MCB 324 MICROBIAL ECOLOGY

(3 credit units)
BY

DR. FATOKUN, E.N.

DEPARTMENT OF BIOLOGICAL SCIENCE AND BIOTECHNOLGY,

COLLEGE OF PURE AND APPLIED SCIENCE

CALEB UNIVERSITY, IMOTA, LAGOS STATE

1 of 54
 COURSE OUTLINE

1. UNIT I: Microbes and Ecological Theory

2. UNIT II:
3. A. Physiological, and Morphological Adaptations of Microorganisms to their
Environment
4. B. Genetic Adaptations of Microorganisms to their Environment
5. UNIT III: Microbial interactions:
• Neutralism
• Commensalism
• Amensalism
• Mutualism
• Competition
• Predation
6. UNIT IV: Microorganisms in natural ecosystems
• Soil microbiology
• Aeromicrobiology
• Aquatic microbiology
7. UNIT V: The life of microorganisms in air, springs, rivers, lakes and seas
8. Week VI: Cycling of elements in water and sediments

LEARNING OBJECTIVES

At the end of this course students are expected to;

• understand the concepts of microbial ecology
• know the definition of ecological terms
• familiarized with different microbial groups in the environment
• understand the different types of interactions between microbial populations
• identify possible microbial interactions in the environment
• understand different types of microbial adaptation and application of the concept in
simple problem solving in microbial environment

2 of 54
 • know the effects of microbial interactions and activities in the ecosystem

UNIT 1

INTRODUCTION

Microbes can be found in almost every sphere of physical environment with estimated population
of about 1017, they represent most of the diversity of life on Earth and are found in every
environment. Microbial ecology deals with the study of which microbes are present and how they
interact with each other and their environment, in order to understand how such huge microbial
populations, exist and survive together in a productive fashion. Microbial ecology is therefore a
multidisciplinary field spanning different aspects of the environment. However, it is more
concerned with the microbial activities in terms of the resultant chemical and physical changes
they make in the environment and those aspects of nutrient cycles, polluted water sources,
biochemical capacities of causative organisms to induce infection and diseased patients, etc.

LECTURE I

Microbes and Ecological Theory

Learning Objectives:
At the end of this course students are expected to;
• understand the concepts of microbial ecology
• know the definition of ecological terms
• understand the ecological order of microorganisms

Definition of ecological terms

Individual: This refers to the individual organisms in the population which is unique and distinct
in its characteristics.

Population: This is the collection of individual microbial species. It is homogenous and specific,
comprising microbes which share basic characteristics.

3 of 54
Ecosystem: This is a combination of biotic and abiotic components of a specific environment.
Usually, such a unit has a collection of organisms and abiotic components which are unique to it
and as such, one eco-system is different from another.

Community: This is a collection of microorganisms inhabiting a given site in the ecosystem; that
is, the ecosystem without the environmental or abiotic factors.

Each ecosystem has, associated with it certain physical, chemical and biological characteristics.
These factors govern the composition of the community by dictating which of the individual
microorganisms will be successfully established, and out of those established, some will be
dominant while others are limited and other groups are totally eliminated. Therefore, selection by
environmental factors is important. Those organisms that are established are those that are better
adapted to the abiotic conditions (PH, temperature, moisture, water activity, oxygen concentration
etc.) in that particular environment. Organisms that cannot cope with the prevailing conditions are
eliminated. The environment builds the community through selection. It is as a result of this
relationship with a community that we have certain Species of micro-organism as dominant.

The Habitat: A habitat is an area having a degree of uniformity in terms of the abiotic components.
The size of the habitat is not important because it varies considerably. The important factor is that
certain sets of conditions are uniform to that area. Habitats are therefore also considered to be of
ecological significance, examples include surfaces of plants and animals, soil, open sea, blood, air,
nasal passages, and alimentary canal, etc.

Niche: The role of a particular organisms in a particular place is the niche. Each microbe has its
specific role based on variation in the ability of microorganisms to make use of resources available
in their habitat.

Microorganism could be divided into types depending on their functions in the different habitats,
those with narrow and those with broad range of tolerance. Those with narrow niche are highly
specialized and perform single function or role e.g. obligate parasites, autotrophic organisms,
while those that carry out a range of functions are said to have a broad niche e.g. heterotrophic
organism. Those that occupy a narrow niche are easily eliminated if there is a change in
environmental conditions especially as it affects their survival, but they however, flourish
luxuriantly when their conditional requirements are met. Examples are photosynthetic micro-

4 of 54
organisms which are adversely affected when the source of light is blocked but they grow rapidly
when there is light. On the other hand, those that have a broad niche are not severely affected by
changes in the environmental conditions.

Hierarchy and ecological order of microorganisms

In the hierarchy and ecological order of microorganisms we consider that individual cells of the
same type multiply to form populations. Metabolically related populations constitute groups called
guild. Mixtures of different guilds conducting complementary physiological processes interact to
form microbial communities. Microbial communities then interact with communities of
macroorganisms and the physicochemical environment to determine an ecosystem.

Concept of microbial ecology

There are many organisms yet to be discovered, and this is the goal of microbial ecology. Each
type of microorganism has at least one ecological niche, that is, a function that it can successfully
compete for in a habitat. Countless microbial niches exist in the biosphere and are to a great extent
responsible for the countless metabolic diversity and biodiversity of microorganisms on earth.
Since microbes are small, their habitats are small and their ecological niches can also cover small
spatial scales; nevertheless, they affect ecosystem on greater scales. The concept of
microenvironment becomes important in understanding how microbes actually live and metabolize
within their natural habitats. Such microenvironments commonly undergo profound changes in
physicochemical characteristics, resulting in gradients. Example is the change in microbial
population in human mouth during respiration from aerobic to anaerobic microbes resulting in
different physiological condition of the individual.

EXERCISE

Define the following ecological terms:

a) Habitat
b) Niche
5 of 54
 c) Ecosystem
d) Community

LECTURE II

COLONIZATION AND SUCCESSION

When an area is denuded or freshly exposed e.g., when we have an earth quake which exposes the
earth’s surface, or when a tissue is freshly exposed or wounded, a number of microorganisms will
be deposited on such surfaces. The first microorganisms to arrive on such surfaces are called
pioneers. These organisms grow and multiply to form the pioneer community and from the time
the exposed areas are occupied by microorganisms, it is said to be colonized. After the
establishment of the pioneer community, they feed on the substrates, produce by products and
other waste materials or metabolites, and so the environment becomes modified. The modified
environment paves way for colonization by other organisms, while the pioneer communities are
gradually eliminated. Thus, we have a situation whereby one community will out-grow and replace
another. This phenomenon is referred to as succession.

Climax Community: When colonization has taken place, succession follows and there is a
continuous modification of the environment. However, at a stage the community remains constant
for at least some time and the process of succession is stopped; and a community that is
characteristic of that habitat results. This is called the climax community.

The species composition at in a climax community is maintained reasonably constant for a period
of time. The stability in composition does not mean that the organisms do not die but the number
of organisms dying is quickly replaced and this is a reflection of dynamic equilibrium. The climax
community therefore is a self-replicating entity where the microorganisms and the physical
environment are in constant equilibrium.

Often, there are alternations in the physical conditions e.g., when a large quantity of pollutants is
introduced into a stream, the organic matter component is eliminated and the climax community
is distorted. However, such disturbances are temporary and the original climax community is
restored with time or as soon as the disturbance is removed.

6 of 54
 SUCCESSION IN NATURAL HABITATS

1. Succession of Micro-organisms on Cellophane Film

Tribe (1960) studied the colonization and breakdown of cellophane film (pure regenerated
cellulose). The breakdown of cellophane buried in a number of soils was studied. Though
variations existed in the soil type, a general pattern of colonization was observed.

1. The first colonizers were fungi and out of these, based on morphological and vegetative
characters, three (3) classes were identified. (a) Those Characterized by coarse mycelium which
ramifies through the surface of the cellophane and rapidly initiates decomposition by lysis of the
cellulose adjacent to their hyphae. Such fungi are mostly in the form genus Rhizoctonia and were
clearly cellulolytic and dominant species at that stage. (b) Members of the second group are mostly
species of the well-known cellulolytic genera e.g Chactomium species and Humicola species
which exist as co-dominants. These fungi did 14 not ramify extensively with the cellophane but
rather they penetrated the thickness at scattered sites by means of “rooting” hyphae which then
branches to form a kind of circular hyphal system. (c) The third group consists of chytrids which
develop on the cellophane pieces. At this stage, the cellophanes are no longer intact but in pieces.
The presence and activities of the initial colonizers (pioneer community) were obviously related
to their ability to produce “cellulases”. Though, other factors must have been involved because the
soil contains other cellulolytic organisms which rarely appear on cellophane. Bacteria are
relatively uncommon during this initial stage of fungal attack. During mycelium senescence
however they rapidly increase and presumably utilize either materials diffusing from the hyphae
or the hyphae itself.

2. The second colonizers are the bacteria. In turn bacteria support a population of nematodes and
protozoa. After the micro-organisms have colonized the cellophane/cellulose, mites, springtails
and other worms become active and the substrate becomes unrecognizable by their passage

7 of 54
through the guts of these organisms. Cellophane decomposition therefore involves a wide range of
micro-organisms and small animals whose occurrence depends on nutrient availability.

2. Succession of Micro-organisms on Dung.

If a fresh dung is placed under a bell jar and a fairly suitable humidity is maintained, a succession
of fungal fruitifications can be observed. The first to appear are Zygomycetes followed by
Ascomycetes and then Basidiomycetes. Each group has been considered to represent sugar,
cellulose and lignin utilizers respectively. Harper and Webster (1964) while confirming the
sequence have shown that it is not a succession based on nutritional factors. They grew a number
of fungi involved under a variety of conditions and showed that each group had a characteristic
minimum time before commencement of growth and appearance of fruiting bodies. If the fungi
are listed in the order based on the minimum time, the sequences is also found to be the same as
on dung. According to these authors, the succession of fruiting bodies on dung is connected with
the duration of necessary developmental periods rather than different assimilatory abilities.

3. Colonization of Sterile Human Hair.

Griffin (1960) made a sequential study of sterile human hair placed on the surface of various soils.
In general, his observations showed that the first colonizers where Fusarium species, Penicillium
species and some Mucorales. These species rely on simple sugars. The second group of colonizers
includes Chaetomium cochloides, Humicola species, Gliocladium roseum and Penicillium species.
The first two are cellulolytic while the last two are polysaccharide users. The third group are
keratinolytic members of Gymnoascaccae which are mainly Ascomycetes. In this case, succession
is based on nutrition. This is more clearly shown in the late predominance of species utilizing the
most resistant component of the substrate (Keratin).

EXERCISE

a) Describe a Climax Community.

b) Explain the order of succession of a cow dung; and state the basis on which this succession
is taking place.

8 of 54
 LECTURE III

MICROORGANISMS IN ECOSYSTEMS
Introduction

Microbes are present in every known ecosystem, they represent most of the diversity of life on
Earth and are found in every environment. Microbes constitute a vital part of the ecosystem and in
this section we shall consider the various environments where microbes can exist. The microbial
environment however, is complex and constantly changing. It often contains low nutrient
concentrations (oligotrophic) and exposes microbes to many overlapping gradients of nutrients
and other environmental factors. The types, physicochemical factors that govern the growth and
survival of microbes in these environments and the methods employed in their isolation, study and
quantification shall be considered.

Types of microbes

Microorganisms are divided into six groups: Archaea, Bacteria, Fungi, Protists, Viruses and
Prions. The last two types of microbes are not actually living cells. They are included with
microbes because they can only be viewed with the aid of microscope, and have the ability to
replicate inside living cells.

Archaea

Archaea are the first living relatives to the first organisms on earth. They resemble bacteria due to
similarity in size and shape, although a few have strange shapes, e.g. the flat and square-shaped
cells of Haloquadratum walsby. Archaea lack cell nucleus which make them prokaryotes. They
live mostly as single cell and have cell walls which unlike that of bacteria lack peptidoglycan,
rather composed of glycoproteins and polysaccharides. The RNA polymerase of archaea is very
similar to that of eukaryotes. Archaeans are anaerobic and their habitat is mostly in environments
with extreme conditions. There are three kingdoms of Archaea:

a) Crenarchaeota: are characterized by their ability to tolerate extreme temperature and acidity
(e.g. Hyperthermophiles and Thermoacidophiles). Examples include Pyrolobus fumarii (live in

9 of 54
temperatures between 90 and 113℃), and Sulfolobus acidocaldarius (found near volcanic
environments in hot, acidic springs containing sulfur).

b) Euryarchaeota: include the methane producers and halophiles (e.g. Methanogens and
Halophiles). They produce methane gas as a by-product of metabolism. They can be found in
environments such as swamps, wetlands, ice lakes, the guts of animals (humans, cow and deer),
and in sewage. Examples are Halobacterium (include several species of halophilic organisms that
are found in salt lakes and high saline ocean environments), Methanococcoides burtonii (these
psychrophilic methanogens were discovered in Antarctica and can survive extremely cold
temperatures), and Methanococcus spp. (they are methanogen found near hydrothermal vents).

c) Korarchaeota (also also known as Xenarchaeota): a recently proposed and little characterized
kingdom comprising groups of other Archaeans. Not very much is known about this kingdom.
However they are thought to be very primitive life forms, they are thermophilic and have been
found in hot springs and sediments from Obsidian Pool in Yellowstone National Park.

Importance of Archaea:

i. They are useful in commercial processes such as production of enzymes that work in
different industrial processes and those that work at very high temperatures, such as
conversion of starch into dextrins, detergent making and the Taq polymerase enzyme used
for gene amplification by polymerase chain reaction (PCR).
ii. They are used for Biogas production by decomposition of cow dung into methane.
iii. Some species such as Methanobacterium ruminantium are present in the gut of ruminants
helping the digest cellulose.
iv. Archaea may also be useful in cleaning up contaminated sites, e.g. oil spillage.

Bacteria

Bacteria are unicellular prokaryotic microbes like Archaea. They have circular DNA and lack
membrane bound organelles. Bacteria grow in many different habitats including animals and
plants. Examples of bacteria are Salmonella, Azotobacter, Chlamydia, etc.

Positive importance of bacteria

i. They are used in antibiotics production.

10 of 54
 ii. They help in the fermentation processes such as baking, cheese making and brewing.
iii. Bacteria help to produce vitamin K in human intestine.
iv. They help Ruminants to digest cellulose in grass.
v. Bacteria are used in tobacco curing.
vi. They are used in leather and hides tanning.

Harmful effects of bacteria

i. Bacteria such as Staphylococcus cause food poisoning, leading to diarrhoea and vomiting.
ii. Food spoilage bacteria cause rottenness of fruit, vegetables, meat, etc.
iii. Some bacteria e.g. Spirochete cytophaga causes deterioration of materials such as leather,
cotton and wood.
iv. Soil sulphate can be lost by its conversion to hydrogen sulphide by Desulfovibrio.

Fungi

These are microbes having certain features as plants but lack chlorophyll and are heterotrophic,
being unable to manufacture their food. Their mode of feeding could be saprophytic, parasitic
or symbiotic depending on the type of fungus.

Importance of fungi

i. They can be used in food industries like in baking, brewing and cheese making process.
ii. They are used in antibiotics production.
iii. Some fungi such as mushrooms, truffles and morels are used as food, as rich source of
proteins, minerals, etc.
iv. Fungi aid in decomposition of organic matter thereby adding to soil nutrient.
v. They play a very important role in the biosphere in nutrient recycling in all terrestrial
habitat.
vi. They are vital for good growth of most plants through the formation of mycorrhizal
association with certain plants.
vii. Some types of fungi example the Chinese caterpillar fungi which parasitize insects can
be used as biocontrol agents for controlling insect pests of crops.

11 of 54
Adverse effects of fungi

i. They induce human and animal diseases e.g. mycosis caused by Aspergillus, Cryptococcus
and Trichoderma.
ii. Fungi cause spoilage of food including fruit, vegetables and all kinds of foodstuff.
iii. Many fungi are plant pathogens, causing diseases in important crops.

Protists

Protists are microbes that occur either as single cells or a colony of similar cells. They live in water
or moist habitats. They can be found in other multicellular organisms in parasitic or symbiotic
relationship with their hosts. Examples are amoeba, paramecium and euglena.

Importance of protists
i. They play a vital role in decomposition of matter which helps to free up resources for use
by plants.
ii. Photosynthetic members of protists help in providing oxygen in the atmosphere.
iii. They are used in thickening of ice cream and bread.
iv. They are used in toothpaste production

Viruses

Although regarded as microbes, viruses are non-living cells. They cannot carry out replication
independently without a host cell, they are inactive outside of a cell. Viruses are obligate
intracellular parasites and can infect cells of many organisms including bacterial cells, plants,
animals and human cells. Viruses are extremely smaller than bacteria, up to a million viruses can
fit into a bacterium! Viruses that infect bacteria are called bacteriophage, and they are cell specific.
Which means, a virus that infects one type of bacterium will not infect others. Example of viruses
include Polio virus, Rubella (measles), Rabies virus and Hepatitis B virus.

Effects of viruses

i. Viruses cause diseases in animal e.g. Rabies virus, HIV/AIDS and corona virus.
ii. They affect the immune system.

12 of 54
 iii. Some are plant pathogens e.g. Tobacco mosaic virus, Tomato yellow leaf curl virus and
African cassava mosaic virus.

Prions

The term prions was derived from the phrase proteinaceous infectious particle. Prions are
transmissible particles that are devoid of nucleic acid and seem to be composed exclusively of a
modified protein (PrPSc). Prions are sometimes classified as microbes due to their ability to cause
disease. However they are unprecedented infectious pathogens that cause a group of invariably
fatal neurodegenerative diseases and like viruses they are non-living cells that are proteins (consist
of amino acids). Unlike most disease causing microbes, prions occur naturally within human and
other mammalian brains as normal cellular prion protein (PrP). Prion diseases may present as
genetic, infectious, or sporadic disorders, all of which involve modification of the normal cellular
prion protein (PrP). The normal cellular PrP (PrPC) is converted into PrPSc through a
posttranslational process during which it acquires a high beta-sheet content. This β-sheet-rich
structure has properties that allow for greater stability and are responsible for the ability of PrPSc to
form aggregates; such PrPSc aggregates are capable of forming amyloid fibrils. These amyloid
fibrils are deposited in the tissues, where they are associated with the pathology of the disease such
as multiple neurodegenerative disorders.

Effects of prion

Prions cause a group of fatal sometimes zoonotic transmissible spongiform encephalopathies

(TSEs) also known as prion diseases. Although they belong to the class of neurodegenerative
disorders that includes Alzheimer's disease (AD), Huntington's disease (HD), and Parkinson's
disease (PD), prion diseases affect both animals and humans. Examples of prion diseases in
animals include scrapie disease, bovine spongiform encephalopathy (mad cow disease) and
chronic wasting disease. Prion diseases in humans include Fatal Familial Insomnia (FFI),
Gerstmann-Straussler-Scheinker (GSS) syndrome, Kuruetic disease and Creutzfeldt-Jakob disease
(CJD)

Differences between viruses and prions

i. Viruses contain nucleic acid (DNA or RNA) while prions do not, instead they consist of
protein materials.

13 of 54
 ii. Prions exist in multiple molecular forms while viruses exist in a single form with distinct
ultra-structural morphology.
iii. Viruses almost always provoke immune response (immunogenic) in the host being
infected. Prions on the other hand are non-immunogens.
iv. Prions are not easy to decompose biologically/resistant to digestive enzymes/resistant to
high temperature, disinfectants and radiation.

EXERCISE

1. Differentiate between a virus and a prion.

2. State three kingdoms of Archaea and their unique environment.

UNIT 2

LECTURE I

Morphological and Physiological adaptations of Microorganisms to their

Environment

Introduction

Microorganisms experience numerous environmental factors over their evolutionary history,

including those that remain essentially constant over long periods (e.g., geological eras), change

slowly (e.g., general increase in annual temperatures), fluctuate periodically (e.g., day-night cycles

and seasonal variations), or change frequently and somewhat randomly (e.g. unpredictable nutrient

loading). These changes occur over diverse timescales, ranging from the lifetime of an individual

cell to multiple generations. Accordingly, microbes have evolved unique strategies to deal with

the peculiarities of their environment. Hence adaptation of microorganism implies that it has

14 of 54
evolved molecular mechanisms that allow it to grow optimally under the varying physicochemical

conditions of its environment.

Environmental adaptation of biological systems can be considered from three evolutionary

perspectives: (i) acclimatization of existing cellular machinery to operate optimally in a new

environmental niche; (ii) acquisition of entirely new capabilities through horizontal gene transfer

or neofunctionalization of gene duplications and (iii) reorganization of network dynamics to

appropriately adjust existing physiological processes to match dynamic environmental changes.

In this units, we shall consider the various adaptations of microorganisms that enable them to

survive in their ecosystems.

Microbial adaptation is the ability of microbes to withstand and adjust to the selective pressure

of their environment.

Morphological adaptations

Morphological adaptations give rise to specialized body parts/structures that enable an organism

live, survive and reproduce in its natural habitat. The prokaryotes exhibit a variety of

morphological and behavioural adaptations as a reaction to environmental stimuli. These can be

observed in the colony and cellular morphology of the microorganism.

a) colony morphology such as shape, height, margin (entire/smooth, undulating, filiform); surface

refraction (smooth, dull, glistering/mucoid, rough); opacity and colour (transparent, translucent,

opaque, pigmented, hemolytic).

b) cellular morphology such as size and shape (bacilli, cocci, spiral).Prokaryotic cells as small as

0.5 μm and as large as 0.3-0.5 mm are known, and some species display truly unusual shapes. A

15 of 54
small cell size is advantageous for efficient nutrients uptake and waste products elimination. Small

cells are especially abundant in low nutrient environments. Microscopic examination of the

planktonic bacterial community in the oligotrophic ocean reveals that most of the cells are smaller

than 1 μm, often even smaller than 0.5 μm. In some cases it has been proven that the smallness of

the cells is an inherent property of the species. In other cases, cell size may depend on the

nutritional status: nutrient-starved cells are often much smaller than cells growing in the rich

medium in which all required nutrients are present in excess. Attempts to isolate bacteria adapted

to life at low nutrient concentrations often yield spirally-shaped cells, increasing the surface-to

volume ratio not by size reduction but by their specialized cell morphology. Cells with a large

surface area relative to their total intercellular volume are able to maximize nutrients uptake and

can therefore grow more quickly than their larger neighbours. Thus, the majority of microbes

growing in nutrient-limited or oligotrophic open oceans are between 0.3 μm and 0.6 μm. Such

microbes have evolved to maximize their surface area to volume ratio in oligotrophic conditions.

Another strategy to increase the surface-to-volume ratio and thus to increase the area of the cell

membrane and enhancing the potential of nutrient uptake is the formation of prosthecae,

appendages consisting of extrusions of cytoplasm, bounded by the cell wall.

c) The outer layers of the microbial cell: different structures of bacterial cell wall lead to

differences in Gram staining reaction. Strains of the fungal Antarctic genus Cryomyces due to their

high pigmentation, is presumed to show higher resistance to UV radiation than the strains of the

Antarctic filamentous species Arthrobotrys ferox.

d) Special Intracellular Structures: many prokaryotes contain a variety of cytoplasmic inclusions

such as intracellular membrane system and storage materials. They produce complex intracellular

membrane system to increase the surface area where energy production processes occur. The

16 of 54
structures can be storage granules or inclusion bodies (which are nuclear or cytoplasmic aggregates

of stainable substances, usually proteins).

These intracellular membranes can be found in photosynthetic, nitrifying and methane-oxidizing

bacteria. Cigar-shaped structures called chlorosomes which contain light-harvesting

bacteriochlorophylls can be found in photosynthetic members of the Chlorobiales and

Chloroflexales. Prokaryotic cells may also contain a variety of storage materials (SM), found as

cytoplasmic inclusions. These SM are in most times surrounded by a membrane, and are assumed

to allow bacterial survival in hostile or nutrient-depleted environments. Cyanobacteria and some

other bacteria may accumulate glycogen as a storage product; phosphorus is stored in many

bacteria as polyphosphate granules; and elemental sulfur granules are deposited in sulfur oxidizing

chemoautotrophic and purple sulfur bacteria.

At the other extreme is an unusual marine microbe found off the coast of Namibia in West Africa.

Thiomargarita namibiensis, (meaning Sulphur pearl of Namibia) is considered to be the world’s

largest bacterium. Individual cells are usually 100-300µm in diameter. Sulfide and nitrate are used

by the organism as electron donor and acceptor respectively. In this case, nitrate from the overlying

seawater, penetrates the anoxic sulfide-containing mud only during storms. When this short term

mixing occurs, this species takes up and stores the nitrate in a large internal vacuole which occupies

98% of the bacterium volume. The vascular nitrate can approach a concentration of 800mµ. The

elementary sulfur granules appear near the cell edge in a thin layer of cytoplasm. Between storms,

the organism lives using the stored nitrate as an electron acceptor. These unique bacteria are

important in sulfur and nitrogen cycling in these environments.

Most estuaries undergo large scale tidal flushing and this forces organisms to adapt to changes in

salt concentrations on a daily basis. Microbes living under such conditions combat the resulting

17 of 54
osmotic stress by adjusting their intracellular osmolarity to limit the difference with that of the

surrounding water. Most protists and fungi produce osmotically active carbohydrates for this

purpose; whereas prokaryotic microbes regulate internal concentrations of potasium or special

amino acids. Most other microbes that inhabit estuaries are halotolerant, distinct from halophilic.

Halotolerant microbes can with-stand significant changes in salinity, halophilic micro-organisms

have an absolute requirement for high salt concentrations.

e) Surface features: When prokaryotes decide to strike out for greener pastures, they make and

use special structures called flagella. Flagella function like little flippers, but they look like whips.

Flagella can be at either the poles of the cells or all over the cell. Bacteria can use their flagella to

swim towards beneficial substance (food) and away from harmful materials (toxins), a process

called chemotaxis. In some environments it is best to stay put and let the food come to you. One

such environment, from a bacterial view, is the intestine. Human intestines for instance, are full of

bacteria that help digest food.

In order to stay put and enjoy the bounty, rather than, err, slip out the other end, bacteria can stick

to the intestines by using small appendages called pili (singular: pilus)

or fimbriae (singular: fimbria). Pili help bacteria and archaea stick to various surfaces including

rocks, plastic, glass, and the intestines. Pili are made up of units of a protein called pilin. Pili also

help bacteria stick to each other to form biofilms or exchange DNA in a process called conjugation.

Furthermore, zoosporic organisms adapt to life in the water by having asexual reproductive spores

with a single whiplash flagellum e.g. chytrids. Another important group is the filamentatous fungi

that sporulate under water. These include the hyphomycetes known as ‘Ingoldian fungi'. The

ecology of these aquatic fungi is that they produce a unique tetraradiate conidium on the vegetative

mycelium which grows inside decomposing leaves. When the vegetative hyphae differentiate into

18 of 54
an aerial mycelium, conidia are released into the water. The released conidia are then transported

and often are present in surface foams. When the conidia come in contact with leaves, they get

attached and establish new points of growth.

e) Endospore formation (central, lateral and terminal): One way that some bacteria cope

with downturns in their environment is to sporulate (make spores). Spores are similar to

the seeds of plants, except seeds are multicellular and packed with nutrients, and spores are

not. Spores can survive high temperatures that sterilize other things. The upshot of

sporulation is that if conditions are bad, every component of the cell is protected. Spores

can outlast many extreme conditions and survive for millions of years. Two important

genera that form spores are Bacillus and Clostridium. Certain Bacillus spores are

responsible for the disease anthrax. Certain Clostridium spores are responsible for the

disease tetanus.

LECTURE II

Physiological adaptations are systems present in an organism that enable the performance of

certain biochemical reactions, growth and development, temperature regulation, ionic balance and

other aspects of homeostasis. Physiological adaptation could involve the coordination of thousands

of chemical reactions in response to constantly changing environment such as temperature, nutrient

availability, pH and harmful agents. These chemical reactions are controlled by enzymes which

are themselves encoded by genes. Bacteria can sense food as well as harmful chemicals in their

environment. Chemotaxis of a bacterium, a type of motion guided by perception of metal or

chemical stress and its motility, largely depends on its physiological capability to utilize or resist

the substance in the environment. In addition, bacteria within a developing biofilm may require

19 of 54
chemotaxis and/or motility to move along the surface, thereby facilitating the growth and spread

of the biofilm.

Physiological adaptation can be observed in the diauxic growth pattern, a diphasic (two-phase)

growth response, usually interpreted as an adaptation to maximise population growth in multi-

nutrient containing two or more carbon sources environments. For instance, when by E. coli is

cultured in a minimal medium supplemented with glucose and lactose, a diauxic growth pattern is

exhibited by the microbe. An initial rapid growth of the E. coli is accompanied with depletion of

glucose level. Growth is paused when glucose is exhausted, and resumed at a slower rate, using

the lactose. E. coli detects and preferentially utilizes the glucose while shutting down other carbon

source metabolic pathway, until the preferred carbon source is exhausted.

Fig. 1. Diauxic growth of E. coli on glucose and lactose medium

Features for physiological adaptation include possession of membrane transport protein for the

direct uptake of available substrates, cofactors required for growth, specialized efflux pumps and

ability to secrete requisite enzymes. Physiological adaptation occurs both because of genetic and

20 of 54
physiological toughness to withstand stress that accumulates over many generations and latent

genetic variance that is revealed after environmental discomfort.

EXERCISE

1. Highlight the morphological characteristics of microbial adaptation to the environment.

2. Explain the physiological adapation of E. coli to a multinutrient.

LECTURE III

Genetic adaptations of Microorganisms to their Environment

Genetic Adaptation

Microorganisms, especially bacteria thrive in a seemingly limitless range of extreme

environments, accompanied by unusual metabolisms and rather refined behaviours. These are

made possible through their ability to acclimatize their existing cellular machinery in order to

operate optimally in a new environmental niche. Genetic adaptation of microorganisms can be

brought about by i) Mutations ii) Horizontal gene transfer (HGT). iii) Recombination iv) Gene

duplications v) Combinations of these events. These modifications can affect the expression of

gene function and could lead to the acquisition or loss of function within the whole community.

Genetic recombination is an important mechanism employed by bacteria to rapidly adapt to

selective pressures such as environmental pollution. Acquisition of new genetic materials helps in

construction of new metabolic pathways necessary for the microbial adaptation to a change in their

environment. Bacteria that degrade organic xenobiotics have revealed that they can adapt to these

compounds by expressing new catabolic pathways, including new functions to resist the potential

toxic effects of the xenobiotics or to use them as alternative source of essential nutrients, such as
21 of 54
those involved in carbon, nitrogen or free energy metabolism. At least some of them appear to

have evolved by pieced assembly of horizontally transmitted genes and subsequent mutations and

gene rearrangements. For example, with extensive evolution, mercury-resistant bacteria obtain

the mer (mercuric ion resistance) operon in their genome to respond to stress from toxic mercury

compounds. The mer operon enables bacteria to survive in the presence of mercury and reduce it

to volatile, less-toxic Hg0, which diffuses out of the cell.

Changes in gene expression are important processes in adaptation to abiotic and biotic

environmental changes, and studies demonstrate that they are involved in adaptive evolution as

well. Investigating microbial adaptation at the genetic level is a way to assess and follow the

biodegradation capacity of an organism or a community in different environments.

EXERCISE

3. What is the possible genetic adaptation of bacteria to the presence of xenobiotics in their
environment?

LECTURE IV

Factors Affecting the Morphological, Physiological and Genetic Adaptations

of Microorganisms to their Environment

Introduction

Microorganisms are adapted for optimum functioning in their normal physiological environments.
Any extreme change in environmental conditions from the optimum inflicts a stress on an
organism. The extent of the change will determine whether the organism is killed, ceases growth,
or has an increased lag time and reduced growth rate. Most bacteria are able to tolerate small
changes in an environmental parameter and can adapt over the time scale of minutes, hours, or

22 of 54
days. Microorganisms do this by both yielding to the stress conditions and making suitable
provisions for survival or attempting to resist the stress. Changes in environmental conditions away
from the optimal value can cause the induction of many elaborate stress responses. These strategies
are generally directed at survival rather than growth.

I. Effect of temperature: Because of the impact of temperature on all reactions of the cell,
adaptation to fluctuations in temperature is possibly the most common response researched.
However, the sensitivity of cells to temperature stress is dependent on several factors
including temperature, culture medium, and microbial strain. Growth of microorganisms
at temperatures below or above the optimum for growth can cause a number of
physiological and morphological changes. Temperature can influence the response of
microorganisms either directly, by its effects on growth rate, enzyme activity, cell
composition, and nutritional requirements, or indirectly by its effects on the solubility of
solute molecules, ion transport and diffusion, osmotic effects on membranes, surface
tension, and density.

Temperature-induced changes in cell membrane fatty acid composition: Microorganisms adjust

their membrane lipid composition in response to changes in growth temperature to ensure
membrane function such as enzyme activity and solute transport. Incubation at low temperatures
can change the lipid composition of microbial cells. There is an increased proportion of unsaturated
fatty acids in bacteria and yeast as the growth temperature decreases which allows the membrane
to retain fluidity, gel formation is prevented and membrane function is maintained. Unsaturation
of fatty acid chains increases the fluidity of the membrane because unsaturated fatty acid groups
create more disturbance to the membrane than saturated chains and is achieved by desaturases
situated in the membrane itself and thus are able to react quickly. The average fatty acid chain
length may be shortened, which would have the effect of increasing the fluidity of the cell
membrane because there are fewer carbon-carbon interactions between neighbouring chains.

Effect of temperature on solute uptake: For the cell to function normally, the membrane lipid
bilayers need to be largely fluid so that the membrane proteins can continue to pump ions, take up
nutrients, and perform respiration. Evidence over the years has shown that in order for
microorganisms such as psychrotrophs to grow rapidly at reduced temperatures, they must be able
to effectively transport soluble molecules across the cytoplasmic membrane. Example, a cold-

23 of 54
resistant sugar transport system was present that provided high concentrations of intracellular
substrates to stimulate growth of psychrotrophic Listeria monocytogenes.

II. Maintaining pH homeostasis: Acids generally inhibit molecular reactions essential to the
microorganisms by increasing the hydrogen ion concentration, which results in a decrease
in internal pH (pHi). This fall in pHi is a major cause of growth inhibition by weak acids.
Microorganisms like bacteria can only survive in acidic environments because of their
ability to regulate their pHi, a process primarily driven by the controlled movement of
cations across the membrane. The ability of a microorganism to maintain its pHi at a value
close to neutral(pH homeostasis) is achieved by a combination of passive and active
homeostasis mechanisms. However there are short-, medium-, and long-term adaptations,
which can aid microbial survival in acid conditions, and the rate of acidification affects the
acid tolerance observed.

Membrane response to low pH stress: At very acidic pH values, it has been proposed thatalterations
in the structure of the outer membrane may be a mechanism for enhancing microbial survival.
Some adaptations to low pH have also been noted in the lipid composition of the inner membrane,
which interacts with the periplasm. For instance, when Clostridiumacetobutylicum is grown at a
low pH, a decrease in the ratio of unsaturated to saturated fatty acids coupled with an increase in
the amount of cyclopropane fatty acids is observed; while the membrane composition of acid-
adapted E. coli has more cyclopropane derivatives and fatty acids present, compared with strains
that have not been exposed to low pH conditions.

Other effects of low pH stress: Studies with E. coli have shown that cells will move away from
acidic environments (chemotaxis) by sensing the decrease in pH via the transmembrane
transducer, a single protein, one part of which is exposed to the cytoplasm and the other to the
periplasm; ATPase and protein synthesisare important for maintaining the internal pH gradient
at low pH conditions for Enterococcusfaecalis. Morphological changes such as cell elongation in
Bacillus polymyxa and Clostridium tyrobutyricum as a stress response to suboptimal pH conditions
has been observed.Once the cells are put back into favourable conditions, the cells reverted and
gave a rapid apparent increase in cell numbers. Other stress responses, such as chilled
temperatures for Salmonella enteritidis and high salt concentrations for L. Monocytogenes similar
results.

24 of 54
Acids generally inhibit molecular reactions essential to the microorganisms by increasing the
hydrogen ion concentration, which results in a decrease in internal pH (pHi). This fall in pHi is a
major cause of growth inhibition by weak acids.

III. Osmotic Stress (aw)

A well-established response to the temporary loss of turgor pressure after a hyperosmotic shock
(for example, a reduction in aw surrounding the cell) is osmoregulation. If the aw of the environment
is reduced because of an increase in solutes unable to be transported across the cell membrane,
then the bacteria raise their internal solute levels.

Osmoregulation: Bacteria are constantly in contact with their surroundings, and the barriers
surrounding the cell are water permeable and thus ensure that bacteria come into rapid equilibrium
with their environment (Gutierrez and others 1995). Generally, the internal osmotic pressure in
bacterial cells is greater than that of the surrounding environment and so pressure is exerted
outward on the cell wall; this is called turgor pressure.A well-established response to the
temporary loss of turgor pressure after a hyperosmotic shock (for example, a reduction in aw
surrounding the cell) is osmoregulation.

Osmoregulation is initiated after the reduction in turgor of the cell following loss of cell water or
an increase in the external solute concentration that cannot cross the membrane. At high
osmolarities, bacteria have evolved to accumulate high cytoplasmic levels of a certain class of
solutes (compatible solutes) that do not interfere too seriously with the functioning of cytoplasmic
enzymes. This results in an increase in internal osmotic pressure and restores turgor pressure.The
internally accumulated solutes allow continued activity of cytoplasmic enzymes at lower water
activities. Osmoregulation also regulates the activity of porins, transport proteins, and potassium
in the cell membrane.

EXERCISE
List two adaptive features of cell membrane response to osmotic stress.

25 of 54
 UNIT 3

MICROBIAL INTERACTIONS
LECTURE I

Introduction

Microbial ecology as considered so far involves microbial communities in complex ecosystems.

However, the ecology of microorganisms also involves the metabolism, physiology and behaviour

of microbes as they interact with one another and with higher organisms. In this section, a number

of microbial interactions shall be defined and describe and also various examples shall be

illustrated.

Various associations of two or more microbes have been described in systematic terms and these

are normally based on aspect of nutrition. All these associations however, may be described by a

few basic types of interactions which can be illustrated in the simplest interacting system, i.e., a

two membered mixed population containing organisms A and B. There are only three possible

responses a growing population e.g., population A, can make to the presence of the second

population B. These responses are as follows:

1. The growth and metabolic activities of microbial population A may have a beneficial or

positive effect on the growth of microbial population B. For example, this could occur if

population A excretes a compound which stimulates the rate of growth of population B,

compared with its rate in the absence of population A. Alternatively, the same positive

effect might be achieved if population A utilized a compound initially present in the

common habitat which was toxic to population B and hence restricted its development.

26 of 54
2. The presence of microbe A could have a detrimental or negative influence on the growth

of microbe B. This situation could arise if microbe A excreted a metabolite which was toxic

to organism B.

3. It is also possible that with the growth of microbe A, its metabolic activities and its

demands upon the resources of the common environment will have no effect on the growth

of microbe B. A neutral response of this kind would be shown by similar growth patterns

for population B whether or not population A was present.

Common microbial interactions are as described below.

1. Neutralism (00): This is simply a case of non-interaction between component species of

an environment. It has been reported that the mixed growth of a Lactobacillus species and

a Streptococcus species in a chemostat culture produced individual population sizes which

were the same as those in separate monocultures under the same growth conditions.

2. Commensalism (+0): This is the situation where one member of a community benefits

from the presence of a second population which itself does not derive any advantage or

disadvantage from the activity of the first organism. Commensalism is an extremely

common interaction in nature and the process of organism succession can be thought of as

a chain of commensal relationships; the growth of one population generating a particular

set of conditions thereby enabling a second population to develop.

a) Metabiosis: this term is used as an alternative to commensalism, which is the relationship

when an organism causes a change in the conditions which then favours the development of

other species associated with it.

Causes of Metabiosis:

27 of 54
(i) Supply of Nutrients: One organism may produce a substance which becomes a nutrient for

another organism e.g. the breakdown of complex molecules into readily available simpler

molecules like the breakdown of starch by Micrococcus rouxianus to maltose for use by other

micrococci or the breakdown of starch by Aspergillus oryzae to glucose which are used by

yeasts. Supply of nutrients can also be by synthesis of an essential nutrient which is not

supplied by the substrate; e.g. yeasts and molds produce vitamin B which is used by

Lactobacillus species. The yeast Saccharomyces cerevisiae produces riboflavin (vitamin B2)

which is needed by Lactobacillus casei for growth. The stability of this community was

verified to be due to a second interaction, namely competition for growth limiting quantities

of carbon and other sources of energy, glucose. The bacterium has a greater affinity for glucose

than the yeast but if the Lactobacillus species used too much of the carbon source, it would

cause a decrease in the size of the yeast population and hence a decrease in the rate of the

riboflavin supply and this ensured that the populations equilibrated to constant sizes under

constant growth conditions.

(ii) Changes in Oxygen or Tension Electron Potential (Eh): In cheese manufacture, the Eh is

reduced to about-119mV to encourage the growth of microaerophiles. Streptococcus species

grow on whale meat and reduces the Eh to a level that enables the anaerobic clostridia to grow.

(iii) Changes in pH: One organism may alter the pH of an environment to favour the growth

of others e.g. Leuconostoc mesenteriodes produces acid which lowers the pH for Lactobacillus

species to grow (in the production of yoghurt).

(iv) Alternation of water activity (aw): by one organism may encourage the growth of other

organisms e.g. osmophilic yeasts can grow in the presence of high sugar concentrations,

breakdown the sugar and lower the aw so that less tolerant organisms can grow in the solution.

28 of 54
(v) Alteration of Cellutar Structures: Biological structures of some foods constitute a physical

barrier. However, if this barrier is breached in some way, contamination and growth by

invading organisms are encouraged e.g. fruit rotting fungi destroy the skin of the fruits thereby

laying it open for the entry and growth of other organisms mainly yeasts.

(vi) Elimination of antimicrobial factors: One organism may neutralize or destroy an

antimicrobial factor which has been inhibiting the growth of a second organism e.g. nisin

which is synthesized by some strains of Streptococcus lactis is active against Gram positive

bacteria including spores of Clostridium and Bacillus species. However, some strains of

Lactobacillus species are capable of inactivating nisin against these other organisms.

LECTURE II

3. Amensalism (0-). This is an interaction in which the growth of one population is restricted

by the presence of a second population which is unaffected by the metabolism of the

inhibited population. Amensalism occurs when organisms produce inhibitory compounds

such as antibiotics or colicins or through nonspecific effects such as the elevation of the

dissolved oxygen tension or changes in pH.

Amensalism can be alternatively referred to as antagonism, in which case one organisms

makes the growth conditions less favourable for other organisms.

Antagonism can be achieved in several ways which include:

(i) Consumption of essential nutrients: Here, one organism with a more rapid growth rate

quickly consumes the essential nutrients in the medium thereby limiting or inhibiting others.

(ii) Accumulation of major metabolites to toxic levels: There are many metabolites that are

produced up to toxic levels as end products of metabolism e.g. acids which are inhibitory both

29 of 54
to other organism as well as the producer. Growth slows down as acidity increases until it stop

eventually. This is clearly indicated in the case of alcohol and cheese production.

(iii) Production of antibiotics: Nisin is produced by Lactococcus lactis that are found

naturally in many products. Nisin is active against Gram positive bacteria, and inhibits

undesirable organism like Clostridium species.

4. Synergism (++): Relationship between two microbial populations in which both members

benefits from the relationship. It is not obligatory because each member can produce its

own food individually. It is a loose relationship because one member can be replaced by

another microorganism. It allows microbial population to perform such functions which it

may not be able to produce individually. E.g. population 1 which is able to utilize

compound A and it breaks it down to compound B but it cannot go beyond that stage, but

population 2 can breakdown compound B to compound C. at the end both population 1 and

2 can utilize compound C to produce energy + CO2. also called syntrophism/when two

populations provide nutrient for each other

5. Mutualism (++): This type of interaction occurs when both members of the mixed culture

derive some advantage from each other’s presence in terms of increased growth rates or

increased population sizes. It is an obligatory interaction between two populations in which

both of them benefit. It usually requires close proximity between one another. The

interactions are highly selective and cannot be replaced by related species. It can be

considered to be an extended form of synergism. When they exist separately the physical

tolerance and metabolic activites will be different between symbionts. Yeoh, Bungay and

Krieg (1968) described a two membered mixed culture of Bacillus polymyxa and Proteus

vulgaris grown in a carbon-limited chemostat in a simply growth medium which could not

30 of 54
 sustain the growth of either population on its own. This indicates that each organism was

in some way completely dependent on the other population to complement its minimum

growth requirements. The Proteus species produces nicotinic acid which is essential for the

growth of B. polymyxa, while the Bacillus species reciprocated by excreting the vitamin

biotin which promotes Proteus vulgaris growth. However, in this case regular oscillations

were established and ascribed to the effect of a third interaction between the two

populations. P. vulgaris produces a proteinaceous compound which inhibited the growth

of B. polymyxa and caused a decrease in its population size. This in turn reduced the rate

of biotin addition to environment and as its concentration declined, it could not maintain

the original proteus population size which also went into decline. At a point, the

concentration of the inhibiting protein was lowered sufficiently to cause a resurgence of

the B. polymyxa population and the whole cycle was repeated.

6. Competition (- -): In this case both populations are limited either in terms of growth rate

or final population size by a common dependence on an external factor required for growth.

Competition is very important because it provides a selective mechanism for evolution.

Competition as Gause observed is the basis of the struggle for existence.

7. Predation (prey-predator) relationship (+-): Here one organism, the predator gains

directly at the expense of the second organism, the prey since the prey forms the complete

nutritional requirements of the predator. In extreme cases, the prey may go into extinction;

but typically in open growth systems, continuous oscillations of the two populations can

be established with the increasing phase of the predator population lagging behind the

increase in the prey population. This has been observed in the case of Dictyostelium

31 of 54
 discoidium (amoebae) feeding on Escherichia coli and a number of models have been

proposed to describe the population fluctuations.

EXERCISE

1. Outline the causes of metabiosis.

2. Briefly explain the following terms:

i. Mutualism

ii. Synergism

iii. Predation

UNIT 4

MICROORGANISMS IN ECOSYSTEMS

LECTURE I

AEROMICROBIOLOGY

Introduction

Biological material including microorganisms and toxins can be found in air or the atmosphere,
and the study of this area is termed ‘aeromicrobiology.’ The transportation of microorganisms in
the air, nature of the atmosphere as a microbial habitat, and the factors that influence microbial
survival in the air are described. This is followed by aerosolization of indigenous soil pathogens;
microbiology in the clouds; airborne pathogens and microbial toxins. Practical application and
importance of aeromicrobiological studies is also considered.

Atmospheric aerosols (or particulate matter) are solid or liquid particles or both suspended in air
with diameters between about 0.002 µm to about 100 µm. Aerosol particles vary greatly in size,
source, chemical composition, amount and distribution in space and time, and how long they
survive in the atmosphere.

32 of 54
Primary atmospheric aerosols are particulates that are emitted directly into the atmosphere (for
instance, sea-salt, mineral aerosols (or dust), volcanic dust, smoke and soot, some organics).

Secondary atmospheric aerosols are particulates that are formed in the atmosphere by gas-to-
particles conversion processes (for instance, sulfates, nitrates and some organics). They are formed
by chemical reactions of the primary aerosols.

Bioaerosols are airborne biological substances; that is, biological particles suspended in the
atmosphere (aerosolized biological matter).

Bioaerosols are generated when bubbles break on the surface of water containing microbes, and
(as recently reported by Joung et al., 2017), by bubbles, tens of micrometres in size, formed
inside the raindrops which disperse micro-droplets containing soil bacteria during raindrop
impingement. A single raindrop can transfer 0.01% of bacteria on the soil surface and the
bacteria can survive more than one hour after the aerosol generation process. However, bacteria
transfer by rain is highly dependent on the regional soil profile and climate conditions.
Bioaerosols may also be generated by transportation of dust particles contai ning
microorganisms by the wind, movement of animals and by activities of man such as cultivation
and digging of soil.

Bioaerosols play an important role in climate change, human health and agricultural
productivity. In the atmosphere, bioaerosols can influence on the global climate; they are key
elements in the life cycle of many organisms and ecosystems, and they may affect the water
cycle by promoting cloud formation and ice nucleation even though their fraction is relatively
small compared to all the atmospheric aerosols. On the ground, bioaerosols can change micro -
biogeography faster than many other transport mechanisms; because bioaerosols can lead to
dispersion of biological contaminants over long distances relative to terrestrial transport
mechanisms, they significantly affect changes in biodiversity and ecology as well as the
propagation of biological pollutants. Furthermore, bioaerosols can be effective carriers of
pathogenic organisms of plants, animals and humans, resulting in the spread of diseases.
Specifically, pollen and spores have been suggested to enhance asthma, allergies and other
respiratory conditions during thundershowers. To date, aerosols generated at water/air
interfaces are considered one of the main mechanisms for transferring microbes to the
environment.

33 of 54
The components of the aerial environment are varied and mostly include dust particles, pollen
grains, fungal and bacterial spores, and spores of bryophytes and pteridophytes, fungal and
actinomycetes hyphal fragments, etc.

LECTURE II

Transportation of microorganisms in the air

Usually, micro-organisms in the air are in a state of suspended animation. Many of them are easily
killed by ultra-violet rays, desiccation, and other unfavorable conditions. Therefore the living
microbes are either usually resistant or have been in the air for some time. Resistant spores are
capable of producing pigments and other means of adaptations.

The dispersal of air borne particles involves 3 stages: Liberation and take off into the air,
Dispersion in air current, and Deposition on surfaces at the end of the transit before germination
and growth.

Liberation: Before a particle becomes airborne, a number of problems have to be overcome.

Example, energy is required to overcome the adhesive forces attaching the particles to a surface;
also the particle has to be of a size and feature that will be airborne. The degree of adaptation to
air borne dispersal varies greatly between different groups of micro-organisms and this is reflected
in their relative abundance in the air. Viruses and bacteria are poorly adapted while fungi have
developed many adaptations mechanisms to enable their spores become readily air-borne. While
some have long sporophores (stalk) which lift their spores well into the air, some others have ways
of forcefully ejecting their spores into the air. Some others rely on passive means. Rain splash,
mechanical disturbance and other physical adaptations help a lot in spore liberation into the air.
Dispersion: The dispersion of air-borne micro-organisms can be considered at two levels. Fate of
individual spores; and the behavior of groups or cloud of spores. These aspects are related and
depend on the physical characteristics of the spores and that of the atmosphere. The important
characteristics of spores in this respect are size, shape, degree of surface roughness, density and
electrostatic charges; while those of the environment include wind movements, turbulences,
layering convention, wind gradient near the ground and the pattern of atmospheric circulation.
Because they are heavier than air, spores tend to settle under gravity but because they are also

34 of 54
blown by air, they are affected by electrostatic charges. The distance traveled by a spore depends
on the interrelationship of the various factors mentioned.

Deposition: The final stage of airborne dispersal of microorganisms is deposition. The microbes
are returned to the surface layer of plants, animals or soil so that they can no longer be blown by
normal wind, though they may still be washed off. Deposition may occur in precipitation or from
dry air by several different methods such as sedimentation, impaction, rain washing, etc.

Factors affecting microbial concentration in the atmosphere

A number of factors can directly or indirectly affect the number of micro-organisms and their
survival structures in air. Such factors may include temperature, wind speed, humidity, rain,
pigmentation, vegetation and human activities.

Temperature: During the dry season, those air-borne spores that are thin walled are easily
dehydrated to the advantage of those with thick warty walls which are more adapted to survive
high temperatures. There is also a relationship between temperature and humidity, as well as
temperature and wind movement. Freezing temperature is likely to be encountered by air-borne
microbes above 3-5 km in the air (the higher you go the cooler). Depending on how well adapted
the structures of the microbes are, the very low temperatures may or may not have a damaging
effect on the survival structures of micro-organisms.

Wind Speed: Fast moving air blows force with it and so readily provides energy for detachment
of spores from their vegetative structure and other surfaces. Usually, it is difficult for spores to be
deposited at a spot except where there is an obstacle or a wind breaker along the wind course.

Humidity: The amount of water in the air is usually referred to in terms of relative humidity; that
is the ratio of the actual vapour pressure when the air is saturated with water at the same
temperature. Vapour pressure varies greatly with temperature and thus relative humidity is low
when temperature is high and vice- visa. Relative humidity is a good indicator of the drying effect
air on micro-organisms. A wide range of relative humidity may be found in the atmosphere from
10- 20% in desert regions to saturation or super saturation where cloud formation occurs at ground
level resulting in dews or frost. Different micro-organisms have different relative humidity
requirements for their survival in the air. The lower limit of relative humidity for fungal growth is
about 65%, while bacterial species require more.

35 of 54
Rain Splashes: Rain washes air-borne spores to the soils and as such the amount of rain received
by an area may have some influence on the number of air-borne spores and microorganisms. Where
an area has a clearly defined raining and dry seasons, the amount of dust particles and spores in
the air may vary with the seasons of the year.

Pigmentation and ultra-violet rays: Ultra violet (UV) radiation in the air originate from the sun
much of which is reflected or absorbed before reaching the earth’s surface. Micro-organisms
carried into the higher regions of the atmosphere may be exposed to the damaging doses of UV
radiation. Though ultra-violet radiation of about 265mm is most lethal, other short waves radiation
even within the visible region can also be damaging. Pigmented spores especially those of
dermatophytes can resist strong ultra- violet rays from the sun. Generally speaking, radiation,
desiccation and temperature all interact to affect the survival of micro-organisms in the air. The
manner of interaction is not well understood but desiccation and freezing may protect micro-
organisms against radiation damage.

Man’s Activities: Some human practices such as open rubbish dump sites, construction of poor
or lack of drainage systems, etc. can lead to microbes in rubbish dumps and dry feacal materials
being blown up into air. Other activities including road construction, cultivation and digging of
soil may release soil-borne spores into the atmosphere. This may explain why some farmers in
some parts of the world suffer from lung and pulmonary tracts s infections caused by Aspergillus
species, a disease called aspergillosis.

Vegetation: This can affect the presence of microbial spores in air in two different ways. Leaves
can trap spores when washed down by the rain. Some may germinate when conditions are suitable.
On the other hand, when the leaves dry off the spores can be blown back into the atmosphere and
thus increasing the number of air-borne spores.

EXERCISE

1. Write a short note on bioaerosols.

2. Describe the stages of aerogenous dispersal of air particles.

36 of 54
 LECTURE III

Airborne Pathogens and Microbial toxins

Though there are significantly less atmospheric microorganisms than there are in oceans and in
soil, there is still a large enough number that they can affect the atmosphere. Once suspended in
the air column, these microbes have the opportunity to travel long distances with the help of wind
and precipitation, increasing the occurrence of widespread disease by these microorganisms. These
aerosols are ecologically significant because they can be associated with disease in humans,
animals and plants. Numerous plant and animal pathogens are spread by the aeromicrobiological
pathway that costs billions of dollars each year. Typically microbes will be suspended in clouds,
where they are able to perform processes that alter the chemical composition of the cloud, and may
even induce precipitation.
Droplet Formation

The emission process mentioned above, in which microbes are lifted in the air often involves
microbes being suspended in droplets, which are large enough to keep the microbes hydrated and
large enough to maintain a virulent amount of pathogen, but are still small enough to stay
suspended in the air.

Microbial Communities and aerosolization of indigenous soil pathogens

Many different microorganisms can be in aerosol form in the atmosphere, including viruses,
bacteria, fungi, yeasts and protozoans. In order to survive in the atmosphere, it is important that
these microbes adapt to some of the harsh climatic characteristics of the exterior world, including
temperature, gasses and humidity. Many of the microbes that are capable of surviving harsh
conditions can readily form endospores, which can withstand extreme conditions. Geo-indigenous
pathogens are those found in soils and are able to reproduce, metabolize and grow. Many of these
microbes are mostly spore formers, such spores can potentially be aerosolized and cause human
infections. Many of these microorganisms can be associated with specific and commonly known
diseases.

37 of 54
In the outdoor (extramural) environment, spread of pathogenic microorganisms such as wheat rust
fungi, and some gastrointestinal pathogens is highly important. Several factors such as the UV
radiation, temperature, and relative humidity modify the effects of bioaerosols by limiting the
amount of time aerosolized microorganisms remain viable. However, the conditions of indoor
environments such as limited circulation of external air and much less UV radiation exposure, are
suitable for the accumulation and survival of microorganisms.

Airborne diseases
Airborne diseases are illnesses spread by tiny pathogens in the air; it occurs by airborne
transmission in which infective particles are discharged into the air in aerosols droplet nuclei
produced by human expiratory actions such as sneezing, coughing and sputtering of those already
infected. Infections are mostly viral, fungal and some bacterial diseases e.g. tuberculosis,
meningitis and pneumonia. In most cases, an airborne disease is contracted when someone breathes
in infected air, and a person also spreads the disease through their breath, particularly by talking,
sneezing, coughing, through phlegm, skin shedding, or resuspension from surfaces.

There are documented six conditions for aerogeneous diseases transmission:

o The resistance of infective agents in droplets

o The droplet nuclei or dust
o Whether the infective agent can survival for long in droplet form.
o The ability to infect from secondary aerosols formed when dust is re-suspended;
o The host range
o Whether there are alternative means of transmission

Airborne vs Droplets transmission

CDC divides diseases between those believed to be spread by:

-large droplets that hit mucous membranes

-small particles that are inhaled.

However many droplet diseases have an airborne route of transmission. Particle size determines
the time pathogen stays suspended in air, distance travelled, body site deposition (upper or lower

38 of 54
respiratory track, etc.), survivability and infectivity of the pathogen, approaches to biosecurity
methods (particle size dependent).

Droplets can be classified using particle sizes. For example it is generally accepted that:

i. small particles of < 5–10 μm aerodynamic diameter that follow airflow streamlines are
potentially capable of short and long range transmission; particles of < 5 μm readily
penetrates the airways all the way down to the alveolar space, and particles of < 10 μm
readily penetrates below the glottis.
ii. Large droplets of diameters > 20 μm refer to those that follow a more ballistic trajectory
(i.e. falling mostly under the influence of gravity), where the droplets are too large to follow
inhalation airflow streamlines. For these particle sizes, for example, surgical masks would
be effective, as they will act as a direct physical barrier to droplets of this size that are too
large to be inhaled into the respiratory tract around the sides of the mask (which are not
close-fitting).
iii. ‘Intermediate particles’ of diameters 10–20 μm, will share some properties of both small
and large droplets, to some extent, but settle more quickly than particles < 10 μm and
potentially carry a smaller infectious dose than large (> 20 μm) droplets.

Aerosols would also include ‘droplet nuclei’ which are small particles with an aerodynamic
diameter of 10 μm or less, typically produced through the process of rapid desiccation of exhaled
respiratory droplets. However, in some situations, such as where there are strong ambient air cross-
flows, larger droplets can behave like aerosols with the potential to transmit infection by this route.

Table 1. Characteristics of airborne and droplet transmission of disease

Airborne transmission
Relatively small numbers of organisms in
inoculum-virulence required
Transmission beyond a meter-shared breathing
volume
Access to vulnerable site e.g. alveoli in the
case of TB)
Hand washing not effective.
Droplet transmission
Relatively large numbers of organisms in
inoculum (small inoculum may be tolerated)
Transmission is within a meter of the source
Access to vulnerable site (mucosal membranes
of eye, nose, mouth, trachea, etc.)
Hand washing may be effective.

39 of 54
If an infected patient produces infectious droplets of varying sizes by breathing, coughing or
sneezing, transmission between individuals by both short-range large droplets and airborne small
droplet nuclei are both possible, depending on the distance from the patient source.
Fig. 1. illustrates these potential routes of short and long-range airborne transmission, as well as
the downstream settling of such droplets onto surfaces (fomites). From such fomites, they may be
touched and transported by hands to be self-inoculated into mucosal membranes (e.g. in the eyes,
nose and mouth) to cause infection, depending on the survival characteristics of individual
pathogens on such surfaces, and the susceptibility (related to available, compatible cell receptors)
of the different exposed tissues to infection by these pathogens.

Fig. 1. Short and long-range airborne transmission and downstream droplets settling on surfaces

Aeromicrobial toxins

Microbial toxins are toxins produced by micro-organisms, including bacteria and fungi.
Microbial toxins promote infection and disease by directly damaging host tissues and by disabling
the immune system. Aeromicrobial toxins are bioaerosols of viable microbial cells containing
hazardous agents such as gram-negative endotoxins, or b-1,3-glucan, or mycotoxins. Exposure
to such substances could induce respiratory symptoms.

40 of 54
Endotoxins are lipopolysaccharide (LPS) found in the cell walls of pathogenic
(e.g., Salmonella and Pseudomonas) and nonpathogenic (e.g., Escherichia coli) Gram-negative
bacteria. They can be shed in trace amounts from living cells or released in larger quantities when
such cells disintegrate. Injection or inhalation of endotoxins can cause fever, chills, and shock.
LPS is highly antigenic biological agent that when associated with airborne particles such as dust,
is often linked with acute respiratory symptoms such as chest tightness, coughing, shortness of
breath and fever.

Exotoxin is a toxin excreted by a microbe, including bacteria, fungi, algae and protozoa. They are
highly potent and can cause major damage to the host. They may be secreted or released during
cell lysis. Examples of exotoxins include botulinum and diphtheria toxins produced by Clostridium
botulinum and Corynebacterium diphtheria respectively. Botulinum toxin is a neurotoxin which
although normally associated with ingestion of contaminated food, may be aerosolized and
disseminated by inhalation of the lethal dose which is as low as 0.3µg. Death is due to paralysis of
respiratory muscles and occurs 12 hours after exposure. Another exotoxin produced by bacteria is
staphylococcal enterotoxin. On occasion, this toxin can be fatal with the lethal dose estimated to
be 25 µg by inhalation. The symptoms include cramping, vomiting and diarrhoea, which occur
within 1 hour of exposure by aerosolization.

Mycotoxins (fungal toxins) including aflatoxins from Aspergillus flavus, Aspergillus parasiticus;
ochratoxins (several species of Aspergillus, Penicillium), lactones, lactams, for example, patulin,
stachybotrylactones, stachybotrylactams (Penicillium, Stachybotrys) have been implicated in
airborne infections transmission. More recently, concerns that toxins from microorganisms that
grow in damp indoor environments may play a role in illnesses reportedly associated with living
or working in damp buildings have focused attention on the adverse health effects of inhaling
mycotoxins. In an unventilated area, pathogens, pollutants, and moisture can build up to unsafe
levels.

Control of airborne pathogen transmission

Ventilation, use of biocidal agents and cleaning the air with a filter is another part of keeping an
area as free of pollutants and pathogens as possible. A few basic filtering methods include
mechanical air filters, UV purification, and HEPA filters. In addition, isolating an infected
individual is a basic way of checking transmission of airborne pathogens, as well as the use of face

41 of 54
masks and personal protective equipment (PPE), especially for health workers or people most
likely exposed to an infected individual. The efficient aeromicrobiology pathway sampling,
monitoring, detection, and modelling also, have the ability to aid in the control of airborne
pathogens.

Table 2. Some Airborne Pathogens and Diseases

Some important diseases of humans transmitted from person to person by inhaled airborne
particles

Virus diseases Bacterial diseases

(virus type in brackets)
Chickenpox (Varicella viruses)
Flu (Influenza viruses)
Measles, Rubeola (Morbillivirus)
German measles, rubella (Rubivirus)
Middle East respiratory syndrome
(coronavirus)
Mumps (Mumps virus)
(bacterial name in brackets)
Pulmonary anthrax (Bacillus anthracis)
Whooping cough (Bordetella pertussis)
Meningitis (Neisseria species)
Diphtheria (Corynebacterium diphtheriae)
Pneumonia (Mycoplasma pneumoniae,
Streptococcus species)
Tuberculosis (Mycobacterium tuberculosis)

Several other diseases, below, are acquired by inhaling particles from environmental
sources, not directly from an infected person.
Disease Source
Dried, powdery droppings from infected birds
Psittacosis (Chlamydia psittaci)
(parrots, pigeons, etc.)
Legionnaire's disease (Legionella
Droplets from air-conditioning systems, water
pneumophila)
storage tanks, etc., where the bacterium grows.

Acute allergic alveolitis (various fungal and

Fungal or actinomycete spores from decomposing
actinomycete spores)
organic matter (composts, grain stores, hay, etc.)
Aspergillosis (Aspergillus fumigatus, A. Fungal spores inhaled from decomposing organic
flavus, A. niger) matter

Spores of the fungus, in old, weathered bat or bird

Histoplasmosis (Histoplasma capsulatum)
droppings

42 of 54
 Spores in air-blown dust in desert regions (Central,
Coccidioidomycosis (Coccidioides immitis)
South and North America) where the fungus grows
in the soil

Practical application and importance of aeromicrobiology

I. The application of aeromicrobiology is of great importance in disease epidemiology,
forecasting and modelling. Epidemiology is the study of incidence, distribution and control
of diseases within populations or the sum of factors controlling the presence or absence of
a disease or pathogen. Epidemiology therefore concerns the interaction between the
pathogen, its host and the environment. Aeromicrobiology can make valuable contributions
to the epidemiology of animal as well as plant diseases. Even non-infectious diseases can
occur epidemically as a result of air-borne infection e.g. coccidiomycosis and
histoplamosis, when a population is exposed to large number of causal fungal spores.

II. Aeromicrobiological methods can be used to detect the presence and quantity of infective
agents in primary and secondary aerosols. Their persistence in air and relationship with
infection can also be known. This was the case in identifying the occupational and
community risks associated with the aerosolization process in relation to disposal of
biosolids and manure in agricultural land application.
III. In Agriculture, aeromicrobiological methods have been widely used in area of plant
pathology, to determine the number of spores of a plant pathogens in the air. The epidemic
spread of wheat rust and the resulting economic destruction produced are indicative of the
impact that airborne microbial pathogens can have on agriculture. A factor that complicates
the control of such diseases is that chemical treatment for the control of pathogens is
viewed as undesirable. This is because many pesticides have long half-lives and their
residence in an ecosystem can be extremely harmful. Another method used for controlling
phytopathogenic (plant pathogenic) fungi is spore monitoring as a disease control strategy.
In this approach, the life cycle of the fungi, especially the release of spores, is monitored,
and fungicide application is timed to coincide with spore release. This approach minimizes

43 of 54
 use of harmful chemicals. Thus, efficient aeromicrobiology pathway sampling, monitoring,
detection and modelling have the ability to aid in the control of airborne pathogens.
IV. Aero microbiological studies can also be used in forensic and crime detection by plating
out pieces of materials from suspects and matching the microbial isolates with those of the
aerial environment where the crime was committed.

EXERCISE

1. What is the role of microorganisms in cloud formation?

2. Define airborne diseases.
3. Differentiate between airborne and droplet transmission of diseases.

LECTURE IV

AQUATIC MICROBIOLOGY
Micro-Organisms in Natural Waters
Most microbial environments are aquatic, in that sometimes, the vegetative organism live in
aqueous media such as animal and plant fluids, soil, water and many other related habitats. Water
is also usually required for the movement of various reproductive structures. Aquatic microbiology
however refers to microorganisms which live in the earth’s natural waters ranging from the small
ponds to great oceans. Most of the earth’s water is contained in the oceans (97.1-97.6%), while
smaller quantities are maintained in Polar Regions as ice and glaciers (2.1%) and ground water
(0.3-0.8%) and in land waters.

Lakes – 0.009% and

Rivers - 0.00009%

In spite of the wide range of conditions encountered in the various aquatic habitats, micro-
organisms are found in all types of aquatic habitats.

Types of aquatic environments

44 of 54
Aquatic environment are often divided into oceans and inland waters. Inland waters can be
classified into ground and surface waters. Ground water is that water contained in permeable rocks
below the water table. It accumulates as water in the soil percolates through it. Many of the
nutrients are therefore filtered out. Because of this, ground water is only able to support a limited
population of micro-organisms.

Surface water comprises of lotic or running waters consisting of springs, streams and rivers. The
second group are lentic or standing waters comprising of lakes, ponds, swamps and bogs. Springs
can occur where ground water breaks the surface and thus like ground water, they are nutrient poor
near the origin. Specialized springs occur in certain regions such as hot springs in regions of
volcanic activities. We can also have mineral springs and this depends on the surrounding
geological conditions. They may occur when water accumulates dissolved mineral as it passes
through geological formations. Examples, hard water and springs found in many lime stone areas.
Springs eventually become rivers as their flow is supplemented by tributaries, land run offs and
precipitation. A number of factors however determine the rate of flow. Such factor include
gradients, transverse conditions of the river valleys etc. Lentic waters differ in size ranging from
the smallest ponds to the deepest known lake. Often, distinction between lakes and ponds are not
clear but generally, the bottom of ponds are colonized by submerged plants whereas lakes are too
deep to be colonized by plants.

The oceans cover approximately 70% of the earth’s surface and the depth is variable ranging from
200m to 10000m or more. Because of this great depth much of the sea is in near total darkness. Of
great importance to abiotic and biotic components of oceans is the salt content which varies 32%
to 38% with an average of 35%. Because of the additional dissolved salts in the sea, the specific
heat capacity is high and the freezing point temperature is affected. Salinity is the major
phenomenon which is often used to distinguish between water bodies. On this basis, classification
of water bodies based on the salt content are as follows

0.5% = fresh water

0.51%-29.9% = brackish water

30.0% and above = marine (sea and ocean) water

Special aquatic habitats

45 of 54
Just like any other habitat, important special habitats can be found in aquatic environments and the
micro-organism inhabiting such habitats have special features of survival in such areas. Such
feature may be structural or physiological. The aquatic habitats can be categorised as the planktons,
benthic, biofilm and microbial mat.

Plankton: from Greek word meaning “wanderer” or “drifter,” are organisms that live suspended
in the open water column and drift with the currents, with little or no ability to control their
horizontal location. Enough bodies of water surface may be heavily colonized by these freely
suspended micro-organisms, and physical and chemical conditions occurring at the surface may
provide micro-environment much like that of the surrounding water. There are three functional
groups of plankton, each with microbial members: phytoplankton, bacterioplankton and
zooplankton. Pelagic microbial populations can be referred to as bacterioplankton (though
notably, despite the name, these include archaeans as well as bacteria), and include
photoautotrophs, chemoautotrophs and heterotrophs. The phytoplankton are the photoautotrophic
plankton, which include microbes (cyanobacteria) and eukaryotes (algae, especially the single-
celled dinoflagellates and diatoms). The zooplankton are larger heterotrophic plankton, including
protozoans such as the intricate foraminiferans and radiolarians.

Benthos: this is one of the specialized habitats in any water body found in bottom sediments and
particulate matter called the benthic region. The benthos is characterized by a dramatic increase in
microbial numbers and activity that supports the formation of adjacent aerobic and anaerobic
microenvironments as well as cycling of essential nutrients. The region varies considerably from
sand to mud and silt. These can be classified into three major components according to the origin.

a). Lithogeneous components: these are primarily derived from rock, soil and volcanic ash.

b). Biogenious components: they are composed of skeletal remains of macro- and micro-
organisms e.g. diatoms.

c). Hydrogenous components: these components result from inorganic and chemical reactions
occurring in the water.

Biofilms: Biofilms are described as a collection of microorganisms and their extracellular products
bound to a solid surface. This special aquatic habitat is the environments provided by surfaces of
plants, animals and non-biological structures such as stones on which microbial communities are

46 of 54
formed. Biofilms are characterized by the presence of bacterial extracellular polymers, and their
roles in nutrient cycling and pollution control within the aquatic environment. They range from a
few cell layers to a maximum of a few millimetres in thickness. Biofilms are important components
of stream ecosystems and are considered a good bioindicator of environmental health, not only
because of their high abundance in most natural environments but also because of their sensitivity
to environmental changes with short life cycle. Biofilms are a basic component of freshwater food
webs

Microbial mat (Benthic biofilms): Microbial mats are vertically layered, and self-sustaining
microbial communities that develop in the liquid–solid interface of benthic sediments (benthic–
planktonic interface). Microbial mats range from several millimetres to several centimetres in
thickness, and are vertically stratified into distinct layers. They are autotrophic, the fixation
of inorganic carbon into biomass occurs either photosynthetically or chemosynthetically, although
in many cases all necessary trophic levels (e.g., primary producers, consumers, and decomposers)
may be present. Furthermore, they comprise millions of microorganisms belonging to different
species, which interact and exchange signals, embedded in a matrix of exopolysaccharides, and
nutrients to enable a greater flow of resources and energy for the survival of the community.
Benthic biofilms have successional stages of development much like a terrestrial forest
ecosystem. Microbial mats, therefore, may be considered complex biofilms.

Physicochemical Factors in aquatic environments

The development of microorganisms in water is influenced by a large number of chemical and

physical factors which, in various ways, interact or oppose each other. They have an influence on
the size, species and composition of the microbial biocenosis as well as on their appearance and
life processes. Within water ecosystems two groups of factors that have a crucial influence on the
quantitative and qualitative relationships between microorganisms may be distinguished:

• Abiotic factors - light and thermal energy, water wave, pressure, salinity, dissolved gases
such as oxygen, carbon dioxide, methane and others, dead organic matter and non-organic
compounds in water).

47 of 54
 • Biotic factors - all water living organisms such as plants, animals, microorganisms and the
relationship between them.

This section, we shall be considering the abiotic factors in aquatic environment.

ABIOTIC FACTORS IN AQUATIC ENVIRONMENT

Light: plays a critical role in determining the amount of carbon fixation into inorganic compounds
through photosynthesis. The amount of light penetrating different layers of water strictly depends
on the position of the sun, transparency, colour and depth of water. The lesser the incidence angle
(the position of the sun in relation to the water surface) the smaller the loss of sun rays due to
reflection. Much of the sun’s radiation does not reaches the earth’s surface since it is absorbed and
scattered by atmosphere and cloud cover. Some of the radiation which reach the water surface is
reflected back to atmosphere and the small amount that penetrates, suffers further the attenuation
through scattering and differential absorption. In pure water, approximately 53% the total light is
dissipated as heat and reduced at the first meter of water depth.

In most natural waters, light extinction may be considerably affected by the amount of dissolved
solids and suspended materials (turbidity); and in water with appreciable dissolved and particulate
materials, the general effect on light penetration is that there is a general decrease is transmittance.
The intensity and specific composition of light penetrating water surface and to any depth has a
profound effect on all resident microbial activity since it is the available light which largely
determine the potential for productivity. Depending on the level of insolation and water turbidity,
the biologically active sun rays usually penetrate water somewhere between 10-150 m.
Undoubtedly, sea waters are clearer and less polluted than inland waters, consequently light can
penetrate much further down through these waters. Sun rays penetrate sea waters down to about
150 m creating the so called photic zone where photosynthesis takes place. Due to different light
conditions the development of photoautotrophs isn't identical throughout the entire water mass.
Generally, photosynthesis increase in relation to light intensity until the photosynthetic system
becomes light saturated. The indicator of the illumination quantity is often the lower boundary
(limit) of algae incidence; their greatest development takes place at a depth of 0.5-2 m. Most algae
possess an ability to change and adapt their colouring to the light conditions. Light is harmful to
those microorganisms which are deprived of any pigments. Both the ultraviolet and the longer
wavelength may have a negative effect. For instance, blue light (wave length 366-436 nm) inhibits

48 of 54
the process of nitrite oxidation by Nitrobacter vinogradskyi. Light also has an influence upon water
fungi development. Blue and green rays have a greater impact than red rays.

Turbidity measurement have been used as a measure of light penetrance, and transparency disc is
often employed for this purpose.

Temperature: The amount of thermal energy entering a body of water depends primarily on the
incidence angle which varies with the latitude, time of the day, seasons and the water conditions.
However the distribution of heat within the water body is dependent on it morphological
characteristics and mixing by wind turbulence. Lotic waters such as rivers have a steady
temperature throughout their mass due to constant mixing by the water flow. However, such a
water habitat is characterised by daily temperature fluctuations especially in shallow rivers. In
lentic (stagnant) waters such as lakes, where the water current is very weak or nonexistent, the
temperature fluctuates during the annual cycle. Lakes, especially deep ones, are characterized by
vertical stratification (the formation of layers that vary according to their composition and
temperature). Illuminated warm and near-surface waters have a lower density than the dark and
cold waters from below. The difference in density prevents mixing of the layers. The warm water
layer is called the epilimnion. The cooler layers from below form a thermocline or metalimnion
and become cooler with depth. The temperature falls by 1°C with each meter. In the lowest layer
– hypolimnion, the water is at 4°C and has the highest density.
The thermocline works as a barrier between the epi- and hypolimnion. The upper waters do not
mix throughout the year due to their different density. Water is only moved within the epilimnion
layer by the wind. The biogenes present near the bottom are not available for the organisms living
in the upper layers thus, in late summer; the top layer has a deficit of trophic substances. In the
autumn the surface waters begin to cool down, slowly falling while pushing the warmer waters
upwards, which also cool down. As the waters continue to exchange (autumn circulation) and are
mixed by the wind they oxygenate and at the same time lose CO2 by releasing it to the atmosphere
especially from the bottom waters. A slight inversion of temperature occurs in the winter since the
water at less than 4°C has a lower density than the 4°C water and it rises towards the surface.
Different circulation occurs in the spring as the surface waters warm up. Then, the entire body of
water is rich in oxygen and biogenes. The mixing of water also causes organisms to move.

49 of 54
 Fig. 1. Thermal stratification of deep lake

However, in shallow lakes there is no stratification because there is a steady mixing of the water.
The range of temperature in oceanic surface water is from – 1.7℃ in Polar Regions to 25- 30℃ in
tropical and subtropical waters. Whereas in deeper waters, temperature remains fairly constant at
a few degrees above freezing point.

In the oceans and inland waters in cold climate areas where predominant water temperatures are
less than 5℃, the resident bacterial are mainly psychrophiles and they can grow event at 0℃. In
warmer inland waters, mesophilic bacteria and fungi are the predominant species. Usually if
temperature is more than that required for the organisms, the cell components are destroyed or
denatured and this results in death. Whereas dropping in temperature below the normal range may
not necessarily kill the organisms, it slows down metabolic activity. Within a given range, bacterial
metabolism increases with increase in temperature and so there is increased growth with increased

50 of 54
temperature, but at temperatures higher than the optimum, growth rate is reduced. Temperature
has a profound effect on enzymatic activity.

Water wave

Mixing of water is of great importance to both the temperature distribution and for the balance of
the chemical composition (gasses, nutrients, substances that equalize the osmotic pressure, water
pH etc.). The movement of water is caused by the following:

• Variations in density caused by different temperatures and contents of soluble

• Suspended compounds

• Winds

• Difference in the levels at the bottom (lotic waters)

• Specific hydraulic engineering processes.

Pressure: Hydrostatic pressure is not an important factor in inland waters but can be of
considerable importance in oceans at great depths. In water the pressure gradually increases with
depth at about 1 atm per 10 m. Therefore, in large oceans and some deep lakes the pressure is quite
high; in most seas it is approximately 100 atm. Increased pressure affects dissociation constants of
carbonic acid and thus results in a decrease in pH. The pressure requirements of organisms differ
greatly even among the species. The term barophilic is used to describe a group of abyssal
microorganisms, which grow preferably or exclusively at high pressures which occur at depths of
10,000 m. These barophiles grow and develop not only under great pressures, but also at very low
temperature (3 -5°C), but their growth is very slow. Some other microbes which survive at high
pressures without injury but are normally active at atmospheric pressure condition are called
barotholerant or baroduric. The barophobic microbes do not develop when the pressure exceeds
200 atm. Most fresh water bacteria are in this category, although not all bacteria are affected to the
same extent.

51 of 54
A number of barophilic bacteria have been isolated from deep seas and from brines in deep oil
wells. Studies have shown that there is a relationship between pressure and temperature, whereby
high pressure tend to raise optimum growth temperature.

pH (Hydrogen ion concentration): The optimum pH for most aquatic bacteria is between 6.5-
8.5 which corresponds with the pH of most aquatic environment. The approximate pH of sea water
is usually between 8-8.3 while that of lakes is approximately 7. Consequent on the high content of
carbonates and their buffering effect, the pH of water does not usually fluctuate significantly. But
when there is a rapid growth of photosynthesising organisms the pH may increase rather
considerably. Some mineral springs and inland waters with a high content of humus compounds
may be acidic. Under these conditions the number of acidophilic fungi increases. Relatively large
changes in pH can be observed in eutrophic lakes where the pH varies between 7-10, which has
an obvious influence on the populations of bacteria and fungi. The effect of pH is also related to
enzymatic activities, and drops in pH beyond the organism’s normal range can affect its
physiology, and when extreme, can lead to death. Morphological changes can also occur such as
enlargement of cells and irregular swelling and branching. Photosynthesis is affected by pH
through its influence on carbon dioxide and carbonic acid equilibrium; pH varies inversely with
dissolved carbondioxide concentration and directly with bicarbonate concentration. In aquatic
environments, all photosynthetic plants use free carbondioxide with undissociated carbonic acid
for photosynthesis. However lack of carbon dioxide at high pH may not be a limiting factor for
photosynthesis for some plants which have enzymes that convert bicarbonates to carbondioxide.

Dissolved gases: Water possesses an ability to dilute gases but the solubility decreases as the
temperature and salinity increase; it is lower in sea waters than in the fresh water basins. The two
most important dissolved gases in aquatic environments are oxygen and carbon dioxide. Oxygen
is impotent because of its importance in aerobic bioprocesses and in relation to redox (oxidation –
reduction) potentials; while carbondioxide is important for photosynthesis and pH equilibrium.
The concentration of oxygen in water is dependent on the water temperature, partial pressure,
salinity and biological activities. Oxygen concentration in water is usually expressed in terms of
millilitres of oxygen in one litre of water (ml/L). Carbondioxide is very important in aquatic
environments since it aids the regulation of hydrogen ion concentration. In water, an equilibrium
is established between carbondioxide, carbonic acid and bicarbonate as follows:

52 of 54
CO2+ H2O = H2CO3 HCO3+H+ CO32- +2H+

Apart from these two gases, a number of other dissolved gasses also occur in natural waters e.g.
nitrogen which is not utilized by many aquatic micro- organisms but is involved in special
microbial processes (nitrogen fixation). Other gasses produced by microbial activities are methane,
H2, HN3, H2S, NH4 etc.

Salinity: Most microorganisms that live in clean rivers and lakes are halophobic and in natural
conditions do not live in waters in which the salinity exceeds 10%. Although salinity is not itself
a physical factor, changes in salinity can have profound osmotic effect which sometimes can be
lethal and can also be toxic through denaturation of cellular components. Most marine bacteria and
fungi are halophilic and some have specific requirements for sodium ions and some will not
tolerate too high salt concentrations. The optimal salinity range for most halophilic bacteria and
fungi varies between 25-40%; an average 32-38% in the oceans, and a much greater range in closed
seas (salty lakes). Increase in salinity level may have morphological and physiological effects as
well as influence on the generation cycle of bacteria and fungi; e.g. rod-shaped bacteria may form
filaments with an increase in salinity and the microbial oxidation of organic acids and sugars are
affected.

Organic substances: Organic substances are either secreted by living cells or the products of their
autolysis. However, the greatest amounts of organic compounds are introduced into water by
sewage. Organic compounds occur in water in the form of solutions or as suspended matter. First
of all they serve as food for heterotrophic bacteria and fungi. Microorganisms that often occur on
the surface of the suspensions, especially upon the particles of the detritus which absorb the organic
substances from water, enjoy favourable feeding conditions. The development and metabolic
changes of microorganisms are influenced, more by the content of readily available organic
compounds (such as carbohydrates, organic acids, proteins and lipids) rather than the amount of
the organic substances in general. Their depletion from water occurs rather quickly. When there is
a lack of organic substances bacteria do not reach their proper size and their cell division is slowed
down.

53 of 54
EXERCISE

1. a) Outline the specialized aquatic habitats.

b) Which of 1a can serve as bioindicator of environmental health and why?
2. What groups of microbes can you identify, based on their hydrostatic pressure
requirements?

54 of 54