Lecture 3

Microbial Metabolism
 Microbial Metabolism
• Is the means by which a microbe obtains the
energy and nutrients (e.g. carbon) it needs to
live and reproduce.
• Microbes use many different types of
metabolic strategies & species can often be
differentiated from each other based on
metabolic characteristics.
 Microbial Metabolism Cont…
• The specific metabolic properties of a microbe
are the major factors in determining that
microbe's ecological niche & often allow for
that microbe to be useful in industrial process
or responsible for biogeochemical cycles.
 Microbial Metabolism
• All microbial metabolisms can be arranged
according to three principles:
• 1. How the organism obtains carbon for
synthesizing cell mass:
– Autotrophic - carbon is obtained from carbon
dioxide (CO2)
– Heterotrophic - carbon is obtained from organic
cpds
– Mixotrophic - carbon is obtained from both
organic cpds & by fixing carbon dioxide
 Microbial metabolism
• 2. How the organism obtains reducing equivalents used
either in energy conservation or in biosynthetic reactions:
– Lithotrophic - reducing equivalents are obtained from inorganic
cpds.
– Organotrophic - reducing equivalents are obtained from organic
compounds

• 3. How the organism obtains energy for living & growing:

• Chemotrophic - energy is obtained from external chemical
cpds.
• Phototrophic - energy is obtained from light
 Microbial Metabolism cont…
• In practice, the terms are almost freely
combined. Typical examples are as follows:
• chemolithoautotrophs obtain energy from the
oxidation of inorganic compounds and carbon
from the fixation of carbon dioxide. Examples:
Nitrifying bacteria, Sulfur-oxidizing bacteria,
Iron-oxidizing bacteria, Knallgas-bacteria
 Microbial Metabolism cont…
• photolithoautotrophs obtain energy from light
and carbon from the fixation of carbon dioxide,
using reducing equivalents from inorganic
compounds
• Examples:
– Cyanobacteria (water (H2O) as reducing equivalent
donor)
– Chlorobiaceae, Chromatiaceae (hydrogen sulfide
(H2S) as reducing equivalent donor)
– Chloroflexus (hydrogen (H2) as reducing equivalent
donor)
 Microbial Metabolism cont…
• chemolithoheterotrophs obtain energy from the
oxidation of inorganic compounds, but cannot fix
carbon dioxide (CO2)
• Examples:
– some Thiobacilus,
– some Beggiatoa,
– some Nitrobacter spp.,
– Wolinella (with H2 as reducing equivalent donor),
– some Knallgas-bacteria,
– some sulfate-reducing bacteria
 Microbial Metabolism cont…
• chemoorganoheterotrophs obtain energy,
carbon, and reducing equivalents for
biosynthetic reactions from organic
compounds
• Examples: most bacteria, e. g. Escherichia coli,
Bacillus spp., Actinobacteria
 Microbial Metabolism cont…
• photoorganoheterotrophs obtain energy from
light, carbon and reducing equivalents for
biosynthetic reactions from organic compounds.
Some species are strictly heterotrophic, many
others can also fix carbon dioxide and are
mixotrophic. Examples: Rhodobacter,
Rhodopseudomonas, Rhodospirillum,
Rhodomicrobium, Rhodocyclus, Heliobacterium,
Chloroflexus(alternatively to
photolithoautotrophy with hydrogen)
Heterotrophic microbial metabolism
• Most microbes are heterotrophic (more
precisely chemoorganoheterotrophic), using
organic compounds as both carbon and
energy sources
• Heterotrophic microbes live off of nutrients
that they scavenge from living hosts (as
commensals or parasites) or find in dead
organic matter of all kind (saprophages)
 Heterotrophic microbial metabolism

• Many eukaryotic microorganisms are

heterotrophic by predation or parasitism

• Properties also found in some bacteria such as

Bdellovibrio (an intracellular parasite of other
bacteria, causing death of its victims) &
Myxobacteria such as Myxococcus (predators
of other bacteria)
 Heterotrophic microbial metabolism

• Most pathogenic bacteria can be viewed as

heterotrophic parasites of humans or the
other eukaryotic species they affect

• Heterotrophic microbes are extremely

abundant in nature and are responsible for
the breakdown of large organic polymers such
as cellulose, chitin or lignin which are
generally indigestible to larger animals
 Heterotrophic microbial metabolism

• Biochemically, prokaryotic heterotrophic

metabolism is much more versatile than that
of eukaryotic organisms
• However, many prokaryotes share the most
basic metabolic models with eukaryotes, e. g.
a) using glycolysis (also called EMP pathway) for
sugar metabolism
b) the citric acid cycle to degrade acetate,
producing energy in the form of ATP and reducing
power in the form of NADH or quinols
 Fermentation
• Fermentation is a specific type of heterotrophic
metabolism that uses organic carbon instead of
oxygen as a terminal e- acceptor

• Means that these organisms do not use an e-

transport chain to oxidize NADH to NAD+
& therefore must have an alternative method of
using this reducing power and maintaining a
supply of NAD+ for the proper functioning of
normal metabolic pathways (e.g. glycolysis)
 Fermentation cont…
• Fermentative organisms are anaerobic

• Many organisms can use fermentation under

anaerobic conditions & aerobic respiration
when oxygen is present. Such organisms are
called facultative anaerobes
 Fermentation cont…
• To avoid the overproduction of NADH,
obligately fermentative organisms do not have
a complete citric acid cycle

• Instead of using an ATP synthase as in

respiration, ATP in fermentative organisms is
produced by substrate-level phosphorylation
where a phosphate group is transferred from
a high-energy organic cpd to ADP to form ATP
 Fermentation cont…
• As a result of the need to produce high energy
phosphate-containing organic cpds (in the form of
Coenzyme A-esters) fermentative organisms use NADH
& other cofactors to produce many different reduced
metabolic by-products, often including hydrogen gas
(H2)

• These reduced organic compounds are generally small

organic acids & alcohols derived from pyruvate, the
end product of glycolysis. Examples include ethanol,
acetate, lactate, & butyrate
 Fermentation cont…
• Not all fermentative organisms use substrate-
level phosphorylation

• Instead, some organisms are able to couple the

oxidation of low-energy organic cpds directly to
the formation of a proton (or sodium) motive
force and therefore ATP synthesis
• Examples of these unusual forms of fermentation
include succinate fermentation by
Propionigenium modestum and oxalate
fermentation by Oxalobacter formigenes
 Fermentation cont…
• Humans and other higher animals also use
fermentation to produce lactate from excess NADH,
although this is not the major form of metabolism as it
is in fermentative microorganisms
• Fermentative organisms are very important industrially
and are used to make many different types of food
products
• The different metabolic end products produced by
each specific bacterial species are responsible for the
different tastes and properties of each food
 Special metabolic properties

– Methylotrophy
– Methanogenesis
– Sulfate reduction
– Nitrogen fixation
– Sulfur compounds (H2S, S0, etc.)
– Syntrophy
– Ferrous iron (Fe ) 2+

– Ammonia (NH ) or nitrite (NO)

3

– Hydrogen (H )2

– Sulfur compounds (H2S, S0, etc.)

 Special metabolic properties
Methylotrophy
• Methylotrophy refers to the ability of an
organism to use C1-compounds as energy
sources
• These compounds include methanol, methyl
amines, formaldehyde, and formate
• Several other less common substrates may also
be used for metabolism, all of which lack carbon-
carbon bonds
• Examples of methylotrophs include the bacteria
Methylomonas and Methylobacter
 Special metabolic properties
Methylotrophy
• Methanotrophs are a specific type of
methylotroph that are also able to use methane
(CH4) as a carbon source by oxidizing it
sequentially to methanol (CH3OH),
formaldehyde), formate (HCOO−), and carbon
dioxide CO2 initially using the enzyme methane
monooxygenase
• As oxygen is required for this process, all
(conventional) methanotrophs are obligate
aerobes
 Special metabolic properties
Methylotrophy
• Methylotrophs and methanotrophs are not
autotrophic, because they are able to
incorporate some of the oxidized methane (or
other metabolites) into cellular carbon before
it is completely oxidized to CO2 (at the level of
formaldehyde), using either the serine
pathway (Methylosinus, Methylocystis) or the
ribulose monophosphate pathway
(Methylococcus), depending on the species of
methylotroph
 Special metabolic properties
Methylotrophy

• In addition to aerobic methylotrophy,

methane can also be oxidized anaerobically.
This occurs by a consortium of sulfate-
reducing bacteria and relatives of
methanogenic Archaea working
syntrophically
 Special metabolic properties
Methylotrophy
• Methanogenesis is the biological production of
methane
• It is carried out by methanogens, strictly anaerobic
Archaea such as Methanococcus, Methanocaldococcus,
Methanobacterium, Methanothermus,
Methanosarcina, Methanosaeta and Methanopyrus
• The biochemistry of methanogenesis is unique in
nature in its use of a number of unusual cofactors to
sequentially reduce methanogenic substrates to
methane, such as coenzyme M and methanofuran
 Syntrophy
• Syntrophy, in the context of microbial
metabolism, refers to the pairing of multiple
species to achieve a chemical reaction that,
on its own, would be energetically
unfavorable. The best studied example of this
process is the oxidation of fermentative end
products (such as acetate, ethanol and
butyrate) by organisms such as
Syntrophomonas
 Anaerobic respiration
• While aerobic organisms during respiration use oxygen
as a terminal electron acceptor, anaerobic organisms
use other electron acceptors
• These inorganic cpds have a lower reduction potential
than O2, meaning that respiration is less efficient in
these organisms and leads to slower growth rates than
aerobes.

• Many facultative anaerobes use either O2 or alternative

terminal e- acceptors for respiration depending on the
environmental conditions
 Denitrification
• Most respiring anaerobes are heterotrophs,
although some do live autotrophically

• Assimilative pathways for many forms of

anaerobic respiration are also known;
Denitrification — nitrate as electron acceptor
 Denitrification
• Denitrification is the utilization of nitrate (NO−3)
as a terminal electron acceptor
• It is a widespread process that is used by many
members of the Proteobacteria
• Many facultative anaerobes use denitrification
because nitrate, like oxygen, has a high reduction
potential
• Many denitrifying bacteria can also use ferric iron
(Fe3+) and some organic electron acceptors
 Denitrification
• Complete denitrification is an environmentally
significant process because some intermediates
of denitrification (nitric oxide and nitrous oxide)
are important greenhouse gases that react with
sunlight and ozone to produce nitric acid, a
component of acid rain
• Denitrification is also important in biological
wastewater treatment where it is used to reduce
the amount of nitrogen released into the
environment thereby reducing eutrophication
 Sulfate reduction — sulfate as
electron acceptor
• Sulfate reduction is a relatively energetically poor
process used by many Gram negative bacteria
found within the δ-Proteobacteria, Gram-positive
organisms relating to Desulfotomaculum or the
archaeon Archaeoglobus. Hydrogen sulfide (H2S)
is produced as a metabolic end product. For
sulfate reduction electron donors and energy are
needed
• Many sulfate reducers are organotrophic, using
carbon cpds such as lactate & pyruvate (among
many others) as electron donors
 Acetogenesis — carbon dioxide as
electron acceptor
• Acetogenesis is a type of microbial metabolism
that uses hydrogen (H2) as an e- donor & CO2 as
an e- acceptor to produce acetate, the same e-
donors & acceptors used in methanogenesis (see
above). Bacteria that can autotrophically
synthesize acetate are called homoacetogens.
CO2 reduction in all homoacetogens occurs by the
acetyl-CoA pathway
• This pathway is also used for carbon fixation by
autotrophic sulfate-reducing bacteria and
hydrogenotrophic methanogens
 Ferric iron (Fe3+)
• Ferric iron (Fe3+) is a widespread anaerobic terminal
electron acceptor both for autotrophic and heterotrophic
organisms
• Electron flow in these organisms is similar to those in
electron transport, ending in oxygen or nitrate, except that
in ferric iron-reducing organisms the final enzyme in this
system is a ferric iron reductase.
• Model organisms include Shewanella putrefaciens and
Geobacter metallireducens. Since some ferric iron-reducing
bacteria (e.g. G. metallireducens) can use toxic
hydrocarbons such as toluene as a carbon source, there is
significant interest in using these organisms as
bioremediation agents in ferric iron-rich contaminated
aquifers
 Metabolism
• Microbial growth requires the polymerization of
biochemical building blocks into proteins, nucleic acids,
polysaccharides, and lipids.
• The building blocks must come preformed in the growth
medium or must be synthesized by the growing cells.
• Additional biosynthetic demands are placed by the
requirement for coenzymes that participate in enzymatic
catalysis.
• Biosynthetic polymerization reactions demand the transfer
of anhydride bonds from ATP.
• Growth demands a source of metabolic energy for the
synthesis of anhydride bonds & for the maintenance of
trans-membrane gradients of ions & metabolites
 Focal Metabolites
• The biosynthetic origins of building blocks &
co-enzymes can be traced to relatively few
precursors, called focal metabolites e.g.
a. Glucose-6-phosphate
b. Phosphoenolpyruvate
c. Oxaloacetate
d. Αlpha-ketoglutarate
They give rise to most biosynthetic end products
 Focal Metabolites
• Glucose 6-Phosphate & Carbohydrate Inter-
conversions; (see charts)
 Focal Metabolites
• Phosphoenolpyruvate (see charts)
 Focal Metabolites
• Oxaloacetate (see charts)
 Focal Metabolites
• Αlpha-ketoglutarate (see charts)
 Four General Categories of Microbial
Metabolism
1. Assimilatory pathways for the formation of
focal metabolites,
2. Pathways for the inter-conversion of focal
metabolites,
3. Biosynthetic sequences for the conversion of
focal metabolites to end products, and
4. Pathways that yield metabolic energy for
growth & maintenance.
 The Principle that Determines
Metabolic Pathways
• The primary principle that determines metabolic
pathways is that they are achieved by organizing
relatively few biochemical type reactions in a specific
order.
• Enzymes tend to be called into play only when their
catalytic activity is demanded.
• The activity of an enzyme may be changed by varying
either the amt of enzyme or the amt of substrate.
• In some cases, the activity of enzymes may be altered
by the binding of specific effectors, metabolites that
modulate enzyme activity.
 Synthesis of Macromolecules
• When provided with building blocks & a source of
metabolic energy, a cell synthesizes macromolecules.
• The sequence of building blocks within a
macromolecule is determined in one of two ways.
– In nucleic acids and proteins, it is template-directed: DNA
serves as the template for its own synthesis & for the
synthesis of the various types of RNA;
– Messenger RNA serves as the template for the synthesis of
proteins.
– In carbohydrates & lipids, on the other hand, the
arrangement of building blocks is determined entirely by
enzyme specificities.
 The Assemble of Macromolecules
• Once the macromolecules have been
synthesized, they self-assemble to form the
supra-molecular structures of the cell, e.g.
ribosomes, membranes, cell wall, flagella &
pili.
 Biosynthesis Balance
• The rate of macromolecular synthesis & the
activity of metabolic pathways must be
regulated so that biosynthesis is balanced.
• All of the components required for
macromolecular synthesis must be present for
orderly growth
• Control must be exerted so that the resources
of the cell are not expended on products that
do not contribute to growth or survival.