Microbial Ecology and Diversity

Course No. Microbiol. 102

Professor Dr. Md. Anisur Rahman Khan (ARK)

Department of Microbiology,
University of Dhaka
 Abiotic limitations to microbial growth
Effects of Abiotic Factors on Microorganisms
Environmental Factors that Influence Microbes

Professor Dr. Md. Anisur Rahman Khan (ARK)

 Environmental determinants
There are a large numbers of abiotic physical and chemical
factors that influence the growth, survival and metabolic
activity of microorganisms.
A variety of physical measurements and analytical
procedures are needed in order to characterize the abiotic
factors .
The effect of one abiotic factor on a microbial population is
influenced by another abiotic factors.
In some cases, microbes are limited in their activities by the
availability of some nutrients.
In other cases, some environmental factor may be exceed the
maximum or minimum tolerance of a particular population.
 Environmental Conditions

Various abiotic factors strongly influence the ecologi­

cal distribution and functioning of microbial popula­
tions.

Abiotic Limitations To Microbial Growth

Liebig's Law of the Minimum

Justus Liebig, a German agricultural chemist active

during the middle of the nineteenth century, recog­
nized that like atoms in a molecule, elements in a liv­
ing organism are present in distinct proportions
(Liebig 1840).
 Liebig’s Law of the
Minimum (1840)
Cellular constituents are required in the proportions that
they exist in the cell.
Justus Liebig, a German agricultural scientist (middle of
nineteenth century) stated that
“ Like atoms in molecule, elements in a living organism are
present in proportions”
According to this law, the total yield or biomass of any
organism will be determined by the nutrient present in the
lowest concentration in relation to the requirements of that
organisms.
This law applies to microbes just as it applies to plants and
animals.
 According to Liebig's law,
The total yield or biomass of any organism
will be determined by the nutrient present
in the lowest (minimum) con­centration in
relation to the requirements of that
organism.
To grow, microorganisms must obtain vari­
ous substances (nutrients) from their
environment and use them for the
production of energy and for the
biosynthesis of cellular macromolecules.

6
Water composes a large part of the cell by weight,
about 70-90%, and therefore is an essential
nutrient. The remaining solids of the cell are
largely composed of hydrogen, oxygen, carbon,
nitrogen, phosphorus, and sulfur.

Also vital for proper cell functioning, although in

substantially smaller amounts, are metal cations
of potassium, magnesium, calcium, iron,
manganese, cobalt, copper, molybdenum, and
zinc, as well as anions such as chloride, and for
some microorganisms, growth factors such as
vitamins. Each nutrient plays an important role
in the overall growth of the cell (Table 8.1).
• In any given ecosystem, there will be some
limiting nutritional factor. For example,
crop yield cannot be increased by the
addition of excess phosphorus if the soil is
suffering from a shortage of nitrogen.
• Liebig's law of the minimum applies to
microorganisms just as it applies to plants
and animals.

8
Increase in the conc. of a particular limiting nutrient allows
the affected population to grow or reproduce until another
factor becomes limiting.
In any given ecosystem there will be some limiting
nutritional factor, e.g. crop yield can’t be increased by
addition of excess P if soil is suffering from a shortage of N.
In a given ecosystem, the growth of one microbial
population may be limited by conc. of available P and
adding N will not permit additional growth of that
population.
Within the same ecosystem, growth of another microbial
population may be limited by conc. of available N and the
addition of N would permit further growth of those
organisms.
 Shelford’s Law of Tolerance
(1913)
The occurrence and abundance of organisms in an
environment are determined not only by nutrients
but also by various physicochemical factors such as
temperature, redox potential, pH, and many others.
Shelford's law of tolerance describes how such abiotic
parameters control the abundance of organisms in an
ecosystem.
It states that for survival and growth each organism
requires a complex set of conditions (Shelford 1913).
 Shelford’s Law of Tolerance
(1913)
The long term survival of a population is
controlled by physical/chemical factors.
Only populations that tolerate the prevailing
conditions will become established.
Population survival depends on conditions
remaining within their range of tolerances.
The occurrence and abundance of organisms in
an environments are determined not only by
nutrients, but also by various physiochemical
factors such as temperature, redox potential, pH
and many others.
 Shelford’s Law of Tolerance
(1913)
In essence Shelford's law says that there are bounds for
environmental factors above and below which
microorganisms can not grow and survive.
For an organism to succeed in a given environment, each of
these conditions must remain within the tolerance range
of that organism; if any condition, such as temperature,
exceeds the minimum or maximum tolerance of the
organism, the organism will fail to thrive and will be
eliminated.
Shelford’s Law of Tolerance describes how such
abiotic parameters control the abundance of
organisms in an ecosystem, and states that for
survival & growth each organisms require a
complex set of conditions.
For an organism to succeed in a given
environment, each of the conditions must remain
within the tolerance range of that organism.
For example, if temperature is too high or low for
an organism then its not possible for that
organisms to survive and grow.
 Shelford’s Law of Tolerance
(1913)

Consequently, psy­chrophilic microorganisms cannot grow in

ecosystems with high temperatures; obligately anaerobic
microor­ganisms cannot survive conditions of high oxygen
tension; obligately halophilic microbes cannot grow in
freshwater lakes; and so forth.
The tolerance ranges of microorganisms and the
fluctuations of chemical and physical factors in an
ecosystem do not determine which microorganisms are
present at any one moment, but rather which
microorganisms can be pres­ent on a sustained basis in
that ecosystem.
 Shelford’s Law of Tolerance
(1913)

In reality, the presence and success of an organism or a

group of organisms in an ecosystem depend both on
nutrient requirements and on environmental tolerance
(Odum 1971).
The population levels of most organisms are controlled in
an ecosystem by the quan­tity and diversity of materials
for which they have a minimum requirement, by critical
physical factors, and by the tolerance limits of the
organisms themselves to these and other components of
the environment
 Shelford’s Law of Tolerance
(1913)

Tolerance ranges for a given parameter are somewhat

interactive with other parameters; thus, a microorganism
that is not able to survive at a particu­lar temperature in
an ecosystem with a particular hydrogen ion
concentration may be able to survive at that same
temperature in another ecosystem with a different
hydrogen ion concentration.
The interactive nature of environmental determinants
complicates the task of microbial ecologists in defining
precisely the controlling or limiting factors in natural
ecosystems.
The interactions among microbial populations can alter
the environment in such a way to allow for or prevent
the growth of other microbes.
Example, a microbe may carry out a metabolic activity ,
such as N fixation, whose by products are required for
growth by another microbes.
Another important of limitation or tolerance factors is
availability.
A nutrient may be present in an ecosystem but in
unavailable form.
Lack of availability may also occur because the chemical
is in wrong form. Such as toxic material as bonded with
clay is unavailable for interaction with microbes. Another
example N gas, unavailable Phosphorous and iron.
Reduced availability of the required substances can
prevent microbial growth.
 Shelford’s Law of Tolerance

In classical ecology, the ecology of the individual falls in the realm of

autecology, whereas synecology deals with ecological interactions
in a population, community, or ecosystem. Microbial ecologists
deal with individual populations but not with individual
microorganisms.
Accordingly, in microbial ecology, autecology studies the
interaction of isolated microbial populations with environmental
determinants, and
synecology considers the interactions of populations with each
other.
Autecology of individual microbial populations includes the study
of environmental determinants, their effect on microbial
populations, and the adaptation mechanisms that microorganisms
have evolved to cope with them. Our discussion of autecology will
include adaptations to environmental extremes and an
examination of the environments where these extremes prevail.
Shelford’s Law of Tolerance

A wide or a narrow tolerance range to an environmental

determinant is described by the eury- or steno­prefixes,
respectively.
A euryhaline microorganism tolerates wide fluctuations of
salt concentrations that typically occur in estuaries and
tidal rivers. In contrast, a stenohaline microorganism is
confined to a freshwater or a marine habitat.
Preference for a partic­ular determinant is expressed by
the -phile suffix, as in halophile or thermophile.
Microorganisms that have predominantly broad (eury-)
tolerance ranges grow in a wide variety of habitats;
microorganisms with one or more narrow (steno-)
tolerances grow only in a few special environments.
 Shelford’s Law of Tolerance

Stenothermal psychrophiles or thermophiles will grow only

in permanently cold or hot environments, respectively,
and will not thrive in environments where the
temperatures fluctuate within the mesophilic range.
Some microorganisms are particularly well adapted for
survival in extreme habitats where other organisms
cannot survive.
Their limits of tolerance to specific stress factors
determine, in large part, the inhabitants of extreme
environments, such as salt ponds, hot springs, alkaline
soda lakes, and desert soils (Table 8.2).
Environmental Determinants
Temperature
Radiation Hydrogen Ion Concentration (pH)
Pressure Redox potential
Magnetic Force
Salinity
Organic Compounds
Water activity Inorganic Compounds
Movement
Many microorganisms that inhabit extreme environments, e.g
hot springs, salt lakes etc. and have special adaptive features that
permit them to survive and function at that environment.

The membranes and enzymes of these microbes have distinct

modifications .
 Temperature
Temperature has an effect on growth rate metabolism,
reproduction rate metabolism and morphology.
There are no organisms that can grow at all temperatures.
Most bacteria will grow in the range of 30-40 degrees.
Three temperature ranges are-
Minimum - cells fail to divide below this temp (usually not lethal)
Optimum - highest reproduction rate
Maximum - cells fail to divide above this temp (frequently lethal)
Survival in very hot environments is difficult due to the fact
that even a slight increase in temp speeds up enzyme reactions
and may cause denaturation of the protein enzymes.
Both the optimal growth temperature and the range of
temperatures that particular microbes can tolerate determine
whether that microbe will survive and what role it will play in
a given ecosystem.

22
 Cardinal temperature
For every microorganism, there is a minimum
temperature below which growth is not
possible, an optimum temperature at which
growth is most rapid, and a maximum
temperature above which growth is not
possible.
These three temperatures are called the
cardinal temperatures, and are characteristic for
any given microbe.
 Temperature
Microorganisms are classified as psy­chrophiles,
mesophiles, thermophiles, and hyperther­
mophiles, respectively, if their optimal growth
temper­atures are low (<0-<20°C), moderate
(20-<40°C), high (40-<80°C), or very high (80-
110°C). Some hyperthermophiles have been
reported with growth temperature optima at
105°C and no growth below 85°C.
 Temperature classes of organisms
Microorganisms can be grouped at least in four
groups in relation to their growth temperature
optima.
Psychrophiles, with low temperature optima;
Mesophiles, with midrange temperature
optima;
Thermophiles, with high temperature optima;
Hyperthermophiles, with very high
temperature optima.
 Temperature Range
C Minimum Optimum Maximum
Psychrophiles <0 <15 ~20

Mesophiles 20-25 25-40 ~45

Thermophiles ~45 >55 100+

Hyperthermophiles 55 80-100 >100

Categories of Microbes Based
on Temperature Range
Temperature and growth relations in different temperature
classes of microbes

Temperature (oC)
The temperature optimum of each example organism is shown on the graph.
 Temperature classes of organisms: their
habitats
Mesophiles are widespread in nature. found in warm-
blooded animals and in terrestrial and aquatic
environments.

Psychrophiles and thermophiles are found in unusually

cold and unusually hot environments, respectively.

Hyperthermophiles are found in extremely hot habitats:

hot springs, geysers, and deep sea hydrothermal
vents.
 Escherichia coli as for example
E. coli is a typical mesophile. Its cardinal
temperature is precisely defined.
The minimum is 8oC.
The optimum is 39oC for most of its strains.
The maximum is 48oC.
Hence, the temperature range for E. coli is
40 degrees, near the high end for
prokaryotes.
 Psychrophiles
Grow in oceans, glaciers and other constantly cold
environments.
Can exist in cold environments because they have high
concentrations of unsaturated fatty acids in the
phospholipids of their cell membranes which helps
maintain fluidity.
Seldom cause problems in food preparation.
No bacterial growth occurs in frozen solid conditions but
remain dormant or in a state of suspended animation.
Some mesophilic bacteria that continue to grow in cold
environments (refrigerator) are termed as
psychromesophiles.
 Mesophiles
Most common types of bacteria. Optimum temperature
range is 25- 40C. Saprophytes also known as
mesophiles grow best at 37C.

Human pathogens grow best at 37C. This group

includes most of the spoilage and disease-causing
organisms.

In most mesophilic microorganisms, a control

mechanism shuts off protein synthesis if temperatures
fall to 5C or lower.
 Thermophiles
Optimum growth temperature is between 50-60C, e.g. the
temperature of hot tap water.
Some members of Archaea grow optimally at temp > 80 C and
are considered hyperthermophiles and grow near
hydrothermal vents in the ocean, sulfur is important in their
metabolic activity (record is 110C near vent, kept from
boiling due to ocean water pressure)
Grow on soil surfaces that get to 50-70C in deserts, power
plants, compost heaps, hot springs.
To survive denaturation of proteins, bacteria rapidly
regenerate enzymes resist to high temperature and use more
heat-stable amino acids.
Thermophilic bacteria are not considered a public health
problem.
 Effect of High & Low Temperature

Effect of temperature on proteins

At too high temperature, proteins are denatured
Alter tertiary structure
Effect of temperature on lipid-containing
membranes of cells and organelles
At too low temperature, membranes become rigid and
fragile
At too high temperature, membranes become too fluid
and cannot contain the cell or organelle
Microbial Growth at High Temperature
High proportions of saturated lipids are present on
cell membrane of thermophilic microbes which
prevent melting at high temperature.

Enzymes produced by many thermophiles are not

denatured at high temperature.

These may have unusual amino acid sequences

occur within the proteins of thermophiles,
stabilizing these proteins at elevated temperatures.

Exhibit amino acid and growth factor requirements

that are absent at optimum temperature.
Microbial Growth at High Temperature
The membranes of thermophilic organisms have major
proportion of high MW and branched fatty acids that
permit them to maintain their semipermeable properties at
high temperature.
Have relatively high proportion of guanine and cytosine in
their DNA that raise melting point and add stability to
DNA.
Thermophiles have reverse DNA gyrase, a unique enzyme,
that introduces positive supercoiling in the chromosome.
Thermophiles have special chaperonins that re-fold
denatured proteins.
At temperature above 75C few bacteria can survive and
grow, some e.g are
Thermus and Sulfolobus
Bacillus stererothermophilus is dominant at 55-70ºC
Cyanobacteria and algae also can grow
 Hydrogen Ion
Concentration (pH)

37
Hydrogen Ion Concentration (pH)

Every microorganism has a pH range within which

growth is possible and typically shows a well-defined
growth pH optimum.

Most organisms show a growth pH range of 2–3 units.

Most natural environments have pH values between 4 and 9, and
organisms with optima in this range are most commonly
encountered.
Only a few species can grow at pH values of lower than 3 or
greater than 9.
Hydrogen Ion Concentration (pH)
Microorganisms can not tolerate extreme pH values.
Enzyme activity and protein structure depends upon
the ionic state of the amino acid side chains
at low pH functional groups will be protonated
at high pH functional groups will be
deprotonated
Extreme pH values cause irreversible denaturation
of proteins.
pH also indirectly affects growth by altering
solubility of nutrients and gases.
The pH scale
The optimal pH values and tolerance ranges for
various bacteria are shown below:

pH
organism min. opt. max.

Escherichia coli 4.4 6 - 7 9.0

Thiobacillus thiooxidans 1.0 2 - 2.8 6.0
Thermoplasma acidophilus 1.0 1.5 4.0
Sulfolobus acidocaldarius 1.0 2.5 4.0
Bacillus acidocaldarius 2.0 3.5 6.0
Bacillus alcalophilus 8.5 9.5 11.5
41
 Acidophiles
Organisms that grow optimally at low pH (< pH
6), are called acidophiles.
Fungi as a group tend to be more acid tolerant
than bacteria. They grow best at ≤5.
Many prokaryotes are also acidophilic. Some
of these are obligate acidophiles, unable to
grow at neutral pH.
Obligately acidophilic bacteria include
species of Acidithiobacillus and several
genera of Archaea, including Sulfolobus,
Thermoplasma, and Ferroplasma.
 Alkaliphiles

Microbes showing growth pH optima of 9 or

higher are called alkaliphiles. A few
extremophiles have very high pH optima for
growth, as high as pH 11. For example, Bacillus
firmus (pH range 7.5 to 11).
Some extremely alkaliphilic bacteria are also
halophilic, and most of these are Archaea.
Habitat: highly alkaline habitats, such as soda
lakes and high-carbonate soils.
Hydrogen Ion Concentration (pH)

Many fungi are acidotolerant, but most bacteria are

not. Some acidotolerant bacteria, like Lactobacil­lus,
and acidophiles, like Thiobacillus and Sulfolobus
(Table 8.8), create their own low pH environment by
producing acids. Lactobacillus is a mixed acid fer­
menter and Sulfolobus produces sulfuric acid. Bacillus
acidocaldarius and Thermoplastna acidophilu.s are
heterotrophic thermoacidophiles that live in acidic
environments created by chemolithotrophic sulfur
oxidizers but do not produce acids themselves.
 pH - Adaptations
Bacteria have evolved mechanisms to maintain
their cytoplasm near neutrality rather than
having evolved enzymes that function at pH
extremes.
The adaptations that allow this are not well
understood.
Depending on the pH adaptation microbes can
be divided into two broad groups-
Acidophiles (acid-loving)
Alkaliphiles (alkali-loving)
 Acidophiles
Microbes that can tolerate and grow at
extreme low pH.
They can usually grow at pH 0-3.
They are mainly found in
Geothermal areas
Acid mine drainage
Acidophiles are diverse.
• Eukaryotes
– Fungi (numerous)
– Algae (Cyanidium)
– Protozoa (flagellates, ciliates, amoebae)
• Bacteria
– Heterotrophs (Bacillus, Acidiphilium, Sulfobacillus)
– Autotrophs (Acidithiobacillus)
• Archaea
– Numerous heterotrophs and autotrophs, many
thermophilic (Thermoplasma, Sulfolobus, Acidianus,
Metallosphaera)
 Alkaliphiles

• Organisms growing optimally at pH 8.5 –

11
• Very widely distributed in the
environment.
• Prevalent in haloalkaline (soda) lakes.
• Include bacteria, fungi, yeasts
 pH for growth:
• The acidity or alkalinity of an environment can greatly
affect microbial growth. Some organisms have evolved
to grow best at low or high pH, but most organisms
grow best between pH 6 and 8. The internal pH of a
cell must stay relatively close to neutral.
• This is because DNA is acid-labile and RNA is alkaline-
labile; if a cell cannot maintain these key
macromolecules in a stable state, it obviously cannot
survive.
Water Activity (aw)

50
 Water Activity (aw)
• Water is the solvent of life, and water availability is
an important factor affecting the growth of
microorganisms.
• Water availability not only depends on the absolute
water content of an environment, that is, how
moist or dry it is, but it is also a function of the
conc. of solutes such as salts, sugars, or other
substances that are dissolved in the water.
• Dissolved substances have an affinity for water,
which makes the water less available to organisms.
51
 Water Activity (aw)
• Water activity is defined as the ratio of the vapor
pressure of the air in equilibrium with a substance
or solution to the vapor pressure of pure water.
• Thus, values of aw vary between 0 and 1.
expressed in physical terms as water activity (aw).

– For example, water activities in agricultural soils

generally range between 0.90 and 1.

52
 Water Activity (aw)
• The absolute amount of water in a habitat is less
important than the availability of the water
• Availability is expressed as water activity:
vapor pressure of solution
aw =
vapor pressure of pure water

 [solute]   vapor pressure

aw decreases with increasing [solute]

aw = 1 for pure water
aw = 0 for no available water
• The water activity depends on
– The No. of moles of water
– The No. of moles of solutes and
– On the activity of coefficients for water and the
particular solute.
• In soils, aw is measured as water-holding
capacity (WHC).
• Optimum conditions for activity of aerobic soil
microbes occur between 60% and 80% WHC.
• The water content of air is low and limiting for
microbes.
• In tropical areas humidity is sufficient to allow
microbial growth at air.
• Most bacteria require aw > 0.96.
• Permanent wilting point for plants aw  0.90
• The microbes which are capable of growth at water
activity as low as 0.60 are known as xerotolerant, such
as some fungi and lichens.
organism required water activity

Rhizobium 0.97
Pseudomonas 0.93
Bacillus 0.90
Ascomycetes, lichens 0.62 *

* xerotolerant
 Water activity of several substances
• Water activity
of a microbial
habitat is
controlled by
the dissolved
solute conc.
• To survive in
high-solute
environments,
organisms
produce or
accumulate
compatible
solutes to
maintain the
cell in positive
water balance.
 Pressure

Atmospheric Pressure : Atmospheric pressure is the pressure

exerted by the weight of the air column, which at the surface of
the Earth (sea level) is approximately I atmosphere (atm) (760
mm mercury or 101.325 kPa). In general, changes in
atmospheric pressure do not affect microorganisms. At
extremely low atmospheric pressures, such as in the upper
atmosphere or in an arti­ficial vacuum, however, water may
evaporate, and oxy­gen becomes limiting, rendering
microorganisms metabolically inactive (Gregory 1973).

58
 P r e s s u r e

Hydrostatic Pressure: Whereas atmospheric pres­sure reflects the

weight of the air column, hydrostatic pressure is the pressure
exerted by the weight of a water column. A 10-m water column
over a 1-cm2 area weighs 1 kg (1 1 water weighs 1 kg) and exerts
about 1 atm pressure, hence hydrostatic pressure increases by
approximately I atm for every 10 m of depth. Because the
atmospheric pressure at sea level is 1 atm, the pres­sure at 10 m
is approximately 2 atm. The precise pres­sure at a given depth
depends on the weight of the water, and hence pressure is
greater at a given depth in saline water than at the same depth
in fresh water.

59
 Pressure

In response to pressures, organisms are either sen­sitive (they grow

optimally at pressures of about 1 atm, and growth rates decline
as pressure increases), barotolerant (they tolerate elevated
pressures up to given limits without a decline in growth), or
barophilic (they grow optimally at elevated pressures and may
be completely inhibited or even killed at atmospheric pressure).
The existence of obligate barophiles has been a question of
prolonged contro­versy. Sampling and isolation of deep-sea
bacteria without loss of in situ pressure is required in order to
determine the existence of decompression-sensitive strains
(Yayanos and Dietz 1983).

60
 Pressure

In nonbarophilic microorganisms, high hydrosta­tic pressure appears to

inhibit microbial synthesis of RNA, DNA, and protein, membrane
transport func­tions, and rates of activity of various enzymes (Baross
et al. 1972; Hardon and Albright 1974). Enzyme pro­teins, in order to
be active, must be in a proper tertiary configuration. Some
researchers have suggested that high hydrostatic pressures distort
this configuration, leading to low enzyme activity. In the case of a
baro­tolerant organism, the distortion would be minimal. Most
enzymes actually appear to be capable of normal functioning over a
wide range of hydrostatic pres­sures, permitting enzymatic activities
even in the deep sea. Theoretically, an obligately barophilic microor­
ganism might have its enzyme in proper tertiary con­figuration only
at elevated hydrostatic pressure and would not function well at
lower pressures (Kim and ZoBell 1972) (Figure 8.16).

61
 Osmosis
• Water diffuses from regions of high water conc. (low solute
conc.) to regions of lower water conc. (higher solute conc.)
in the process of osmosis. The cytoplasm of a cell has a
higher solute conc. than the environment, so water tends
to diffuse into the cell. Under such conditions, the cell is
said to be in positive water balance.
• However, when a cell finds itself in an environment where
the solute conc. exceeds that of the cytoplasm, water will
flow out of the cell. This can cause serious problems if a
cell has no way to counteract it because a dehydrated cell
cannot grow.

63
 Osmotic Pressure
• Osmotic Pressure is the pressure exerted on a semipermeable
membrane by a solution containing solutes that cannot
freely cross membrane; it is related to the concentration of
dissolved molecules and ions in a solution.
• Hypotonic solutions have lower solute concentrations; cells
placed in these solutions will swell and burst
• Hypertonic solutions have greater solute concentrations;
cells placed in these solutions will undergo plasmolysis
(shriveling of cytoplasm)
– This effect helps preserve some foods
• Restricts organisms to certain environments
– Obligate halophiles – grow in up to 30% salt
– Facultative halophiles – can tolerate high salt concentrations
 Osmotic Pressure
• It is the pressure exerted on a semipermeable membrane by a
solution containing solutes that cannot freely cross
membrane; it is related to the concentration of dissolved
molecules and ions in a solution.
• Hypotonic solutions have lower solute concentrations; cells
placed in these solutions will swell and burst
• Hypertonic solutions have greater solute concentrations; cells
placed in these solutions will undergo plasmolysis (shriveling
of cytoplasm)
– This effect helps preserve some foods
– Organisms able to live in environments high in sugar as a solute
are called osmophiles.

• Restricts organisms to certain environments

65
 Osmotic Pressure
• Whereas high hydrostatic pres­sure is restricted to special
habitats, all microorgan­isms must cope with osmotic pressure,
which results from differences in solute concentrations on
opposite sides of a semipermeable membrane. In order to equi­
librate and equalize solute concentrations, water mol­ecules
attempt to move across the membrane in the direction of the
higher solute concentration. In some hypotonic habitats, water
molecules attempt to move into microbial cells, which could
expand and rupture the cells; in hypertonic habitats, water
molecules attempt to move out of the cells, which could dehy­
drate and shrivel the cells.

66
 Osmotic Pressure
Microorganisms have evolved adaptive mecha­nisms that
permit them to tolerate osmotic pressure within
certain ranges. The rigid cell walls of bacteria and other
microorganisms protect these organisms from osmotic
shock by preventing the pressure exerted by incoming
water molecules from expanding and bursting the cells.
The pressure buildup within the cell at equilibrium
prevents the entry of additional water. The contractile
vacuoles of some protozoa pre­vent osmotic swelling in
hypotonic solution by pump­ing out excess incoming
water.

67
 Osmotic Pressure
• The majority of microorganisms can withstand
the low osmotic pressures that prevail in distilled
water, rainwater, and freshwater habitats either
by building up intracellular pressure or by
actively pumping out excess water from the cell.
Fewer microorganisms can withstand the high
osmotic pressure of concen­trated solutions. In
traditional terminology, microor­ganisms that
tolerate or prefer high concentrations of organic
solutes (usually sugars) are called osmotoler­ant
or osmophilic, respectively (Jennings 1990
68
 Osmotic Pressure
• Honey, sap flows, flower nectar, molasses, and
other sugar syrups provide habitats for
osmotolerant and osmophilic microorganisms.
These may cause spoilage of fruit preserves,
syrups, and other food items normally stabilized
by their high sugar concen­tration. Debaromyces
hansenii and Zygosaccha­romyces rouxii are
osmophilic yeasts; Aspergillus and Penicillium
molds are osmotolerant.

69
 Osmotic Pressure
The osmotic pressure of concentrated sugar solu­tions tends to
dehydrate microbial cells. Osmotolerant and osmophilic
microorganisms avoid this fate by building up balancing
intracellular concentrations of "compatible solutes." These are
low-molecular­weight organics such as glycerol, various sugars,
glu­tamate, glycine betaine, and similar compounds. These
balance the osmotic pressure and prevent water loss from the
cell. The enzymes of osmotolerant and osmophilic
microorganisms must be capable of func­tioning in the presence
of these high-solute concentra­tions. The more adapted
osmophiles pay a price for this capability.

70
 Osmotic Pressure
Their enzymes function suboptimally at low solute concentrations,
resulting in optimal growth at water activities below 0.9
(Jennings 1990) (Figure 8.17). Osmotic concentrations tend to
change. An osmotolerant or osmophilic microorganism with
high intracellular solute concentration might burst when the
osmotic pressure of the surrounding medium drops. These
microorganisms, however, have the capability of sensing the
changes in outside osmotic pressure and reacting by rapidly
degrading or poly­merizing their intracellular solutes to preserve
their osmotic balance.

71
 Compatible Solutes
• Water activity of a microbial habitat is controlled by
the dissolved solute concentration. To survive in high-
solute environments, organisms produce or
accumulate compatible solutes to maintain the cell in
positive water balance, so that it can obtain water
from its environment.
• The compatible solute is a molecule that is
accumulated in the cytoplasm of a cell for adjustment
of water activity but that does not inhibit biochemical
processes.
72
 Compatible Solutes
• The internal solute concentration can be raised
by either pumping inorganic ions into the cell
from the environment or by synthesizing or
concentrating an organic solute.
• Staphylococcus are notoriously halotolerant
(7.5–10% NaCl), and these organisms use the
amino acid proline as a compatible solute.

73
 Osmophiles and
Xerophiles
• Organisms able to live in environments
high in sugar as a solute are called
osmophiles.
• Organisms able to grow in very dry
environments (made dry by lack of
water rather than from dissolved
solutes) are called xerophiles.
74
75
 Salinity
• High salt conc. tend to denature proteins, i.e. that
disrupt the tertiary protein structure, which is essential
for enzymatic activity.
• At high salt concentrations microbes are dehydrated by
hyperosmotic (hypertonic) environments
• Halotolerant microbes actively exclude sodium and
achieve osmotic balance by concentrating other solutes
(glycerol, KCl)
• Halophiles have evolved cellular structures (enzymes,
ribosomes, etc.) that require high internal concentration
of KCl to adopt the proper conformation
• Some halophilic require high salt conc for their enzyme
activity
Effect of NaCl conc. on growth of micro-organisms of
different salt tolerances or requirements

• The optimum
NaCl conc. for
marine
microbes such
as Vibrio
fischeri is
about 3%.
• For extreme
halophiles, it is
between 15
and 30%,
depending on
the organism.
 Salinity
• Microorganisms that tolerate or require high salt con­
centrations are called halotolerant and halophilic,
respectively (Gilmour 1990). At high salt concentra­tions, the
hypertonic environment tends to dehydrate nonhalotolerant
microorganisms.
• In addition to affecting osmotic pressure, high salt
concentrations tend to denature proteins; that is, they
disrupt the tertiary protein structure, which is essential for
enzymatic activity. Besides denaturing enzymes, high
concentrations of salt dehydrate cells. algal and bacterial
species (Kushner 1968, 1980; Post 1977).

78
 Salinity
• High ­salinity habitats include salt lakes,
which occur in arid regions where
evaporation exceeds freshwater inflow or
where a lake is fed by a salt spring. Partially
land­locked marine lagoons and tidal
evaporation flats can also develop high salt
concentrations. Relatively few organisms can
grow in highly saline waters, and often the
biota of salt lakes are restricted to a few
halophilic and halotolerant

79
 Salinity
• Halotolerant and halophilic microorganisms tend to exclude
from their cell interiors the high and rela­tively toxic sodium ion
concentrations that usually prevail in their environments. They
achieve osmotic balance with their environment by mechanisms
simi­lar to those used by the osmophiles. The halophilic
unicellular green alga Dunaliella that lacks a rigid cell wall builds
up high intracellular glycerol concentra­tions for osmotic balance.
The obligately halophilic Halobacterium, however, achieves
osmotic balance with high intracellular concentrations of
potassium chloride. The ribosomes of Halobacterium require
high concentrations of potassium ions for stability. Its enzymes
also require high salt concentrations for maintaining their active
configuration and functions and are inactivated at low salinity
(Larsen 1962, 1967; Gilmour 1990) (Figure 8.18).

80
 Salinity
• Halobacterium, a het­erotrophic aerobic archaeaon, lacks
murein, and its cell wall appears to require sodium ions for
stability. Some strains of Halobacterium have bacteri­
orhodopsin bilayer membrane components that serve as
light-driven proton pumps. Light energy is used to pump
protons out of the cell and thereby generate an
electrochemical potential. This, in turn, drives ATP synthesis.
The described features make Halobacterium superbly
adapted to live in highly saline, often saturated brine
environments. Halobac­terium is unable to tolerate low
salinities and requires at least 3.0 M NaCI for growth.

81
 Salinity
• Halotolerance is a characteristic of the bacteria Staphylococcus
and Halomonas. Some green algae (Chlorella, Dunaliella), some
diatoms, and other uni­cellular algae are also halotolerant.
Most algae and bac­teria from the marine environments are
moderately halophilic. Some marine microbiologists actually
define marine bacteria as bacteria that require 3% NaCI for
growth. True marine bacteria appear to require - sodium for all
membrane transport systems, whereas sodium-dependent
transport in nonmarine bacteria has so far been shown to occur
only in the case of specific and nonessential metabolites
(MacLeod 1985). Extreme halophiles are the archaea
Halobacterium, Halococcus, Natronobacterium, the anoxypho­
totrophic bacterium Ectothiorhodospira, and the green alga
Dunaliella (Oren 1988; Gilmour 1990).

82
 Halophiles
• Seawater contains about 3% NaCl plus small
amounts of many other minerals and
elements.
• Marine microbes usually have a specific
requirement for NaCl for growing optimally at
the water activity of seawater. Such organisms
are called halophiles. The growth of
halophiles requires at least some NaCl, but the
optimum varies with the organism.
– For mild halophiles, (conc. of NaCl 1–6%)
and
– For moderate halophiles (conc. 7–15%).
 Re d ox Po t e n t i a
• Many enzymatic reactions are oxidation-reduction reactions
in which one compound is oxidized and another compound
is reduced.
• The ability of an organ­ism to carry out oxidation-reduction
reactions depends on the oxidation-reduction state of the
envi­ronment. In a solution, the proportion of oxidized to
reduced components constitutes the oxidation­reduction
potential or redox potential (En).
• Some microorganisms can be active only in oxidizing envi­
ronments, and others can exist only in reducing envi­
ronments

85
 Redox Potentia

The redox potential is a relative value measured against

the arbitrary 0 point of the normal hydrogen
electrode.
Any system or environment that accepts electrons from a
normal hydrogen electrode is a half­cell that is defined
as having a positive redox poten­tial;
Any environment that donates electrons to this half-cell
is defined as having a negative redox poten­tial.
The redox potential is measured in millivolts (mV) and
expressed as Eh value. . A high positive Eh value
indicates an environ­ment that favors oxidation
reactions; a low negative Eh value indicates a strongly
reducing environment.
86
 Re d ox Po t e n t i a
• Strictly aerobic microorganisms can be metabolically active only at
positive redox potentials,
• whereas strict anaerobes are active only at negative redox potentials.
• Facultative anaerobes can operate over a wide range of Eh values
using oxygen as an electron sink at high redox potentials and
fermenting or using alternate electron acceptors, such as ferric iron
and nitrate ions, at low redox potentials.
• The solubility of certain nutri­ents is strongly influenced by the
prevailing redox potential. Chemicals can exist in oxidized or reduced
forms at different redox values.
• At high redox potentials, iron and manganese exist in their trivalent
(ferric) and tetravalent (manganic) forms, respec­tively. These are
insoluble and generally unavailable for microbial uptake. The bivalent
forms of these met­als that exist at low redox potentials are soluble
and readily available.

87
 Redox Potentia

Below the surface of waterlogged soil and sediment, Eh values are

usually negative (Figure 8.22).
Low redox potentials may be caused by extensive growth of
heterotrophic microorganisms that scavenge all available
oxygen. Such is often the case in highly pol­luted ecosystems
where microorganisms utilize the available oxygen for
decomposition processes.
Sedi­ments rich in organic matter can have Eh values as low as -450
mV. At these low Eh values, sulfate reduction yielding H2S and
COz reduction yielding CH4 can readily occur. It should be
pointed out that it is diffi­cult to measure Eh in natural habitats,
and that hetero­geneity is great; the development and use of
micro­electrodes, however, now makes it possible to measure
redox potentials on a scale relevant to micro­bial microhabitats
(Revsbech and Jorgensen 1986).
88
 Radiation
• Sun is the main radiant energy.
• The spectrum of electromagnetic radiation is
continuous from extremely energetic short
wavelength gamma rays to long wavelength
low energy radio waves.
• The portion of this continuous spectrum are
defined as
• UV light
• Visible light
• Infrared radiation etc.
 Radiation

The spectrum of electromagnetic radiation is continu­ous from

extremely energetic, short-wavelength gamma rays to long-
wavelength, low-energy radio waves (Figure 8.10).
Portions of this continuous spec­trum are defined as ultraviolet,
visible, infrared radia­tion, and so forth. The radiant energy of
the sun drives the global ecosystem; photosynthetic
interaction with visible light radiation is of profound
importance for terrestrial life. The other portions of the
electromag­netic spectrum are also ecologically important and
have marked effects on life.
 wavelength in meters

10-12 10-10 10-8 10-6 10-4 10-2 100 102 104

 x-rays UV infrare waves radio waves
rays d
visible light

wavelength in nm

1 380 430 480 530 560 630 680 750

UV Violet Blue Green Yellow Orange Red
 Radiation
• Shorter wavelength equals more energy and
greater penetration
• Radiation described as ionizing or nonionizing
according to effects on cellular chemicals
 Ionizing Radiation

• Wavelengths shorter than 1 nm – electron beams,

gamma rays, and X rays
• Eject electrons from atoms to create ions
• Ions disrupt hydrogen bonding, oxidize double covalent
bonds, and create hydroxide ions; hydroxide ions
denature other molecules (DNA)
 Ionizing Radiation
• Electron beams – effective at killing but do not
penetrate well
– Used to sterilize spices, meats, microbiological plastic ware,
and medical and dental supplies
• Gamma rays – penetrate well but require hours to kill
microbes
– Used to sterilize meats, spices, and fresh fruits and
vegetables
• X-rays require too much time to be practical for growth
control
 Nonionizing Radiation

• Wavelengths greater than 1 nm

• Excites electrons and causes them to make new
covalent bonds
– Affects 3-D structure of proteins and nucleic acids
• UV light causes pyrimidine dimers in DNA
• UV light does not penetrate well
• Suitable for disinfecting air, transparent fluids, and
surfaces of objects
 UV Radiation
Solar radiation includes UV light, visible light and
infrared radiation.
UV (1-320nm) is too energetic for photosynthetic use
and destructive for microorganisms.
strongly bactericidal at 260 nm coincides with absorption
max of DNA so that DNA is damaged.
UV induces the formation of pyrimidine dimers
(dimerization of thymine bases) in DNA stands causes
faulty transcription, resulting defective enzymes.

T T
A G C T T G G C A UV light A G C G G C A
| | | | | | | | | | | | | | | |
T C G A A C C G T T C G A A C C G T
 Visible light
• The Visible light spectrum is relatively narrow band,
ranges from 320 nm to the far end of 800 nm.
• The intensity of light reaching a particular habitat
influences the rate of photosynthesis.
• Some microbes exhibit phototatic behavior; they
move toward or away from light source.
• Cells vary concentration and type of photosynthetic
pigments depending on the intensity and wavelength
of light available
• Cells stratify in the environment according to their
optimum photosynthetic wavelength
 Ionizing Radiation
• These radiations are designated is I.R if their
interaction with matter produces unstable ions and
free radicals that interact with living matter in a
destructive manner.
• Gamma, x-rays (WL 10-11 cm to 10-6cm), etc. are highly
penetrating and interact with matter in a
microorganisms to produce unstable ions and free
radicals leading to significant cellular damage.
• Low level irradiation may cause mutations and high
exposure doses destroy both NA and enzymes and thus
kill microbes.
• Micrococcus radiodurans has evolved remarkable
resistance to ionizing radiation
• Extremely efficient DNA repair mechanisms, rather
than any unusual protective substances are
responsible for resistance.
• Also these cells have stacked chromosomes and can
rapidly repair DNA damage.
• Bacterial endospores resist ionizing radiation of
~ 10 times more than vegetative cells, specially
gamma radiation; it takes 0.3-0.4 Mrads to effect and
90% kill.
• Some cells tolerate 3 Mrad.
• 500 rads is fatal in humans.
 M a g n e t i c F o r c e

The effects of magnetism upon microorganisms have generally

been ignored as most bacteria appear to be totally unaffected
by changes in magnetic fields.
Some bacteria, however, exhibit magnetotaxis, motility directed by
a geomagnetic field (Blakemore 1975, 1982; Moench and
Konetzka 1978; Spring et al. 1993, 1995).
Diverse populations of magnetotactic bacteria have been identified
based on rRNA sequence analy­ses (Spring et al. 1993, 1995).
Magnetotactic bacteria contain dense inclusion bodies, which
may impart a magnetic moment upon the cell (Figure 8.23).

101
 Ma gnetic For ce

Some of these magnetotactic bacteria contain approximately

4% iron by weight. The magnetic iron is in the form of either
magnetite (Fe304) or greigite (Fe3S4) (Farina et al. 1990; Mann
et al. 1990).
The magnetic iron is enclosed in membrane-bound
magnetosomes.
These allow cells to orient themselves in magnetic fields and
actively move by flagellar motion toward one of the
magnetic poles.
Initial enrichments of magnetotactic bacteria from sediments
were obtained by placing magnets next to the culture flasks
and collecting the microorganisms that aggregated near the
magnetii poles

102
 Ma gnetic For ce

The adaptive value of magnetotactic behavior is a yet unclear.

Because the magnetotactic microorganisms that have been
described are microaerophilic o anaerobic, it has been
suggested that magnetotactii orientation may help these
motile organisms to location deeper, more reduced organic
sediments. Experimentation on a pure culture of magnetotac
tic bacterium Aquaspirillum magnetotacticum (Ric( et al.
1991) revealed that even in a pure culture som bacteria are
attracted to the north and others to th south magnetic pole.
Pulse magnetization can alte and even reverse the
orientation of A. magnetotactician cells. However, the
ecological value of magnetic orientation for microorganisms,
if any, remain to be determined.

103
 Chemical Requirements
• water!
• Elements
– C (50% of cell’s dry weight) HONPS
– Trace elements
• Organic
– Source of energy (glucose)
– Vitamins (coenzymes)
– Some amino acids, purines and
pyrimidines
 Source of Carbon, Energy,
and Electrons
• Organisms categorized into two groups based on
source of carbon
– Those using an inorganic carbon source (carbon
dioxide) are autotrophs
– Those catabolizing reduced organic molecules
(proteins, carbohydrates, amino acids, and fatty acids)
are heterotrophs
• Organic compounds can be potential nutrients for
microbes, but some of them act as inhibitors or
poisons, such as alcohols and other acids.
• Some microbes specially excrete allelopathic
substances, such as antibiotics.
 Four Basic Groups of
Organisms
Energy Source
Light (photo-) Chemical compounds
(chemo-)
Carbon Source

Carbon Photoautotrophs Chemoautotrophs

dioxide
(auto-)

Organic Photoheterotrophs Chemoheterotrophs

Compounds
(hetero-)
 Nutritional Categories
• Carbon sources
– CO2 = autotroph
– organic = heterotroph
• Energy sources
– sunlight = phototroph
– organic = chemotroph
 A “Chemoheterotroph”
would…..

• Derive both carbon and energy from

organic compounds
 A “Chemoorganic autotroph would be….

Derives energy from organic compounds and carbon

source from inorganic compounds

A related ancient group…..

Lithoautotroph
Neither sunlight nor organics used, rather it relies
totally on inorganics
 Nutritional Categories
• Saprobe – lives on organic matter of dead
organisms
• Parasite – lives on organic matter of living host
= pathogens
 Classifying Microbes According to Their
Energy and Carbon Sources.

• Based on energy source

– Phototrophs
• Use light as an energy source; photosynthesize.
– Chemotrophs
• Use inorganic and organic chemicals.
• Based on carbon source
– Autotrophs
• Use carbon dioxide.
– Heterotrophs
• Do not use carbon dioxide as their carbon source.
• Carbon sources
• Heterotroph – must obtain carbon in an
organic form such as proteins, carbohydrates,
lipids and nucleic acids, made by other living
organisms
• Autotroph - an organism that uses CO2, an
inorganic gas as its carbon source
– not nutritionally dependent on other living things

113
• Main determinants of nutritional type are:
– carbon source – heterotroph, autotroph
– energy source –
• chemotroph – gain energy from chemical
compounds
• phototrophs – gain energy through
photosynthesis

114
Heterotrophs: This group of bacteria has a simpler set of enzymes so they must use
organic carbon for growth.
It can be further divided into:

Parasitic bacteria: grow in and feed on a different organism.

Saprophytic bacteria: obtain their nutrients from dead or decaying organic matter.

Most of pathogenic bacteria are parasitic bacteria.

Some saprophytic bacteria cause disease by acting on food to produce toxins.
 Nitrogen, Phosphorous,
Sulfur and other elements
N is required for protein formtion in microbes. In some cases,
some chemolithotrophic microbes use ammonia or nitrite as
source of energy. Some use nitrate as terminal electron
acceptor in respiratory pathways, resulting in denitrification.
Phosphate is required for microbial generation of ATP and for
NA and membrane synthesis. High conc may be inhibitory for
microbial growth.
Concentration of available N & P often limit both
productivity and decomposition in aquatic environments.
Controlled addition of N & P can enhance decomposition of
polluting organic compounds, for example, the extent of
petroleum biodegradation of in seawater has been found to be
limited by both N & P. This can be overcome by addition of N
& P fertilizer.
Inorganic S is required by microbes for formation of
proteins and other molecular components.
Some oxidized form of S, e.g SO2 are toxic to microbes,
used as disinfecting agents.
H2S is used by photoautotriphic bacteria as an electron
donor.
Fe is required in cytochromes and other iron proteins.
pH and Eh are depended on Fe.
Ferrous and ferric ions demonstrate different degrees of
solubility, which affects their availability.
Chloride ions are essential for maintenance of
membrane function.
Silicon is required by diatoms, silicoflagellates and
radiolaria for building cell wall structures
 Gas(O2) Requirements:
Oxygen and Bacterial Growth
• Aerobe -grows in presence of atmospheric
oxygen (O2) which is 20% O2
• Obligate aerobe –requires O2
• Anaerobe -grows in the absence of O2
• Obligate anaerobe -usually killed in presence of
O2
• Microaerophiles -requires 2–10% O2
• Facultative anaerobes -do not require O2 but
grow better in its presence –prefer O2
• Aerotolerant anaerobes -grow with or without O2
119
 (O2) Gas Requirements

According to the requirement of O2 during bacteria growth,

bacteria can be divided into groups:

Aerobic Anaerobic
1. Obligate aerobe: Growth No growth
2. Microaerophile: Growth at low O2 No growth
3. Obligate Anaerobe: No growth Growth
4. Facultative aerobe: Growth Growth
 Categories of Oxygen Requirement
• Aerobe – utilizes oxygen and can detoxify it
• Obligate aerobe - cannot grow without oxygen
• Facultative anaerobe – utilizes oxygen but can
also grow in its absence
• Microaerophilic – requires only a small
amount of oxygen

121
 Categories of Oxygen Requirement
• Anaerobe – does not utilize oxygen
• Obligate anaerobe - lacks the enzymes to
detoxify oxygen so cannot survive in an oxygen
environment
• Aerotolerant anaerobes – do no utilize oxygen
but can survive and grow in its presence

122
123