CHAPTER-5

MICROBIAL METABOLISM
Microbial growth is essential for soil ecosystem
function.

Microbial growth in soil is transitory and depends on

the availability of nutrients and adequate
physiochemical conditions.

Different conditions of nutrient availability occur in

soil and, as a result, different growth strategies are
required.
For example, under dry surface soil conditions,
biodegradable nutrients (fecal material, animal
and microbial corpses, plant residues, seeds
and fruits) might accumulate because there is
insufficient water to support microbial activity.
Upon the return of water, a flush of rapid microbial
growth occurs.
This is in contrast to the rhizosphere where a more
consistent supply of nutrients is available or with
the large pool of less labile soil organic matter,
or humus, which can be digested only by
microorganisms equipped with the enzymes
necessary to attack these complex substrates.
Mathematical Concepts of Microbial Growth
Under favourable environmental conditions of
initially nonlimiting nutrients, microbial growth
proceeds through various phases:

• 1. Lag Phase
• 2. Log Phase
• 3. Stationary Phase
• 4. Death Phase
Lag phase:
• Bacteria are first introduced into an environment
or media
• Bacteria are “checking out” their surroundings
• cells are very active metabolically
• # of cells changes very little
• 1 hour to several days
Log phase:
• Rapid cell growth (exponential growth)
• population doubles every generation
• microbes are sensitive to adverse conditions
– antibiotics
– anti-microbial agents
Stationary Phase:
• Death rate = rate of reproduction
• cells begin to encounter environmental stress
– lack of nutrients
– lack of water
– not enough space
– metabolic wastes
– oxygen
– pH
Death Phase:
• Death rate > rate of reproduction
• Due to limiting factors in the environment

During the unlimited growth phase, cell numbers

increase exponentially or double per constant
interval of time.
This time interval is referred to as doubling time, or
generation time (often abbreviated as td).
An Overview of Microbial Metabolism:

Metabolism - all of the chemical reactions

within a living organism
- The processes of
catabolism and anabolism

In discussing metabolic diversity, a central concept

is that the over all goal of all forms of
metabolism is essentially the same;
to obtain energy or carbon in the production of
cellular constituents necessary for growth,
survival and reproduction.
Catabolism ( Catabolic )
– breakdown of complex organic molecules
into simpler compounds
– releases ENERGY
The processes by which a living organism
obtains its energy and raw materials from
nutrients

Anabolism ( Anabolic )
– the building of complex organic molecules
from simpler ones
– requires ENERGY
The processes by which energy and raw
materials are used to build macromolecules
and cellular structures (biosynthesis)
Biochemical reactions in metabolism may
be of two types:

Exergonic: which yield energy

Exergonic reactions result in the production
energy needed to support cellular processes.
They are often referred to as “spontaneous”
because, given the proper conditions, they can
be sustained without the addition of external
energy.
 Endergonic: which consume energy
Enderognic activities result in the biosynthesis of
cellular components and microbial biomass.
These reactions are not spontanous and require a
supply of energy from exergonic reactions to
proceed.

Metabolism involves both types of reactions and is

a highly integrated and interdependent system.
Some Important Basic Concepts
• Reduction and Oxidation
a) An atom becomes more reduced when it
undergoes a chemical reaction in which
it
• Gains electrons
• By bonding to a less electronegative atom
• And often this occurs when the atom
becomes bonded to a hydrogen
b) An atom becomes more oxidized when it
undergoes a chemical reaction in which
it
• Loses electrons
• By bonding to a more electronegative atom
• And often this occurs when the atom
becomes bonded to an oxygen
c) In metabolic pathways, we are often
concerned with the oxidation or reduction of
carbon.
d) Reduced forms of carbon (e.g.
hydrocarbons, methane, fats,
carbohydrates, alcohols) carry a great deal
of potential chemical energy stored in their
bonds.
e) Oxidized forms of carbon (e.g. ketones,
aldehydes, carboxylic acids, carbon dioxide)
carry very little potential chemical energy in
their bonds.
f) Reduction and oxidation always occur
together.
In a reduction-oxidation reaction (redox
reaction), one substance gets reduced, and
another substance gets oxidized.
The thing that gets oxidized is called the
electron donor, and the thing that gets
reduced is called the electron acceptor.
Enzymatic Pathways for Metabolism
– Metabolic reactions take place in a step-
wise fashion in which the atoms of the raw
materials are rearranged, often one at a
time, until the formation of the final product
takes place.
– Each step requires its own enzyme.
– The sequence of enzymatically-catalyzed
steps from a starting raw material to final
end products is called an enzymatic
pathway (or metabolic pathway)
Cofactors for Redox Reactions
– Enzymes that catalyze redox reactions
typically require a cofactor to “shuttle”
electrons from one part of the metabolic
pathway to another part.
– There are two main redox cofactors:
– NAD and FAD.
– These are (relatively) small organic
molecules in which part of the structure can
either be reduced (e.g., accept a pair of
electrons) or oxidized (e.g., donate a pair of
electrons)
ATP: A “currency of energy” for many cellular
reactions
a) ATP stands for adenosine triphosphate.
It is a nucleotide with three phosphate
groups linked in a small chain.
b) The last phosphate in the chain can be
removed by hydrolysis (the ATP becomes ADP,
or adenosine diphosphate).

This reaction is energetically favorable: it has a

G°' of about –7.5 kcal/mol
ATP + H2O  ADP + Phosphate + Energy
(7.5 kcal/mol)
c) ATP hydrolysis is used as an energy source
in many biological reactions that require
energy – for example, active transport in the
sodium-potassium pump
d) During catabolism, energy released from the
oxidation of carbon is captured and used to
synthesize ATP from ADP and phosphate.
C6H12O6 + 6 O2 6 CO2 + 6 H2O + Energy
ADP + Phosphate + Energy ATP + H2O
Microbes obtain energy from a large number of
sources, including organic compounds,
inorganic substances, and light.
Furthermore, microorganisms as a group, and
some times as individuals as well, can use these
sources under both aerobic and anaerobic
conditions.
Thus, to a large extent, the presence of
microogranisms every where reflects their
diverse strategies for obtaining energy.
Two general types of energy-rich compounds are
derived from the exergonic reactions of
metabolism:
• High-energy phosphate compounds and
• Stored electrons associated with specialized
carrier molecules.
Adenosine triphosphate (ATP) is the dominant
high-energy phosphate compound in cells.

The potential energy stored in the “high-energy

phosphate bonds of ATP is useful in wide variety
of biosynthetic reactions.
Electrons released during exergonic metabolism
are generally captured by oxidized electron
carriers such as nicotinamide adenine
dinucleotide (NAD+), NAD phosphate (NADP+)
or related compounds
The reduced forms of these carriers will be
referred to as NADH and NADPH, respectively.
An additional but less energy-rich electron carrier
is flavin adenine dinucleotide (FAD/FADH2).

The electrons stored in these compounds are often

called reducing equivalents or reducing power.
Most organisms obtain cellular energy from the
biodegradation of energy-rich organic
compounds, such as carbohydrates, proteins,
and lipids; this “dismantling” of organic
substances is catabolism.

Alternatively, some organisms obtain energy from

transformations of various inorganic compounds,
whereas others use light as an energy source.

Organisms that derive energy from organic or

inorganic substances are called chemotrophs,
while photorophs convert light energy into
chemical energy to support metabolic process.
Organisms that obtain reducing equivalents from
organic compounds are referred to as
organotrophs, and those that use inorganic
substan-ces are called lithotrophs.

The vast majority of microorganisms encountered

by soil microbiologists fit into three metabolic
groups i.e., chemoheterotrophs, photoauto-
trophs, and chemoautotrophs.
Microorganism can be categorized with respect to
three important metabolic requirements
Source of energy:
chemotrophs or phototrophs
Source of reducing equivalents
organotrophs or lithotrophs
Source of carbon for anabolism
heterotrophs or autotrophs)

Assignment:
Write a comprehensive note on ATP production in
microorganisms (Due after two weeks)
The Role of Enzymes in Metabolism
Although redox chemistry and free energy
principles are useful in predicting energy
relationships in metabolic processes, they
provide no information concerning the rate at
which reactions proceed.

Certain reactions may release energy too rapidly

for cellular processes and are incompatible with
living cells, generally because of heat
production.
Conversely, many chemical reactions do not occur
at appreciable rates even though the
corresponding free energy change is highly
favorable.

This results from the need to satisfy the activation

energy for the reaction- the energy input
necessary to break the existing chemical bonds
within each reactant.

For a reaction to proceed, its activation energy

must either by met by an external energy source
or reduced in magnitude by the presence of a
catalyst.
A catalyst is a substance that promotes a reaction
by reducing the required energy of activation
without itself being altered by the ensuring
reaction.

This catalytic role in living cells is provided by

specialized proteins called enzymes.

Unlike most nonbiological catalysts, enzymes are

highly specific in that they generally promote
only one particular reaction or class of reaction.
Enzymes promote efficient metabolism not only by
facilitating the initiation of biochemical reactions
but also by controlling the rate and extent of
these reactions.

Enzymes do this by temporarily binding the

reactants at the enzyme’s active site and
thereby physically orienting them so as to both
promote and control their interaction.

In this way, enzymes allow reaction to proceed in a

step-by-step fashion with minimum energy input.
Enzyme Components
2 Parts
1. Apoenzyme - protein portion
2. Coenzyme (cofactor) - non-protein
Holoenzyme - whole enzyme
Inhibitors can affect enzymatic activity
1. Competitive Inhibitors
2. Noncompetitive Inhibitors
Microorganims need control of enzyme production
both to promote balanced cell growth and to
minimize unnecessary energy expenditure for
protein production.

Therefore, various strategies have been evolved to

regulate the production and activity of cellular
enzymes.
Enzymes needed for fundamental cellular
processes are generally maintained at constant
levels in the cell, and their production is
unaffected by concentrations of substrate or
products; such enzymes are called constitutive
enzymes.

Alternatively, enzyme production may be

inducible, when production occurs in the
presence of an inducer molecule, or
derepressible, when production occurs in the
absence of a repressor molecule.
Many cataboloic enzymes are inducible in that the
proper degradative enzymes are only produced
in response to the presence of the
corresponding substrate, which functions as an
inducer; for example, lactose (milk sugar) acts
as an inducer for the production of its
degradative enzymes.

Conversely, some anabolic enzymes are

derepressible so as to limit enzyme production
to periods when a specific enzymatic product
has dropped below some critical concentration in
the cell; that product functions as a repressor.
The enzymes responsible for the conversion of
dinitrogen gas to ammonia are example of
derepressible enzymes in that their production is
inhibited by the presence of the product.
Specific examples of enzymes important in soil
microbiology include:

• Cellulases, which degrade the polymer cellulose

into smaller constituents,

• Nitrogenase, which converts dinitrogen gas into

biologically available ammonia,

• Sulfatase, which release sulfate from protein and

certain other organic compounds, and

• Phosphatases, which remove phosphate groups

from organic compounds such as nucleic acids.
Class Representative subclass Types of reactions catalysed
Oxidoreductases Dehydrogenases Catalyse oxidation reduction reactions.
Oxidases Important in fermentation and respiration pathway.
Reductases
Peroxidases
Catalases
Transferases Aminotransferases Catalyse the transfer of molecular substituents among
Kinases molecules.

Hydrolases Glycosidases Catalyse the hydrolytic cleavage of chemical bonds.

Peptidases
Phosphatases
Ribonucleases
Lyases Decarboxylases Catalyse the addition or removal of chemical groups
Synthases such as carbon dioxide, ammonia and water
Lyases

Isomerases Racemases Catalyse inversions at asymmetric carbon atoms and the

Isomerases intramolecular transfer of molecular substituents.

Ligases Synthetases Catalyse the binding of two molecules with the

Carboxylases expenditure of ATP. Important in anabolic pathways.
All enzymes are not intracellular, meaning that
they are produced and are active within the cell.

Enzymes that catalyze the degradation of

polymeric substances added to soil, such as
cellulose from crop residues, are necessarily
extracellular because the polymer is too large to
be transported across the cellular membrane.
However, once the polymer has been reduced to
its smaller subunits, subsequent catabolism may
proceed intracellularly.

Because many enzymes are important in nutrient

cycling and other soil-related processes,
standardized assays have been developed for
measuring their activities.