithotrophic sulfur oxidation

• sulfur-oxidizing microbes that store sulfur granules lack
SoxCD (sulfur dehydrogenase)
• Sulfur can be transported to cytoplasm and oxidized to
SO32– and SO42–.
• Electrons eventually reach electron transport chain and
are transported through to O2.
• generates a proton motive force that leads to ATP
synthesis by ATPase
• Electrons for CO2 fixation come from reverse electron
transport, yielding NADH.
• Some species grow by anaerobic respiration using nitrate
as an electron acceptor (e.g., Thiobacillus denitrificans).

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 14.10 Iron (Fe²⁺) Oxidation

• Aerobic oxidation of ferrous iron (Fe2+) to ferric iron

(Fe3+) supports chemolithotrophic “iron bacteria.”
• Ferric hydroxide precipitates in water, driving down
pH (Figure 14.29).
• Many Fe oxidizers are strongly acidophilic.

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© 2018 Pearson Education, Inc. Figure 14.29
 14.10 Iron (Fe²⁺) Oxidation

• Iron-oxidizing bacteria
• Acidithiobacillus ferrooxidans and Leptospirillum
ferrooxidans grow autotrophically using ferrous iron as
low as pH 1, optimally at between 2 and 3.
• common in acid-polluted environments such as coal-
mining waters
• Ferroplasma (Archaea) grows at pH <0.
• at neutral pH, restricted to locations where Fe2+ is
transition from anoxic to oxic conditions (e.g., anoxic
groundwater springs)

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 14.10 Iron (Fe²⁺) Oxidation
• Energy from iron oxidation
• very electropositive reduction potential of Fe3+/Fe2+
at acidic pH
• Respiratory chain of A. ferrooxidans contains cytochromes,
rusticyanin (periplasmic copper-containing protein), and an
iron-oxidizing membrane protein. (Figure 14.30)
• Ferroplasma (Archaea) grows at pH <0.
• Ferrous iron oxidation begins in the outer membrane by outer
membrane cytochrome c that oxidizes Fe2+ and transfers
electrons into periplasm.
• Rusticyanin then reduces periplasmic cytochrome c; this
reduces cytochrome aa3, which in turn reduces O2 to H2O.
• ATP is synthesized by ATPases; protons consumed during
reduction of O2.

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© 2018 Pearson Education, Inc. Figure 14.30
 14.10 Iron (Fe²⁺) Oxidation

• Energy from iron oxidation

• Autotrophy in Acidithiobacillus ferrooxidans is driven by
the Calvin cycle.
• Energy must be consumed in reverse electron flow to
obtain NADH at expense of proton motive force.
• A. ferrooxidans must oxidize large amounts of Fe2+ to
produce cell material.

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 14.10 Iron (Fe²⁺) Oxidation

• Ferrous iron oxidation under anoxic conditions

• can be done by certain chemolithotrophs and
phototrophic purple and green bacteria (Figure 14.31)
• Fe2+ used either as an electro donor (chemolithotrophs)
or a reductant for CO2 fixation (phototrophs)
• NO3– → NO2– or N2 (chemolithotrophs) or Fe2+ or FeS →
Fe3+ + SO42– (phototrophs)

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© 2018 Pearson Education, Inc. Figure 14.31
 14.11 Nitrification

• Ammonia (NH3) and nitrite (NO2–) are oxidized by

chemolithotrophic nitrifying bacteria during
nitrification.
• Widely distributed in soil, water, wastewater, oceans
• Nitrification uses two sets of reactions: oxidation of
ammonia to nitrite and oxidation of nitrite to
nitrate (NO3–).
• Most nitrifiers can only catalyze one set of reactions
(e.g., Nitrosomonas and Nitrosopumilus are ammonia
oxidizers that oxidize ammonia to nitrite, Nitrobacter
are nitrite oxidizers that oxidize NO2– to NO3–).
• Certain Nitrospira can catalyze both, oxidizing
ammonia to nitrate.
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 14.11 Nitrification

• Bioenergetics and enzymology of ammonia and

nitrite oxidation
• Electron transport reactions establish proton motive
force for ATP synthesis.
• Complete oxidation involves transfer of eight electrons.
• Key enzymes are ammonia monooxygenase
(producing water and hydroxylamine; NH2OH), and
hydroxylamine oxidoreductase oxidizes NH2OH to
NO2–, removing four electrons. (Figure 14.32)

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© 2018 Pearson Education, Inc. Figure 14.32
 14.11 Nitrification

• Bioenergetics and enzymology of ammonia and

nitrite oxidation
• Nitrite oxidizers oxidize NO2– to NO3– with nitrite
oxidoreductase. (Figure 14.33)
• Electron transport reactions establish proton motive
force for ATP synthesis.
• only small energy yields from this reaction

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© 2018 Pearson Education, Inc. Figure 14.33
 14.11 Nitrification

• Carbon metabolism and ecology of nitrifying

bacteria
• Aerobic nitrifying Bacteria use Calvin cycle for
CO2 fixation.
• Most nitrite oxidizers can grow chemoorganotrophically
on glucose and a few other organics.
• Ammonia-oxidizing bacteria are either obligate
chemolithotrophs or mixotrophs.
• Autotrophy in ammonia-oxidizing Archaea is through a
variation of hydroxypropionate cycle.
• Nitrifiers play key roles in nitrogen cycle, sewage and
wastewater treatment, and water column of lakes.

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 14.12 Anaerobic Ammonia Oxidation
(Anammox)
• Anammox: anaerobic ammonia oxidation
• performed by unusual group of obligate anaerobic
bacteria
• NH4+ + NO2– → N2 + 2 H2O
• Brocadia anammoxidans is a Planctomycetes and a
major annamox organism.
• Planctomycetes are unusual because their cytoplasm
contains membrane-enclosed compartments. (Figure 14.34)
• In B. anammoxidans, this is the anammoxosome, where
anammox occurs.
• Several other annamox bacteria are related to Brocadia
and contain ammoxosomes.
• Anammox bacteria fix CO2 using reductive acetyl-CoA
pathway.
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© 2018 Pearson Education, Inc. Figure 14.34
 14.12 Anaerobic Ammonia Oxidation
(Anammox)
• The anammoxosome and Its reactions
• an “organelle”
• Membrane lipids consist of ladderane lipids that prevent
diffusion into cytoplasm.
• Membrane protects cell from toxic intermediates including
hydrazine (N2H4).
• NO2– first reduced to nitric oxide (NO) by nitrite reductase.
• NO reacts with NH4+ to form hydrazine by hydrazine synthase.
• Hydrazine dehydrogenase oxidizes hydrazine to form
N2 + electrons.
• Electron transport chain runs with cyclical electron transfer to
generate proton motive force for ATPases in anammoxosome
membrane.
• Nitrite oxidation provides reducing power for CO2 fixation.
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 14.12 Anaerobic Ammonia Oxidation
(Anammox)
• Ecology of anammox
• NO2– provided by aerobic ammonia-oxidizing
prokaryotes in ammonia-rich habitats including
sewage and wastewater.
• High levels of oxygen inhibit anammox and favor
nitrification.
• very beneficial in the treatment of sewage and
wastewater
• helps reduce input of fixed nitrogen from wastewater
treatment effluents into rivers and streams,
maintaining higher water quality

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 IV. Respiratory Processes Defined by Electron
Acceptor
• 14.13 Nitrate Reduction and Denitrification
• 14.14 Sulfate and Sulfur Reduction
• 14.15 Other Electron Acceptors

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 14.13 Nitrate Reduction and Denitrification

• Inorganic nitrogen compounds are some of the

most common electron acceptors in anaerobic
respiration. (Table 14.4)
• Nitrate (NO3–) can be reduced with two electrons
to nitrite or reduced further to nitric oxide, nitrous
oxide, or dinitrogen (denitrification). (Figure 14.35)
• Some nitrate reducers like Escherichia coli only
carry out the first step.
• Some organisms can reduce nitrite to ammonia in
a dissimilative process.

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© 2018 Pearson Education, Inc. Table 14.4
© 2018 Pearson Education, Inc. Figure 14.35
 14.13 Nitrate Reduction and Denitrification
• Denitrifying microorganisms and their ecological
activities
• Many are Proteobacteria and facultative aerobes (e.g.,
Pseudomonas).
• Many denitrifying bacteria reduce other electron
acceptors (e.g., Fe3+ and organics) anaerobically, and
some ferment.
• Some Archaea and one eukaryote (Globobulimina
pseudospinescens) denitrify.
• detrimental for agriculture because nitrate from
fertilizers is formed
• N2O is a greenhouse gas; NO consumes ozone, NO2–
is part of acid rain.
• beneficial in sewage treatment because fixed nitrogen
triggers algal growth
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 14.13 Nitrate Reduction and Denitrification

• Biochemistry of dissimilative nitrate reduction

• compare aerobic respiration, nitrate respiration, and
denitrification (Figure 14.36)
• first step catalyzed by nitrate reductase
• Synthesis of all enzymes is repressed by O2.
• Proton motive force is established for ATPase to
synthesize ATP.

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© 2018 Pearson Education, Inc. Figure 14.36
 14.14 Sulfate and Sulfur Reduction
• Inorganic sulfur compounds are important
electron acceptors in anaerobic respiration.
(Table 14.5)
• Reduction of SO42– to H2S is done by sulfate-
reducing bacteria (obligate anaerobic bacteria,
e.g., Desulfovibrio).
• Assimilative sulfate metabolism: incorporation of
sulfate for biosynthetic purposes to make
cysteine, methionine, and other organosulfur
compounds
• Dissimilative sulfate metabolism: use of sulfate
as an electron acceptor for energy conservation
and production of large amounts of H2S
© 2018 Pearson Education, Inc.
 14.14 Sulfate and Sulfur Reduction

• Biochemistry and energetics of sulfate reduction

• SO42– is energetically much less favorable as an
electron acceptor.
• If an electron donor is oxidized that yields NADH or
FADH2, sufficient free energy to make ATP is
available.
• H2 is used by nearly all species; some use organics
such as lactate and pyruvate (freshwater) or acetate
and longer-chain fatty acids (marine).
• Only archaeal sulfate-reducer is Archaeoglobus.

© 2018 Pearson Education, Inc.

 14.14 Sulfate and Sulfur Reduction

• Biochemistry and energetics of sulfate reduction

• Reduction of SO42– to H2S requires eight electrons and
many intermediates.
• SO42– must be activated by ATP sulfurylase to form
adenosine phosphosulfate (APS; Figure 14.37a).
• in dissimilative reduction, SO42– in APS reduced directly
to sulfite (SO32–) by APS reductase, releasing AMP
• in assimilative reduction, phosphate added to APS to
form phosphoadenosine phsophosulfate (PAPS), then
SO42– is reduced to sulfite
• Sulfite is reduced to H2S by sulfite reductase.
• In dissimilative reduction, electron transport generates
proton motive force.
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Figure 14.37
 14.14 Sulfate and Sulfur Reduction

• Biochemistry and energetics of sulfate reduction

• Hydrogenase plays central role.
• lactate converted through pyruvate to acetate with
production of H2
• H2 crosses membrane and is oxidized; electrons go back
into system and protons establish proton motive force.
• One ATP produced for each SO42– reduced to HS–.
• If lactate or pyruvate is electron donor, ATP is also
produced by substrate-level phosphorylation (oxidizing
pyruvate to acetate and CO2).
• Marine sulfate-reducers can couple sulfate reduction and
acetate oxidation via acetyl-CoA pathway.

© 2018 Pearson Education, Inc.

 14.14 Sulfate and Sulfur Reduction

• Special metabolisms of sulfate-reducing bacteria

• disproportionation (oxidation and reduction)
• Example: Desulfovibrio sulfodismutans disproportionates
thiosulfate to H2S and SO42– and establishes proton
motive force.
• phosphite oxidation
• Example: Phosphite oxidation and sulfate reduction form
phosphate and sulfide in Desulfotignum phosphitoxidans.
• examples: H2, organic compounds, phosphite

© 2018 Pearson Education, Inc.

 14.14 Sulfate and Sulfur Reduction

• Sulfur reduction
• Sulfur reducers are non-sulfate-reducing prokaryotes
that coexist with sulfate-reducing bacteria.
• Electrons come from H2 or organics (e.g., acetate
or ethanol).
• cannot activate sulfate to APS

© 2018 Pearson Education, Inc.

 14.15 Other Electron Acceptors

• Metal and metalloid reduction

• Fe3+ and Mn4+ most important
• Electrons travel from donor through electron transport
chain, generating proton motive force and terminating in
a metal reductase system forming Fe2+ or Mn2+.
• gram-negatives Shewanella and Geobacter
• Other inorganics can be electron acceptors (e.g.,
selenium, tellurium, arsenic, oxidized chlorine
compounds).
• Chlorate and perchlorate-reducing bacteria form Cl–.
• Desulfotomaculum can reduce arsenate (AsO43–) and
sulfate, forming orpiment (As2S3) and detoxifying arsenic
in biomineralization. (Figure 14.39)

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.39
 14.15 Other Electron Acceptors
• Organic electron acceptors
• most studied is fumarate (reduced to succinate)
• trimethylamine oxide (TMAO) and dimethyl
sulfoxide (DMSO)
• TMAO reduced to trimethylamine (TMA)
• DMSO reduced to dimethyl sulfide (DMS)
• halogenated organic compounds (reductive
dechlorination or dehalorespiration)
• Example: Desulfomonile reduces chlorobenzoate to
benzoate and hydrochloric acid.
• Example: Dehalobacter and Dehalococcoides oxidize H2
and reduce tetrachloroethylene to dichloroethylene and
ethene, respectively.
• Example: Dehalococcoides reduces polychlorinated
biphenyls (PCBs), which are widespread pollutants.

© 2018 Pearson Education, Inc.

 14.15 Other Electron Acceptors

• Proton reduction
• Pyrococcus furiosus
• species of Archaea
• grows optimally at 100°C on sugars; small peptides as
electron donors
• may have the simplest anaerobic respiration mechanism
(Figure 13.54)
• Organism uses modified glycolysis, forming
3-phosphoglyceric acid instead of 1,3-bisphosphoglyceric
acid. (Figure 14.40)
• Reaction is coupled to production of ferredoxin, pumping
protons across membrane via hydrogenase.

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.40
 V. One-Carbon (C1) Metabolism

• 14.16 Acetogenesis
• 14.17 Methanogenesis
• 14.18 Methanotrophy

© 2018 Pearson Education, Inc.

 14.16 Acetogenesis

• Acetogens and methanogens are strict

anaerobes that use CO2 as an electron acceptor
in anaerobic respiration.
• H2 is the major electron donor for both groups
of organisms.
• Acetogenesis and methanogenesis are linked to ion
pumps. (Figure 14.41)

© 2018 Pearson Education, Inc.

 14.16 Acetogenesis

• Organisms and pathway

• Acetogens carry out 4 H2 + H+ + 2 HCO3– →
CH3COO– + 4 H2O.
• Other electron donors include methanol, methoxylated
aromatics, other organics.
• Many acetogens can reduce nitrate and thiosulfate.
• Reduce CO2 to acetate by reductive acetyl-CoA
(Wood-Ljungdahl) pathway: major pathway in obligate
anaerobes. (Table 14.6)
• can grow chemoorganotrophically by fermentation or
chemolithotrophically and autotrophically through
reduction of CO2 with H2 to acetate
• Most acetogenic bacteria are gram-positive (especially
Clostridium and Acetobacterium).
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Table 14.6
 14.16 Acetogenesis

• The reductive Acetyl-CoA pathway and energy

conservation in acetogenesis
• Reductive acetyl-CoA pathway is not a cycle.
(Figure 14.42)
• Carbon monoxide (CO) dehydrogenase is key,
catalyzing CO2 + H2 → CO + H2O.
• CO becomes carbonyl carbon of acetate.
• Methyl originates from reduction of CO2 in reactions
requiring tetrahydrofolate, corrinoid iron-sulfur protein,
and acetyl-CoA synthase.
• Acetogens conserve energy by ion motive force
(Na+ or H+).

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.42
 14.16 Acetogenesis

• Flavin-based electron bifurcation (Figure 14.43)

• Endergonic reduction of reduced ferredoxin by a
hydrogenase is coupled to exergonic reduction of
NAD+ to NADH.
• used by many obligate anaerobes to generate
reduced ferredoxin
• essential in methanogens lacking cytochromes

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.43
 14.17 Methanogenesis

• Methanogenesis, the biological production of

methane, is catalyzed by strictly anaerobic
Archaea called methanogens.
• present in freshwater sediments, sewage sludge
digesters, bioreactors, animal intestines (Figure 14.44)
• Methanogenesis is also a form of anaerobic
respiration.

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.44
 14.17 Methanogenesis

• C1 carriers in methanogenesis
• Methanogenesis requires eight electrons added
two at a time.
• involves a complex series of biochemical reactions
that use novel coenzymes (Figure 14.45)
• C1 carriers carry C1 unit along path of enzymatic
reduction.
• Redox coenzymes donate electrons.

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.45
 14.17 Methanogenesis

• C1 carriers in methanogenesis
• Methanofuran is required for first step.
• Methanopterin resembles folic acid and carries C1
during intermediate steps.
• Coenzyme M is required for last step.
• Coenzyme F430 also required for last step but is not
a carrier.

© 2018 Pearson Education, Inc.

 14.17 Methanogenesis

• Redox coenzymes
• F420: Flavin derivative that resembles flavin
mononucleotide (FMN); oxidized form absorbs light at
420 nm and fluoresces blue-green (Figure 14.46)
• 7-mercaptoheptanoylthreonine phosphate (Coenzyme B)
required for terminal step catalyzed by methyl reductase
enzyme complex

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.46
 14.17 Methanogenesis

• Methanogenesis from CO2 + H2

• H2 is the major electron donor for methanogenesis.
(Figure 14.47)
• CO2 activated by methanofuran-containing enzyme and
reduced to formyl.
• formyl transferred to a methanopterin-containing enzyme;
dehydrated and reduced using F420.
• methyl transferred from methanopterin to a CoM-enzyme
• reduction of Methyl-CoM to methane involving
F430 and CoB
• regeneration of CoM and CoB through flavin-based
electron-bifurcation of H2

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.47
 14.17 Methanogenesis

• Methanogenesis from methyl compounds

and acetate
• Methanogens that reduce methylated compounds (e.g.,
Methanosarcina) typically have cytochromes, in contrast
to methanogens that use H2 + CO2.
• Methanol catabolized by donating methyl groups to form
CH3–corrinoid, then CH3–CoM, then methane.
(Figure 14.48)
• Acetate is activated to acetyl-CoA, then methyl is
transferred to corrinoid.

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.48
 14.17 Methanogenesis

• Autotrophy
• Methanogens use reductive acetyl-CoA pathway.
• Energy conservation in methanogenesis
• occurs via proton or sodium motive force
• no substrate-level phosphorylation
• ATP produced from sodium motive force generated
during methyl transfer.
• In acetate- and methanol-grown cells, energy
conservation linked to methyl reductase and proton
motive force. (Figure 14.49)

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.49
 14.18 Methanotrophy

• Methylotrophs oxidize methane and other C1

organic compounds as electron donors and carbon
sources during catabolism.
• Aerobic methane oxidation
• CH4 → CH3OH → CH2O → HCOO– → CO2
• Not all methylotrophs can use methane.
• Methanotrophs (e.g., Methylococcus capsulatus) are
methylotrophs that use CH4.
• The initial step in aerobic oxidation is catalyzed by
methane monooxygenase (MMO).
• CH4 is converted to CH3OH and H2O. (Figure 14.50)
• CH3OH converted to CO2 or to make new cell material
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Figure 14.50
 14.18 Methanotrophy

• C1 assimilation by aerobic methanotrophs

• serine pathway (Figure 14.51a)
• Acetyl-CoA is synthesized from CH2O (formaldehyde)
and CO2.
• needs two NADH and two ATP
• Ribulose monophosphate pathway (Figure 14.51b)
• All carbon derived from CH2O; no NADH needed.
• uses one ATP per glyceraldehyde-3-phosphate (G-3-P)
synthesized
• Reversal of glycolysis produces glucose.

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.51
 14.18 Methanotrophy

• Anaerobic oxidation of methane (AOM)

• can occur by an association (consortium) of two
organisms: sulfate-reducing bacterium (SRB) and
Archaea (ANME: anaerobic methanotroph)
• thrive in anoxic marine sediments
• coexist in spatially structured aggregates (Figure 14.52)
• ANME oxidizes CH4 by reversing methanogenesis and
transfers electrons to SRB by direct electron transfer,
which reduces SO42– to H2S.
• ANME also associate with denitrifying bacteria in
freshwater sediments.

© 2018 Pearson Education, Inc.

 14.18 Methanotrophy

• Intra-aerobic methanotrophy
• Methylomirabilis oxyfera (Figure 14.53)
• catalyzes AOM linked to NO2– as electron acceptor

• has all genes for aerobic oxidation of CH4 to CO2

• has most genes for denitrification

• reduces nitrite in a novel way: forms O2 from 2 NO →

N2 + O2 and uses O2 as CH4 electron acceptor

• O2 consumed immediately, keeping environment anoxic

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.53
 VI. Fermentation

• 14.19 Energetic and Redox Considerations

• 14.20 Lactic and Mixed-Acid Fermentations
• 14.21 Clostridial and Propionate Fermentations
• 14.22 Fermentations That Lack Substrate-Level
Phosphorylation
• 14.23 Syntrophy

© 2018 Pearson Education, Inc.

 14.19 Energetic and Redox Considerations

• Fermentations: Energy conservation occurs at

expense of other reactions (in contrast
to respiration).
• If terminal electron acceptors are absent from anoxic
habitats, fermentation catabolizes organic compounds.
(Figure 14.54)
• Energy-rich compounds and substrate-level
phosphorylation
• Energy-rich compounds contain an energy-rich
phosphate bond or coenzyme A. (Table 14.7)
• Formation during fermentation allows microbe to make
ATP by transferring the phosphate bond to ADP by
substrate-level phosphorylation.
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Figure 14.54
© 2018 Pearson Education, Inc. Table 14.7
 14.19 Energetic and Redox Considerations

• Redox balance and H2 and acetate production

• redox balance achieved by excretion of fermentation
products (acids, alcohols) as end products
• redox balance often facilitated by production of H2 and
activity of ferredoxin and hydrogenase or by the C1 fatty
acid formate. (Figure 14.55)
• H2 is a powerful electron donor never wasted in microbial
ecosystems.
• Acetate or other fatty acids conserve energy by allowing
the organism to do substrate-level phosphorylation via
coenzyme-A derivatives (e.g., acetyl-CoA to acetyl
phosphate).

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.55
 14.20 Lactic and Mixed-Acid Fermentations
• Fermentations are classified by either the substrate
fermented (e.g., amino acid) or the products formed (e.g.,
alcohol, mixed acid). (Table 14.8 and Table 14.9)
• Lactic acid fermentation
• Lactic acid bacteria are gram-positive nonsporulating bacteria
that produce lactic acid as major or sole fermentation product.
• Homofermentative yields lactic acid only and two
ATP/glucose.
• Heterofermentative yields lactate, ethanol, CO2 (Figure 14.56)
and one ATP/glucose.
• Difference is presence (homofermentative) or absence
(heterofermentative) of aldolase (from glycolysis).
• heterofermentative
• Phosphoketolase converts pentose phosphate to triose
phosphate and acetyl phosphate.
• Triose phosphate is converted to lactic acid and ATP.
• Acetyl phosphate is reduced by NADH to ethanol without ATP.
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Table 14.8
© 2018 Pearson Education, Inc. Table 14.9
© 2018 Pearson Education, Inc. Figure 14.56
 14.20 Lactic and Mixed-Acid Fermentations

• Entner–Doudoroff pathway
• variant of the glycolytic pathway
• Glucose 6-phosphate is converted to pyruvate and
glyceraldehyde 3-phosphate; G-3-P is catabolized
in glycolysis.
• yields half the ATP of glycolysis because pyruvate is
formed directly

© 2018 Pearson Education, Inc.

 14.20 Lactic and Mixed-Acid Fermentations

• Mixed-acid fermentations
• characteristic of enteric bacteria
• generate acetic, lactic, and succinic acids
• ethanol, CO2, and H2 also typically formed
• glycolysis used
• Some produce neutral products such as butanediol.
• formed with ethanol, CO2, H2 (Figure 14.57)

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.57
 14.21 Clostridial and Propionate Fermentations

• Clostridium species are obligately fermentative

anaerobes.
• Ferment sugars, amino acids, purines and
pyrimidines, and other compounds
• ATP synthesis from substrate-level
phosphorylations in glycolysis or hydrolysis of CoA
intermediates

© 2018 Pearson Education, Inc.

 14.21 Clostridial and Propionate Fermentations

• Sugar fermentation by Clostridium species

• “saccharolytic”
• produce butyric acid as major product
• Acetone and butanol can also be products (e.g.,
Clostridum acetobutylicum). (Figure 14.58)
• Pyruvate from glycolysis is split to acetyl-CoA, CO2, and
H2 by the “phosphoroclastic reaction.”
• Actual products influenced by duration and conditions.
• Synthesis of butyrate produces extra ATP.

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.58
 14.21 Clostridial and Propionate Fermentations
• Amino acid fermentation by Clostridium species and
the Stickland reaction
• Proteolytic clostridia degrade proteins released from dead
organisms.
• Some ferment individual amino acids to yield a fatty acid-CoA
derivative, then produce ATP via substrate-level
phosphorylation.
• also produce ammonia (NH3) and CO2
• Some ferment amino acid pairs, with one amino acid as
electron donor and other as acceptor.
• Stickland reaction: coupled amino acid fermentation
(Figure 14.59)
• Products are NH3, CO2, and a carboxylic acid with one fewer
carbon than the oxidized amino acid.
• Purines and pyrimidines lead to many of the same
fermentation products.
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Figure 14.59
 14.21 Clostridial and Propionate Fermentations

• Clostridium kluyveri fermentation

• “caproate/butyrate” fermentation of ethanol (electron
donor) plus acetate (acceptor)
• low ATP yield but unique ability
• This is a secondary fermentation (fermentation of
fermentation products).

© 2018 Pearson Education, Inc.

 14.21 Clostridial and Propionate Fermentations

• Propionic acid fermentation (Figure 14.60)

• Gram-positive Propionibacterium and related bacteria
produce propionic acid as a major fermentation product
from glucose or lactate.
• in nature, lactate probably the major substrate because
lactic acid bacteria and Propionibacterium live in close
association
• important in ripening of Emmental (Swiss) cheese
• pyruvate (from glycolysis of lactate oxidation) converted
to acetate + CO2 or propionate
• Oxidative phosphorylation also occurs.

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.60
 14.22 Fermentations That Lack Substrate-Level
Phosphorylation
• Fermentations of certain compounds do not yield
sufficient energy to synthesize ATP.
• Catabolism is linked to ion pumps that establish a
membrane gradient.
• Propionigenium modestum
• catabolizes succinate under strictly anoxic conditions
• insufficient energy for ATP synthesis by substrate-level
phosphorylation
• pumps sodium ion (Na+) from cytoplasm to periplasm
(sodium motive force)
• Sodium-translocating ATPase forms ATP.
(Figure 14.61a)
• Malonomonas and Sporomusa decarboxylate malonate
and form sodium motive force.
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Figure 14.61
 14.22 Fermentations That Lack Substrate-Level
Phosphorylation
• Oxalobacter formigenes
• catabolizes C2 oxalate, producing formate + CO2
• Formate is excreted from the cell.
• Export of formate from the cell establishes a proton
motive force.
• Proton motive force forms ATP. (Figure 14.61b)

© 2018 Pearson Education, Inc.

 14.22 Fermentations That Lack Substrate-Level
Phosphorylation
• What can be learned from the decarboxylations of
succinate and oxalate?
• decarboxylation-type fermentations from ATP without
substrate-level phosphorylation or electron transport-
fueled oxidative phosphorylation
• Pumping one ion enables ATP synthesis.

© 2018 Pearson Education, Inc.

 14.23 Syntrophy
• Syntrophy: Two different microbes cooperate to
degrade a substance neither can degrade alone.
• Most syntrophic reactions are secondary
fermentations.
• H2 consumption in syntrophy: The metabolic link
• Table 14.10: syntrophs and compounds
• Major compounds are fatty acids and alcohols.
• Most reactions are based on interspecies H2 transfer.
• H2 production by one partner is linked to H2 consumption
by the other.
• example: Fermentation of ethanol to acetate plus H2 by
Pelotomaculum coupled to methane production
(Figure 14.62)
• example: Oxidation of butyrate to acetate plus H2 by
Syntrophomonas (Figure 14.63a)
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Figure 14.62
© 2018 Pearson Education, Inc. Figure 14.63
 14.23 Syntrophy

• Energetics of H2 transfer
• H2 consumption shifts equilibrium toward product
formation, allowing the reaction to be exothermic.
• also possible to have syntrophic associations that only
transfer electrons, such as CH4 consumption by ANME-
sulfate reducer consortium

© 2018 Pearson Education, Inc.

 14.23 Syntrophy

• Energetics in syntrophs
• substrate-level and oxidative phosphorylation
• Many syntrophs also carry out anaerobic respiration by
disproportionation of unsaturated fatty acids (e.g.,
crotonate oxidized to acetate and reduced to butyrate by
Syntrophomonas).
• Syntrophic bacteria have very marginal energy economy.

© 2018 Pearson Education, Inc.

 14.23 Syntrophy

• Ecology of syntrophs
• key links in anoxic steps of carbon cycle
• Under oxic conditions or when alternative electron
acceptors are abundant, syntrophy is unnecessary.
• Characteristic of anoxic catabolism when
methanogenesis or acetogenesis is the terminal process
(e.g., wastewater biodegradation).

© 2018 Pearson Education, Inc.

 VII. Hydrocarbon Metabolism

• 14.24 Aerobic Hydrocarbon Metabolism

• 14.25 Anaerobic Hydrocarbon Metabolism

© 2018 Pearson Education, Inc.

 14.24 Aerobic Hydrocarbon Metabolism
• Oxygenases and aliphatic hydrocarbon oxidation
• Oxygenases catalyze the incorporation of O2 into organic
(and some inorganic) compounds.
• two classes
• dioxygenases: incorporate both oxygen atoms
• monooxygenases: incorporate one oxygen atom with second
reduced to H2O; usually NADH or NADPH-dependent
• In initial oxidation, an O atom is incorporated, usually at a
terminal carbon. (Figure 14.64a)
• End product is a fatty acid the same length as original
hydrocarbon.
• Fatty acid is oxidized by beta-oxidation, forming NADH,
acetyl-CoA, and a new fatty acid two carbons shorter.
• Acetyl-CoA is oxidized through citric acid cycle or used to
make new cell material.
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Figure 14.64
 14.24 Aerobic Hydrocarbon Metabolism
• Aromatic hydrocarbon oxidation
• Typically starts with catechol or structurally related
compound formation via oxygenases. (Figure 14.65)
• Catechol is cleaved and degraded into compounds that
can enter the citric acid cycle.
• Several steps require oxygenases.
• typically oxidized completely to CO2 with electrons
entering electron transport or used to make new cell
material

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.65
 14.25 Anaerobic Hydrocarbon Metabolism
• Aliphatic hydrocarbons
• straight-chain saturated or unsaturated organic
compounds
• Many are substrates for denitrifying and sulfate-reducing
bacteria.
• anoxic hexane metabolism in denitrifying bacteria
well-studied
• appears to be the same for longer chains and other
electron acceptors
• Hexane is modified on carbon atom 2 with fumarate,
forming 1-methylpentylsuccinate. (Figure 14.66a)
• Coenzyme A added and beta-oxidation occurs.
• proton motive force generated and consumed in nitrate or
sulfate reduction
© 2018 Pearson Education, Inc.
© 2018 Pearson Education, Inc. Figure 14.66
 14.25 Anaerobic Hydrocarbon Metabolism

• Aromatic hydrocarbons
• can be degraded by nitrate, ferric iron, and sulfate-
reducing bacteria
• oxygen added by addition of fumarate
• yields benzoyl-CoA, which is degraded by ring reduction
• Multi-ringed hydrocarbons are oxygenated by addition of
CO2 to form carboxylic acid derivative.
• Anaerobic degradation of aromatics occurs via ring
reduction (conversion to benzoate followed by ring
cleavage and benzoyl-CoA pathway). (Figure 14.67)

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc. Figure 14.67